Becky Steck
Matthias Kretzler
Michael Todd Valerius
Sean Mooney
Edison Ong
Ling Wan
Yongqun "Oliver" He
KTAO (Kidney Tissue Atlas Ontology) is a community-based biomedical ontology. Its development is supported by the NIH-NIDDK supported Kidney Precision Medicine Project (KPMP).
OWL-DL
KTAO: A biomedical ontology that represents kidney tissue atlas.
KTAO: Kidney Tissue Atlas Ontology
Vision Release: 1.0.121
BFO OWL specification label
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
Chris Mungall
expand assertion to
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
term_mapping_to_UMLS
term_mapping_to_NCIT
A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source.
The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
Provides an alternative Preferred Name for use in some NCI systems.
The word or phrase that NCI uses by preference to refer to the concept.
Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
Contains a Concept Unique Identifier for those concepts that appear in NCI Metathesaurus but not in the NLM UMLS.
An NCI Thesaurus property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used.
This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software.
A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
has_MedDRA_id
has_meddra_id
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA tools project (http://isa-tools.org)
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
the symbol assigned by the nomenclature authority
symbol from nomenclature authority
the full name assigned by the nomenclature authority
full name from nomenclature authority
NCBI GeneID
NCBI LocusTag
gene map location
modification date
The NCBITaxon ontology ID of an organism.
organism NCBITaxon ID
A chromosome ID where a gene is located.
chromosome ID of gene
an annotation property that specifies the type of a gene
type of gene
an annotation property that specifies a nomenclature status
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association.
has GO association
An annotation property that represents a gene's association with PubMed publication(s).
YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).
has PubMed association
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term
term mapping to NCIT ID
A subproperty of seeAlso that represents a UMLS CUI identifier mapped to the specified term
term mapping to UMLS CUI
An annotation property that refers to a code defined by NCIT
NCIT code
alternative term in Chinese
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
tooth SubClassOf 'never in taxon' value 'Aves'
S never_in_taxon T iff: S SubClassOf in_taxon only not T.
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
Class: ?X DisjointWith: RO_0002162 some ?Y
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
present in taxon
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
Notes on the how instances of this class vary across species.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
An annotation property that represents the trade name of a product.
trade name
The vaccine Prevnar (trade name) has a FDA-defined proper name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein). Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
An annotation property that represents the proper name of a vaccine, which is defined in an official way such as one defined by FDA.
vaccine proper name
The vaccine Prevnar has the manufacturer: Wyeth Pharmaceuticals Inc. Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
An annotation property that represents the manufacturer of a product such as vaccine
manufacturer
The vaccine Prevnar has the indications: - Immunization of infants 2, 4, 6 and 12-15 months of age to prevent invasive pneumococcal disease. - Immunization of infants and toddlers against otitis media caused by vaccine serotypes. Reference: https://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm180017.htm
An annotation property that represents the indications of a vaccine defined by the USA FDA.
FDA vaccine indications
Prevnar has the package insert PDF URL: https://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM137038.pdf . Recorded on 11/26/2018.
An annotation property that represents a URL of the package insert PDF document of a licensed vaccine
vaccine package insert PDF URL
A number that is generated by FDA based on a request from an applicant of a product licensing.
vaccine submission’s tracking number
A metadata relation between a class and its taxonomic rank (eg species, family)
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
An entity responsible for making contributions to the content of the resource.
Contributor
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the resource.
Date
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
The topic of the content of the resource.
Subject and Keywords
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
label
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
inheres in at all times
bearer of
bearer_of
is bearer of
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
[copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
[copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
[copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
[copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
[copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
concretized by at some time
You may concretize a piece of software by installing it in your computer
You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
you may concretize a poem as a pattern of memory traces in your head
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
(forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
(forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]
concretizes at some time
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
A pain s-depends_on the organism that is experiencing the pain
a gait s-depends_on the walking object. (All at some specific time.)
a shape s-depends_on the shaped object
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
the two-sided reciprocal s-dependence of the roles of husband and wife [20
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
BFO2 Reference: specifically dependent continuant\; process; process boundary
To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
specifically depends on at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
occupies spatial region at some time
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
has proper occurrent part
[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has spatial occupant at some time
[copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
[copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
[copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
[copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
[copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
[copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
[copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has specific dependent at some time
[copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
[copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
has spatiotemporal occupant
BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
occupies spatiotemporal region
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
projects onto spatial region at some time
spatial projection of spatiotemporal at some time
projects onto temporal region
temporal projection of spatiotemporal
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
(iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]
bearer of at all times
a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.
(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]
has disposition at all times
has participant at all times
has specific dependent at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
specifically depends on at some time
Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
[copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
part of continuant at some time
[copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
has continuant part at some time
[copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
[copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
part of continuant at all times that whole exists
[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has continuant part at all times that part exists
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
x proximal_to y iff x is closer to the point of attachment with the body than y.
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
A shortcut object property that represents a relation between a biological entity and a material entity inside a human patient where the biological entity is susceptible to be differentially regulated in the material entity (e.g., cell or anatomic entity) of a human patient with a specific disease.
susceptible to be differentially regulated in human disease
A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be differentially regulated in a cell of a chronical kidney disease (CKD) patient.
susceptible to be differentially regulated in CKD in cell
A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be up-regulated in a cell of a chronical kidney disease (CKD) patient
susceptible to be up-regulated in CKD in cell
A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be down-regulated in a cell of a chronical kidney disease (CKD) patient
susceptible to be down-regulated in CKD in cell
A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be differentially regulated in a cell in an acute kidney injury (AKI) patient.
susceptible to be differentially regulated in AKI in cell
A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be differentially regulated in the anatomic location of a chronical kidney disease (CKD) patient.
susceptible to be differentially regulated in CKD in anatomic location
A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be up-regulated in the anatomic location of a chronical kidney disease (CKD) patient.
susceptible to be up-regulated in CKD in anatomic location
A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be down-regulated in the anatomic location of a chronical kidney disease (CKD) patient.
susceptible to be down-regulated in CKD in anatomic location
A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be differentially regulated in the anatomic location of an acute kidney injury (AKI) patient.
susceptible to be differentially regulated in AKI in anatomic location
A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be up-regulated in a cell of an acute kidney injury (AKI) patient
susceptible to be up-regulated in AKI in cell
A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be down-regulated in a cell of an acute kidney injury (AKI) patient
susceptible to be down-regulated in AKI in cell
A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be down-regulated in the anatomic location of an acute kidney injury (AKI) patient.
susceptible to be down-regulated in AKI in anatomic location
susceptible to be up-regulated in AKI in anatomic location
An object property that represents a relation between a gene and a cell type where the gene is the gene marker of the cell type
is gene marker of cell
An object property that represents a relation between a celltype and a gene where the cell has the gene as its gene marker
cell has gene marker
An object property that represents a relation between a disease and a biomarker where the disease has the biomarker.
disease has biomarker
An object property that represents a relation between a disease and a gene where the disease has the gene as a biomarker.
disease has gene biomarker
An object property that represents a relation between a disease and a protein where the disease has the protein as a biomarker.
disease has protein biomarker
An object property that represents a relation between a disease and a RNA where the disease has the mRNA as a biomarker.
disease has RNA biomarker
An object property that represents a relation between a biomarker and a disease where the biomarker serves as a biomarker role for the disease
biomarker of disease
An object property that represents a relation between a gene and a disease where the gene is a biomarkder of the disease.
gene biomarker of disease
An object property that represents a relation between a protein and a disease where the protein is a biomarkder of the disease.
protein biomarker of disease
An object property that represents a relation between a RNA of a gene and a disease where the mRNA expression of the gene is a biomarkder of the disease.
RNA biomarker of disease
biomarker related
is biomarker of cell
encodes protein
An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased.
an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality.
This is a shortcut relation of the following full version: 'has participant' some (participant 'has quality' ) in: process 'has participant' some (participant 'has quality' some quality)
has participant quality
a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in.
AE occurs in
a specific 'preceded by' object property that has a domain of an adverse event.
adverse event preceded by
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
Alan Ruttenberg
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
The inverse property of is_specified_output_of
is_manufactured_by
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
Liju Fan
has_make
has_manufacturer
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
has organization member
A relation between an information content entity and a value specification that specifies its value.
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
is genome of organism
a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
is gene of organism
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
true
A kidney biopsy protocol is executed in a kidney biopsy process.
A shortcut relation that is concretized and realized in some process.
executed in
A 'has part' object property that has the range of a textual question
has question
form generated by
An object property that indicates a relation between a question and an answer
has answer
An object property that represents a relation between a form and a question where the question sets up an exclusion criterion. Specifically, when the answer to the question is Yes, the candidate becomes ineligible for the participation of a study.
has exclusion question
An object property that represents a relation between a form and a question where the question sets up an inclusion criterion. Specifically, when the answer to the question is Yes, then the candidate fulfills a criterion for being eligible for participating in a study. Note that there might be other criteria that the candidate also need to meet in order to be fully eligible. Meanwhile, if the answer is No, the candidate may still be eligible depending on the other restriction.
has inclusion question
has process quality
An object property that represents a relation between a person with a biological sex and a process where the person has a specific susceptbility to a process
has sex-specific susceptibility to
An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding male population
has increased susceptibility compared to male to
Male has increased susceptibility to death due to COVID-19 infection compared to female. Note that in this case, the male can mean one single male individual. however, the female here means the whole female population. It is reported that the ratio of deaths in COVID-19 infected males to females is 1·21:1 in high-income countries, but 2·8:1 in low-income countries (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023692/).
An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding female population
has increased susceptibility compared to female to
An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to the whole population with all sexes included
has increased sex-specific susceptibility compared to sex baseline to
A care_site has a care_site_id (OMOP: http://ohdsi.github.io/CommonDataModel/cdm54.html#CARE_SITE)
An object property that represents a relation between an entity and its corresponding identifier that is owned by the entity.
has identifier
A patient was admitted to the hospital from home or a long-term care facility.
An object property that represents a relation between a patient and a site from which the patient was admitted.
admitted from
After a visit, a person was discharged to home or a long-term care site. Typically this applies only to visits that have a length of stay of a day or more.
An object property that represents a relation between a patient and a site to which the patient was discharged after a visit.
discharged to
An admission diagnosis status has the content of adimission diagnosis (as an information content entity).
An object property that represents a relation between a status and an information content entity where the status has its content information defined by the information content entity.
has status content
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
'inheres in at all times'
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
concretizes
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
has boundary
has_2D_boundary
has 2D boundary
innervated_by
X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
Primitive instance level timing relation between events
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
Relation between a neuron and a material anatomical entity that its soma is part of.
<http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
has soma location
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
has plasma membrane part
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has synaptic terminal in
A overlaps B if they share some part in common.
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
lactation SubClassOf 'only in taxon' some 'Mammalia'
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
connects
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
relation between an artery and the structure is supplies with blood.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
has phenotype
phenotype of
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from
develops into
'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
expressed in
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
directly develops from
directly develops into
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
has active participant
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
adjacent to
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
Relation between occurrents, shares an end boundary with.
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
Any relationship between an exposure event or process and any other entity.
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1.
b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
developmentally replaces
developmentally succeeded by
y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process.
expresses
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
results in development of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
results in morphogenesis of
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
characteristic of part of
inheres in part of
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
results in acquisition of features of
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
ecologically related to
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
genomically related to
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
regulates levels of
enabled by
regulated by
negatively regulated by
positively regulated by
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
has target end location
Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
results in transport along
Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
results in transport across
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
results in transport to from or in
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
formed as result of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
tributary of
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
branching part of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
This relation groups causal relations between material entities and causal relations between processes
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
A relationship that holds between a disease and organism
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
causal relation between material entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
determined by (system to material entity)
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
causally influenced by (material entity to material entity)
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
causally influences (material entity to material entity)
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
A relation that holds between an attribute or a qualifier and another attribute.
placeholder relation to indicate normality/abnormality.
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
Editor note: TODO property chain: disease_has_location <- dhbido o occurs_in
A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
causal relationship with disease as subject
A relationship between a disease and a process where the disease process disrupts the execution of the process.
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
causally upstream of or within, negative effect
causally upstream of or within, positive effect
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
p acts on population of c iff c' is a collection, has members of type c, and p has participant c
acts on population of
results in fusion of
A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.
has synaptic IO in region
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
This relation groups relations between diseases and any other kind of entity.
p has anatomical participant c iff p has participant c, and c is an anatomical entity
results in changes to anatomical or cellular structure
a object property that specifies a relation between a vaccine and a vaccine allergen
a shortcut relation that equals to: 'processed material' and (is_specified_output_of some 'vaccine preparation') and ('has function' some ('vaccine function' and ('is realized by' only ('vaccine immunization' and (realizes some ('vaccine host role' and (role_of some 'organism')))))))). The domain of this relation is a vaccine. The range of this relation is a organism.
a shortcut relation that equals to: processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some ('immunization target role' and (role_of some 'MICROBE')))))))) The domain of this relation is a vaccine. The range of this relation is a microbe (a bacterium, a virus, a fungus, and a parasite)
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).
A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer c if and only if P has_component multiple instances of c and each instance of c is covalently attached to another instance of c.
The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows one to indicate the number of instances of c.
See document https://docs.google.com/document/d/15iVMtMyYbQSlvUDgn2XUaDzpwkB0USZI for full definition.
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
x is a conduit for y iff y passes through the lumen of x.
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
has_proper_part
has measurement value
The data type "last 4 digits of social security number" has digit number of 4.
A data property that represents a relation between a data type and a number of integer digits that the data type has.
has digit number
quality measured by year
Chemical Ingredients [Chemical/Ingredient]
Diseases, Manifestations or Physiologic States
Diseases, Manifestations or Physiologic States [Disease/Finding]
Mental Disorders and Manifestations [Disease/Finding]
Small Ion Transport Pump Interactions [MoA]
Biological Macromolecular Activity [MoA]
G-Protein-linked Receptor-Effector Interactions
G-Protein-linked Receptor Interactions [MoA]
Cytokine Receptor Superfamily Interactions
Cytokine Receptor Superfamily Interactions [MoA]
Cholinergic Nicotinic Receptor Interactions
Cholinergic Nicotinic Receptor Interactions [MoA]
Cellular or Molecular Interactions [MoA]
Immunologic and Biological Factors [MoA]
Malformations of organs or body parts during development in utero.
Congenital Abnormalities [Disease/Finding]
Congenital abnormalities caused by medicinal substances or drugs of abuse given to or taken by the mother, or to which she is inadvertently exposed during the manufacture of such substances. The concept excludes abnormalities resulting from exposure to non-medicinal chemicals in the environment.
Abnormalities, Drug-Induced [Disease/Finding]
Disturbances in the ACID-BASE EQUILIBRIUM of the body.
A pathologic condition of acid accumulation or depletion of base in the body. The two main types are RESPIRATORY ACIDOSIS and metabolic acidosis, due to metabolic acid build up.
An acute organic mental disorder induced by cessation or reduction in chronic alcohol consumption. Clinical characteristics include CONFUSION; DELUSIONS; vivid HALLUCINATIONS; TREMOR; agitation; insomnia; and signs of autonomic hyperactivity (e.g., elevated blood pressure and heart rate, dilated pupils, and diaphoresis). This condition may occasionally be fatal. It was formerly called delirium tremens. (From Adams et al., Principles of Neurology, 6th ed, p1175)
Alcohol Withdrawal-Induced Delirium Tremens
Delirium Tremens, Alcohol Withdrawal Induced
Alcohol Withdrawal Delirium [Disease/Finding]
A pathological condition that removes acid or adds base to the body fluids.
Absence of urine formation. It is usually associated with complete bilateral ureteral (URETER) obstruction, complete lower urinary tract obstruction, or unilateral ureteral obstruction when a solitary kidney is present.
A pathological constriction occurring in the region below the AORTIC VALVE. It is characterized by restricted outflow from the LEFT VENTRICLE into the AORTA.
Aortic Stenosis, Subvalvular [Disease/Finding]
A pathological constriction that can occur above (supravalvular stenosis), below (subvalvular stenosis), or at the AORTIC VALVE. It is characterized by restricted outflow from the LEFT VENTRICLE into the AORTA.
Any disturbances of the normal rhythmic beating of the heart or MYOCARDIAL CONTRACTION. Cardiac arrhythmias can be classified by the abnormalities in HEART RATE, disorders of electrical impulse generation, or impulse conduction.
Accumulation or retention of free fluid within the peritoneal cavity.
Infections caused by bacteria and fungi, general, specified, or unspecified.
Bacterial Infections and Mycoses [Disease/Finding]
Psychiatric illness or diseases manifested by breakdowns in the adaptational process expressed primarily as abnormalities of thought, feeling, and behavior producing either distress or impairment of function.
Hemorrhagic and thrombotic disorders that occur as a consequence of abnormalities in blood coagulation due to a variety of factors such as COAGULATION PROTEIN DISORDERS; BLOOD PLATELET DISORDERS; BLOOD PROTEIN DISORDERS or nutritional conditions.
Blood Coagulation Disorders [Disease/Finding]
Bone Diseases, Metabolic [Disease/Finding]
Cardiac arrhythmias that are characterized by excessively slow HEART RATE, usually below 50 beats per minute in human adults. They can be classified broadly into SINOATRIAL NODE dysfunction and ATRIOVENTRICULAR BLOCK.
Pathologic conditions affecting the BRAIN, which is composed of the intracranial components of the CENTRAL NERVOUS SYSTEM. This includes (but is not limited to) the CEREBRAL CORTEX; intracranial white matter; BASAL GANGLIA; THALAMUS; HYPOTHALAMUS; BRAIN STEM; and CEREBELLUM.
Central Nervous System Disorders, Intracranial
Central Nervous System Intracranial Disorders
Intracranial Central Nervous System Disorders
Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization.
Calcium Metabolism Disorders [Disease/Finding]
An abnormal concretion occurring mostly in the urinary and biliary tracts, usually composed of mineral salts. Also called stones.
Infection with a fungus of the genus CANDIDA. It is usually a superficial infection of the moist areas of the body and is generally caused by CANDIDA ALBICANS. (Dorland, 27th ed)
A clinical syndrome characterized by development, usually in infancy or childhood, of a chronic, often widespread candidiasis of skin, nails, and mucous membranes. It may be secondary to one of the immunodeficiency syndromes, inherited as an autosomal recessive trait, or associated with defects in cell-mediated immunity, endocrine disorders, dental stomatitis, or malignancy.
Candidiasis, Chronic Mucocutaneous [Disease/Finding]
Candidiasis of the skin manifested as eczema-like lesions of the interdigital spaces, perleche, or chronic paronychia. (Dorland, 27th ed)
Candidiasis, Cutaneous [Disease/Finding]
Infection of the mucous membranes of the mouth by a fungus of the genus CANDIDA. (Dorland, 27th ed)
Infection of the VULVA and VAGINA with a fungus of the genus CANDIDA.
Candidiasis, Vulvovaginal [Disease/Finding]
A state of subnormal or depressed cardiac output at rest or during stress. It is a characteristic of CARDIOVASCULAR DISEASES, including congenital, valvular, rheumatic, hypertensive, coronary, and cardiomyopathic. The serious form of low cardiac output is characterized by marked reduction in STROKE VOLUME, and systemic vasoconstriction resulting in cold, pale, and sometimes cyanotic extremities.
Pathological conditions involving the CARDIOVASCULAR SYSTEM including the HEART; the BLOOD VESSELS; or the PERICARDIUM.
Cardiovascular Diseases [Disease/Finding]
Diseases of any component of the brain (including the cerebral hemispheres, diencephalon, brain stem, and cerebellum) or the spinal cord.
Central Nervous System Diseases [Disease/Finding]
A spectrum of pathological conditions of impaired blood flow in the brain. They can involve vessels (ARTERIES; or VEINS) in the CEREBRUM, the CEREBELLUM, and the BRAIN STEM. Major categories include INTRACRANIAL ARTERIOVENOUS MALFORMATIONS; BRAIN ISCHEMIA; CEREBRAL HEMORRHAGE; and others.
Cerebrovascular Disorders [Disease/Finding]
A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused. Coma generally occurs when there is dysfunction or injury involving both cerebral hemispheres or the brain stem RETICULAR FORMATION.
Organic mental disorders in which there is impairment of the ability to maintain awareness of self and environment and to respond to environmental stimuli. Dysfunction of the cerebral hemispheres or brain stem RETICULAR FORMATION may result in this condition.
Consciousness Disorders [Disease/Finding]
A chronic transmural inflammation that may involve any part of the DIGESTIVE TRACT from MOUTH to ANUS, mostly found in the ILEUM, the CECUM, and the COLON. In Crohn disease, the inflammation, extending through the intestinal wall from the MUCOSA to the serosa, is characteristically asymmetric and segmental. Epithelioid GRANULOMAS may be seen in some patients.
Infection with CYTOMEGALOVIRUS, characterized by enlarged cells bearing intranuclear inclusions. Infection may be in almost any organ, but the salivary glands are the most common site in children, as are the lungs in adults.
Cytomegalovirus Infections [Disease/Finding]
A condition produced by dietary or metabolic deficiency. The term includes all diseases caused by an insufficient supply of essential nutrients, i.e., protein (or amino acids), vitamins, and minerals. It also includes an inadequacy of calories. (From Dorland, 27th ed; Stedman, 25th ed)
The condition that results from excessive loss of water from a living organism.
A chronic inflammatory genetically determined disease of the skin marked by increased ability to form reagin (IgE), with increased susceptibility to allergic rhinitis and asthma, and hereditary disposition to a lowered threshold for pruritus. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee. In infants it is known as infantile eczema.
Superficial infections of the skin or its appendages by any of various fungi.
Diseases in any part of the GASTROINTESTINAL TRACT or the accessory organs (LIVER; BILIARY TRACT; PANCREAS).
Digestive System Diseases [Disease/Finding]
Immunologically mediated adverse reactions to medicinal substances used legally or illegally.
Manifestations of the adverse effects of drugs administered therapeutically or in the course of diagnostic techniques. It does not include accidental or intentional poisoning for which specific headings are available.
Abnormal fluid accumulation in TISSUES or body cavities. Most cases of edema are present under the SKIN in SUBCUTANEOUS TISSUE.
Female Urogenital Diseases and Pregnancy Complications
Pathological processes of the female URINARY TRACT, the reproductive system (GENITALIA, FEMALE), and disorders related to PREGNANCY.
Female Urogenital Diseases and Pregnancy Complications [Disease/Finding]
Gastrointestinal disturbances, skin eruptions, or shock due to allergic reactions to allergens in food.
INFLAMMATION of any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM. Causes of gastroenteritis are many including genetic, infection, HYPERSENSITIVITY, drug effects, and CANCER.
Diseases in any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM.
Gastrointestinal Diseases [Disease/Finding]
Pathological processes involving the female reproductive tract (GENITALIA, FEMALE).
Genital Diseases, Female [Disease/Finding]
Pathological processes involving the male reproductive tract (GENITALIA, MALE).
Genital Diseases, Male [Disease/Finding]
The clinical entity characterized by anorexia, diarrhea, loss of hair, leukopenia, thrombocytopenia, growth retardation, and eventual death brought about by the GRAFT VS HOST REACTION.
Cessation of heart beat or MYOCARDIAL CONTRACTION. If it is treated within a few minutes, heart arrest can be reversed in most cases to normal cardiac rhythm and effective circulation.
Impaired conduction of cardiac impulse that can occur anywhere along the conduction pathway, such as between the SINOATRIAL NODE and the right atrium (SA block) or between atria and ventricles (AV block). Heart blocks can be classified by the duration, frequency, or completeness of conduction block. Reversibility depends on the degree of structural or functional defects.
Pathological conditions involving the HEART including its structural and functional abnormalities.
A heterogeneous condition in which the heart is unable to pump out sufficient blood to meet the metabolic need of the body. Heart failure can be caused by structural defects, functional abnormalities (VENTRICULAR DYSFUNCTION), or a sudden overload beyond its capacity. Chronic heart failure is more common than acute heart failure which results from sudden insult to cardiac function, such as MYOCARDIAL INFARCTION.
Pathological conditions involving any of the various HEART VALVES and the associated structures (PAPILLARY MUSCLES and CHORDAE TENDINEAE).
Disorders of the blood and blood forming tissues.
Hematologic diseases and diseases of the lymphatic system collectively. Hemic diseases include disorders involving the formed elements (e.g., ERYTHROCYTE AGGREGATION, INTRAVASCULAR) and chemical components (e.g., BLOOD PROTEIN DISORDERS); lymphatic diseases include disorders relating to lymph, lymph nodes, and lymphocytes.
Hemic and Lymphatic Diseases [Disease/Finding]
Bleeding or escape of blood from a vessel.
Spontaneous or near spontaneous bleeding caused by a defect in clotting mechanisms (BLOOD COAGULATION DISORDERS) or another abnormality causing a structural flaw in the blood vessels (HEMOSTATIC DISORDERS).
Infection of the genitals (GENITALIA) with HERPES SIMPLEX VIRUS in either the males or the females.
A group of acute infections caused by herpes simplex virus type 1 or type 2 that is characterized by the development of one or more small fluid-filled vesicles with a raised erythematous base on the skin or mucous membrane. It occurs as a primary infection or recurs due to a reactivation of a latent infection. (Dorland, 27th ed.)
Virus diseases caused by the HERPESVIRIDAE.
Herpesviridae Infections [Disease/Finding]
Abnormally high level of calcium in the blood.
Abnormally high potassium concentration in the blood, most often due to defective renal excretion. It is characterized clinically by electrocardiographic abnormalities (elevated T waves and depressed P waves, and eventually by atrial asystole). In severe cases, weakness and flaccid paralysis may occur. (Dorland, 27th ed)
Excessive amount of sodium in the blood. (Dorland, 27th ed)
Altered reactivity to an antigen, which can result in pathologic reactions upon subsequent exposure to that particular antigen.
Hypersensitivity reactions which occur within minutes of exposure to challenging antigen due to the release of histamine which follows the antigen-antibody reaction and causes smooth muscle contraction and increased vascular permeability.
Hypersensitivity, Immediate [Disease/Finding]
Persistently high systemic arterial BLOOD PRESSURE. Based on multiple readings (BLOOD PRESSURE DETERMINATION), hypertension is currently defined as when SYSTOLIC PRESSURE is consistently greater than 140 mm Hg or when DIASTOLIC PRESSURE is consistently 90 mm Hg or more.
Reduction of the blood calcium below normal. Manifestations include hyperactive deep tendon reflexes, Chvostek's sign, muscle and abdominal cramps, and carpopedal spasm. (Dorland, 27th ed)
A syndrome of abnormally low BLOOD GLUCOSE level. Clinical hypoglycemia has diverse etiologies. Severe hypoglycemia eventually lead to glucose deprivation of the CENTRAL NERVOUS SYSTEM resulting in HUNGER; SWEATING; PARESTHESIA; impaired mental function; SEIZURES; COMA; and even DEATH.
Deficiency of sodium in the blood; salt depletion. (Dorland, 27th ed)
Absence or reduced levels of prothrombin in the blood.
Syndromes in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.
Immunologic Deficiency Syndromes [Disease/Finding]
Disorders caused by abnormal or absent immunologic mechanisms, whether humoral, cell-mediated, or both.
Immune System Diseases [Disease/Finding]
Diseases of newborn infants present at birth (congenital) or developing within the first month of birth. It does not include hereditary diseases not manifesting at birth or within the first 30 days of life nor does it include inborn errors of metabolism. Both HEREDITARY DISEASES and METABOLISM, INBORN ERRORS are available as general concepts.
Infant, Newborn, Diseases [Disease/Finding]
Infant, Premature, Diseases [Disease/Finding]
Invasion of the host organism by microorganisms that can cause pathological conditions or diseases.
Pathological processes in any segment of the INTESTINE from DUODENUM to RECTUM.
Stones in the KIDNEY, usually formed in the urine-collecting area of the kidney (KIDNEY PELVIS). Their sizes vary and most contains CALCIUM OXALATE.
Pathological processes of the KIDNEY or its component tissues.
The end-stage of CHRONIC RENAL INSUFFICIENCY. It is characterized by the severe irreversible kidney damage (as measured by the level of PROTEINURIA) and the reduction in GLOMERULAR FILTRATION RATE to less than 15 ml per min (Kidney Foundation: Kidney Disease Outcome Quality Initiative, 2002). These patients generally require HEMODIALYSIS or KIDNEY TRANSPLANTATION.
Kidney Failure, Chronic [Disease/Finding]
Lacrimal Apparatus Diseases [Disease/Finding]
Liver disease in which the normal microcirculation, the gross vascular anatomy, and the hepatic architecture have been variably destroyed and altered with fibrous septa surrounding regenerated or regenerating parenchymal nodules.
Pathological processes involving any part of the LUNG.
A nutritional condition produced by a deficiency of magnesium in the diet, characterized by anorexia, nausea, vomiting, lethargy, and weakness. Symptoms are paresthesias, muscle cramps, irritability, decreased attention span, and mental confusion, possibly requiring months to appear. Deficiency of body magnesium can exist even when serum values are normal. In addition, magnesium deficiency may be organ-selective, since certain tissues become deficient before others. (Harrison's Principles of Internal Medicine, 12th ed, p1936)
Generic term for diseases caused by an abnormal metabolic process. It can be congenital due to inherited enzyme abnormality (METABOLISM, INBORN ERRORS) or acquired due to disease of an endocrine organ or failure of a metabolically important organ such as the liver. (Stedman, 26th ed)
General or unspecified diseases of the stomatognathic system, comprising the mouth, teeth, jaws, and pharynx.
Stomatognathic Diseases [Disease/Finding]
A diminution of the skeletal muscle tone marked by a diminished resistance to passive stretching.
Diseases of the muscles and their associated ligaments and other connective tissue and of the bones and cartilage viewed collectively.
Musculoskeletal Diseases [Disease/Finding]
Congenital, Hereditary, and Neonatal Diseases and Abnormalities
Diseases existing at birth and often before birth, or that develop during the first month of life (INFANT, NEWBORN, DISEASES), regardless of causation. Of these diseases, those characterized by structural deformities are termed CONGENITAL ABNORMALITIES.
Congenital, Hereditary, and Neonatal Diseases and Abnormalities [Disease/Finding]
New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.
A collective term for the various histological types of NEOPLASMS. It is more likely to be used by searchers than by indexers and catalogers.
Neoplasms by Histologic Type [Disease/Finding]
A collective term for precoordinated organ/neoplasm headings locating neoplasms by organ, as BRAIN NEOPLASMS; DUODENAL NEOPLASMS; LIVER NEOPLASMS; etc.
Neoplasms composed of primordial GERM CELLS of embryonic GONADS or of elements of the germ layers of the EMBRYO, MAMMALIAN. The concept does not refer to neoplasms located in the gonads or present in an embryo or FETUS.
Neoplasms, Germ Cell and Embryonal [Disease/Finding]
Neoplasms composed of nerve tissue. This concept does not refer to neoplasms located in the nervous system or its component nerves.
Neoplasms, Nerve Tissue [Disease/Finding]
Pathological processes of the KIDNEY without inflammatory or neoplastic components. Nephrosis may be a primary disorder or secondary complication of other diseases. It is characterized by the NEPHROTIC SYNDROME indicating the presence of PROTEINURIA and HYPOALBUMINEMIA with accompanying EDEMA.
A condition characterized by severe PROTEINURIA, greater than 3.5 g/day in an average adult. The substantial loss of protein in the urine results in complications such as HYPOPROTEINEMIA; generalized EDEMA; HYPERTENSION; and HYPERLIPIDEMIAS. Diseases associated with nephrotic syndrome generally cause chronic kidney dysfunction.
Diseases of the central and peripheral nervous system. This includes disorders of the brain, spinal cord, cranial nerves, peripheral nerves, nerve roots, autonomic nervous system, neuromuscular junction, and muscle.
Nervous System Diseases [Disease/Finding]
Clinical signs and symptoms caused by nervous system injury or dysfunction.
Neurologic Manifestations [Disease/Finding]
Disorders caused by nutritional imbalance, either overnutrition or undernutrition.
A collective term for nutritional disorders resulting from poor absorption or nutritional imbalance, and metabolic disorders resulting from defects in biosynthesis (ANABOLISM) or breakdown (CATABOLISM) of endogenous substances.
Nutritional and Metabolic Diseases [Disease/Finding]
An infection caused by an organism which becomes pathogenic under certain conditions, e.g., during immunosuppression.
Opportunistic Infections [Disease/Finding]
Reduction of bone mass without alteration in the composition of bone, leading to fractures. Primary osteoporosis can be of two major types: postmenopausal osteoporosis (OSTEOPOROSIS, POSTMENOPAUSAL) and age-related or senile osteoporosis.
A neural crest tumor usually derived from the chromoreceptor tissue of a paraganglion, such as the carotid body, or medulla of the adrenal gland (usually called a chromaffinoma or pheochromocytoma). It is more common in women than in men. (Stedman, 25th ed; from Segen, Dictionary of Modern Medicine, 1992)
Infections or infestations with parasitic organisms. They are often contracted through contact with an intermediate vector, but may occur as the result of direct exposure.
The abnormal mechanisms and forms involved in the dysfunctions of tissues and organs.
A usually benign, well-encapsulated, lobular, vascular tumor of chromaffin tissue of the ADRENAL MEDULLA or sympathetic paraganglia. The cardinal symptom, reflecting the increased secretion of EPINEPHRINE and NOREPINEPHRINE, is HYPERTENSION, which may be persistent or intermittent. During severe attacks, there may be HEADACHE; SWEATING, palpitation, apprehension, TREMOR; PALLOR or FLUSHING of the face, NAUSEA and VOMITING, pain in the CHEST and ABDOMEN, and paresthesias of the extremities. The incidence of malignancy is as low as 5% but the pathologic distinction between benign and malignant pheochromocytomas is not clear. (Dorland, 27th ed; DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, p1298)
A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
Pathologic processes that affect patients after a surgical procedure. They may or may not be related to the disease for which the surgery was done, and they may or may not be direct results of the surgery.
Postoperative Complications [Disease/Finding]
A common genetically determined, chronic, inflammatory skin disease characterized by rounded erythematous, dry, scaling patches. The lesions have a predilection for nails, scalp, genitalia, extensor surfaces, and the lumbosacral region. Accelerated epidermopoiesis is considered to be the fundamental pathologic feature in psoriasis.
Excessive accumulation of extravascular fluid in the lung, an indication of a serious underlying disease or disorder. Pulmonary edema prevents efficient PULMONARY GAS EXCHANGE in the PULMONARY ALVEOLI, and can be life-threatening.
Respiratory Tract Diseases [Disease/Finding]
Respiratory Tract Neoplasms [Disease/Finding]
Virus diseases caused by the RETROVIRIDAE.
Retroviridae Infections [Disease/Finding]
Diseases due to or propagated by sexual contact.
Sexually Transmitted Diseases [Disease/Finding]
A pathological condition manifested by failure to perfuse or oxygenate vital organs.
Acute hemorrhage or excessive fluid loss resulting in HYPOVOLEMIA.
Clinical manifestations that can be either objective when observed by a physician, or subjective when perceived by the patient.
Diseases of the skin with a genetic component, usually the result of various inborn errors of metabolism.
Skin Diseases, Genetic [Disease/Finding]
Skin diseases caused by bacteria, fungi, parasites, or viruses.
Skin Diseases, Infectious [Disease/Finding]
Physiological and psychological symptoms associated with withdrawal from the use of a drug after prolonged administration or habituation. The concept includes withdrawal from smoking or drinking, as well as withdrawal from an administered drug.
Substance Withdrawal Syndrome [Disease/Finding]
Pathological Conditions, Signs and Symptoms
Abnormal anatomical or physiological conditions and objective or subjective manifestations of disease, not classified as disease or syndrome.
Pathological Conditions, Signs and Symptoms [Disease/Finding]
A disorder characterized by muscle twitches, cramps, and carpopedal spasm, and when severe, laryngospasm and seizures. This condition is associated with unstable depolarization of axonal membranes, primarily in the peripheral nervous system. Tetany usually results from HYPOCALCEMIA or reduced serum levels of MAGNESIUM that may be associated with HYPERVENTILATION; HYPOPARATHYROIDISM; RICKETS; UREMIA; or other conditions. (From Adams et al., Principles of Neurology, 6th ed, p1490)
Loss of the ability to maintain awareness of self and environment combined with markedly reduced responsiveness to environmental stimuli. (From Adams et al., Principles of Neurology, 6th ed, pp344-5)
Low-density crystals or stones in any part of the URINARY TRACT. Their chemical compositions often include CALCIUM OXALATE, magnesium ammonium phosphate (struvite), CYSTINE, or URIC ACID.
Abnormalities in the process of URINE voiding, including bladder control, frequency of URINATION, as well as the volume and composition of URINE.
Pathological processes of the male URINARY TRACT and the reproductive system (GENITALIA, MALE).
Male Urogenital Diseases [Disease/Finding]
Pathological processes of the URINARY TRACT in both males and females.
Inflammation of the vagina characterized by pain and a purulent discharge.
Pathological processes involving any of the BLOOD VESSELS in the cardiac or peripheral circulation. They include diseases of ARTERIES; VEINS; and rest of the vasculature system in the body.
A potentially lethal cardiac arrhythmia that is characterized by uncoordinated extremely rapid firing of electrical impulses (400-600/min) in HEART VENTRICLES. Such asynchronous ventricular quivering or fibrillation prevents any effective cardiac output and results in unconsciousness (SYNCOPE). It is one of the major electrocardiographic patterns seen with CARDIAC ARREST.
Ventricular Fibrillation [Disease/Finding]
Occlusion of the outflow tract in either the LEFT VENTRICLE or the RIGHT VENTRICLE of the heart. This may result from CONGENITAL HEART DEFECTS, predisposing heart diseases, complications of surgery, or HEART NEOPLASMS.
Ventricular Outflow Obstruction [Disease/Finding]
A general term for diseases produced by viruses.
Inflammation of the VULVA. It is characterized by PRURITUS and painful urination.
Inflammation of the VULVA and the VAGINA, characterized by discharge, burning, and PRURITUS.
Disturbances in the body's WATER-ELECTROLYTE BALANCE.
Water-Electrolyte Imbalance [Disease/Finding]
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
Chronic, non-specific inflammation of the GASTROINTESTINAL TRACT. Etiology may be genetic or environmental. This term includes CROHN DISEASE and ULCERATIVE COLITIS.
Inflammatory Bowel Diseases [Disease/Finding]
Viral diseases which are transmitted or propagated by sexual conduct.
Sexually Transmitted Diseases, Viral [Disease/Finding]
Corneal and conjunctival dryness due to deficient tear production, predominantly in menopausal and post-menopausal women. Filamentary keratitis or erosion of the conjunctival and corneal epithelium may be caused by these disorders. Sensation of the presence of a foreign body in the eye and burning of the eyes may occur.
An accidental or deliberate dose of a medication or street drug that is in excess of what is normally used.
Includes the spectrum of human immunodeficiency virus infections that range from asymptomatic seropositivity, thru AIDS-related complex (ARC), to acquired immunodeficiency syndrome (AIDS).
T-Lymphotropic Virus Type III Infections, Human
An excessive amount of fluid in the cornea due to damage of the epithelium or endothelium causing decreased visual acuity.
Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection.
Opportunistic infections found in patients who test positive for human immunodeficiency virus (HIV). The most common include PNEUMOCYSTIS PNEUMONIA, Kaposi's sarcoma, cryptosporidiosis, herpes simplex, toxoplasmosis, cryptococcosis, and infections with Mycobacterium avium complex, Microsporidium, and Cytomegalovirus.
AIDS-Related Opportunistic Infections [Disease/Finding]
A severe irreversible decline in the ability of kidneys to remove wastes, concentrate URINE, and maintain ELECTROLYTE BALANCE; BLOOD PRESSURE; and CALCIUM metabolism.
A collective term for diseases of the skin and its appendages and of connective tissue.
Skin and Connective Tissue Diseases [Disease/Finding]
Any of a variety of eruptive skin disorders characterized by erythema, oozing, vesiculation, and scaling. Etiology is varied.
Skin Diseases, Eczematous [Disease/Finding]
A group of dermatoses with distinct morphologic features. The primary lesion is most commonly a papule, usually erythematous, with a variable degree of scaling on the surface. Plaques form through the coalescing of primary lesions.
Skin Diseases, Papulosquamous [Disease/Finding]
Malignant neoplasms arising in the neuroectoderm, the portion of the ectoderm of the early embryo that gives rise to the central and peripheral nervous systems, including some glial cells.
Neuroectodermal Tumors [Disease/Finding]
Tumors whose cells possess secretory granules and originate from the neuroectoderm, i.e., the cells of the ectoblast or epiblast that program the neuroendocrine system. Common properties across most neuroendocrine tumors include ectopic hormone production (often via APUD CELLS), the presence of tumor-associated antigens, and isozyme composition.
Signs and symptoms of higher cortical dysfunction caused by organic conditions. These include certain behavioral alterations and impairments of skills involved in the acquisition, processing, and utilization of knowledge or information.
Neurobehavioral Manifestations [Disease/Finding]
Delirium, Dementia, Amnestic, Cognitive Disorders
Cognitive disorders including delirium, dementia, and other cognitive disorders. These may be the result of substance use, trauma, or other causes.
Delirium, Dementia, Amnestic, Cognitive Disorders [Disease/Finding]
Disorders related to substance abuse, the side effects of a medication, or toxin exposure.
Substance-Related Disorders [Disease/Finding]
Disorders related to or resulting from abuse or mis-use of alcohol.
Alcohol-Related Disorders [Disease/Finding]
Hemorrhagic and thrombotic disorders resulting from abnormalities or deficiencies of coagulation proteins.
Coagulation Protein Disorders [Disease/Finding]
Neurologic disorders caused by exposure to toxic substances through ingestion, injection, cutaneous application, or other method. This includes conditions caused by biologic, chemical, and pharmaceutical agents.
Neurotoxicity Syndromes [Disease/Finding]
Alcohol-Induced Disorders, Nervous System
Acute and chronic neurologic disorders associated with the various neurologic effects of ETHANOL. Primary sites of injury include the brain and peripheral nerves.
Ethanol Induced Nervous System Disorders
Ethanol-Induced Disorders, Nervous System
Ethanol-Induced Nervous System Disorders
Ethyl Alcohol Abuse Neurologic Syndromes
Nervous System Disorders, Ethanol-Induced
Alcohol-Induced Disorders, Nervous System [Disease/Finding]
Bleeding within the SKULL, including hemorrhages in the brain and the three membranes of MENINGES. The escape of blood often leads to the formation of HEMATOMA in the cranial epidural, subdural, and subarachnoid spaces.
Intracranial Hemorrhages [Disease/Finding]
Disorders stemming from the misuse and abuse of alcohol.
Alcohol-Induced Disorders [Disease/Finding]
An abnormal structural condition of the human body, usually macroscopic, that is common to a variety of different diseases.
Pathological Conditions, Anatomical [Disease/Finding]
Signs and symptoms associated with diseases of the muscle, neuromuscular junction, or peripheral nerves.
Neuromuscular Manifestations [Disease/Finding]
A type of constriction that is caused by the presence of a fibrous ring (discrete type) below the AORTIC VALVE, anywhere between the aortic valve and the MITRAL VALVE. It is characterized by restricted outflow from the LEFT VENTRICLE into the AORTA.
Discrete Subaortic Stenosis [Disease/Finding]
The largest class of organic compounds, including STARCH; GLYCOGEN; CELLULOSE; POLYSACCHARIDES; and simple MONOSACCHARIDES. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n.
A quinazoline-sulfonamide that is considered a thiazide-like diuretic which is long-acting so useful in chronic RENAL FAILURE. It also tends to lower BLOOD PRESSURE and increase POTASSIUM loss.
6-Quinazolinesulfonamide, 7-chloro-1,2,3,4-tetrahydro-2-methyl-3-(2-methylphenyl)-4-oxo-
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
A catecholamine derivative with specificity for BETA-1 ADRENERGIC RECEPTORS. It is commonly used as a cardiotonic agent after CARDIAC SURGERY and during DOBUTAMINE STRESS ECHOCARDIOGRAPHY.
1,2-Benzenediol, 4-(2-((3-(4-hydroxyphenyl)-1-methylpropyl)amino)ethyl)-, (+-)-
One of the catecholamine NEUROTRANSMITTERS in the brain. It is derived from TYROSINE and is the precursor to NOREPINEPHRINE and EPINEPHRINE. Dopamine is a major transmitter in the extrapyramidal system of the brain, and important in regulating movement. A family of receptors (RECEPTORS, DOPAMINE) mediate its action.
A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)
A vitamin that includes both CHOLECALCIFEROLS and ERGOCALCIFEROLS, which have the common effect of preventing or curing RICKETS in animals. It can also be viewed as a hormone since it can be formed in SKIN by action of ULTRAVIOLET RAYS upon the precursors, 7-dehydrocholesterol and ERGOSTEROL, and acts on VITAMIN D RECEPTORS to regulate CALCIUM in opposition to PARATHYROID HORMONE.
A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants, VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K.
A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.
A primary source of energy for living organisms. It is naturally occurring and is found in fruits and other parts of plants in its free state. It is used therapeutically in fluid and nutrient replacement.
A strong corrosive acid that is commonly used as a laboratory reagent. It is formed by dissolving hydrogen chloride in water. GASTRIC ACID is the hydrochloric acid component of GASTRIC JUICE.
The major circulating metabolite of VITAMIN D3. It is produced in the LIVER and is the best indicator of the body's vitamin D stores. It is effective in the treatment of RICKETS and OSTEOMALACIA, both in azotemic and non-azotemic patients. Calcifediol also has mineralizing properties.
A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.
A salt used to replenish calcium levels, as an acid-producing diuretic, and as an antidote for magnesium poisoning.
The sodium salt of racemic or inactive lactic acid. It is a hygroscopic agent used intravenously as a systemic and urinary alkalizer.
Salts or esters of LACTIC ACID containing the general formula CH3CHOHCOOR.
A non-depolarizing neuromuscular blocking agent with short duration of action. Its lack of significant cardiovascular effects and its lack of dependence on good kidney function for elimination provide clinical advantage over alternate non-depolarizing neuromuscular blocking agents.
Isoquinolinium, 2,2'-(1,5-pentanediylbis(oxy(3-oxo-3,1-propanediyl)))bis(1-((3,4-dimethoxyphenyl)methyl))-1,2,3,4-tetrahydro-6,7-dimethoxy-2-methyl-
Macrolide antifungal antibiotic complex produced by Streptomyces noursei, S. aureus, and other Streptomyces species. The biologically active components of the complex are nystatin A1, A2, and A3.
A beta-lactamase inhibitor with very weak antibacterial action. The compound prevents antibiotic destruction of beta-lactam antibiotics by inhibiting beta-lactamases, thus extending their spectrum activity. Combinations of sulbactam with beta-lactam antibiotics have been used successfully for the therapy of infections caused by organisms resistant to the antibiotic alone.
4-Thia-1-azabicyclo(3.2.0)heptane-2-carboxylic acid, 3,3-dimethyl-7-oxo-, 4,4-dioxide, (2S-cis)-
Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)
A thiazide diuretic with actions and uses similar to those of HYDROCHLOROTHIAZIDE. (From Martindale, The Extra Pharmacopoeia, 30th ed, p812)
2H-1,2,4-Benzothiadiazine-7-sulfonamide, 6-chloro-, 1,1-dioxide
Derivative of 7-dehydroxycholesterol formed by ULTRAVIOLET RAYS breaking of the C9-C10 bond. It differs from ERGOCALCIFEROL in having a single bond between C22 and C23 and lacking a methyl group at C24.
An antiviral agent used in the treatment of cytomegalovirus retinitis. Foscarnet also shows activity against human herpesviruses and HIV.
Phosphinecarboxylic acid, dihydroxy-, oxide
Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys.
Magnesium Chloride [Chemical/Ingredient]
A ubiquitous sodium salt that is commonly used to season food. It plays an important biological role in maintaining the osmotic tension of blood and tissues. The OSMOLAR CONCENTRATION this and other SALTS accounts for SALINITY which influences the types of organisms that live in an ENVIRONMENT.
A macrolide isolated from the culture broth of a strain of Streptomyces tsukubaensis that has strong immunosuppressive activity in vivo and prevents the activation of T-lymphocytes in response to antigenic or mitogenic stimulation in vitro.
Organic nitrogenous bases. Many alkaloids of medical importance occur in the animal and vegetable kingdoms, and some have been synthesized. (Grant & Hackh's Chemical Dictionary, 5th ed)
A group of compounds that are derivatives of beta- aminoethylbenzene which is structurally and pharmacologically related to amphetamine. (From Merck Index, 11th ed)
A group of macrocyclic compounds formed by chain extension of multiple PROPIONATES and cyclized into a large (typically 12, 14, 16) membered lactone. They are often glycosylated. Many of them are ANTIBIOTICS.
Negatively charged atoms, radicals or groups of atoms which travel to the anode or positive pole during electrolysis.
Heterocyclic compounds of a ring with SULFUR and two NITROGEN atoms fused to a BENZENE ring. Members inhibit SODIUM-POTASSIUM-CHLORIDE SYMPORTERS and are used as DIURETICS.
Biogenic amines having only one amine moiety. Included in this group are all natural monoamines formed by the enzymatic decarboxylation of natural amino acids.
Biogenic Monoamines [Chemical/Ingredient]
Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. (Grant & Hackh's Chemical Dictionary, 5th ed)
Carboxylic acids that have open-chain molecular structures as opposed to ring-shaped structures.
Inorganic acids with a non metal, other than carbon, attached to hydrogen, or an acid radical containing no carbon.
Acids, Noncarboxylic [Chemical/Ingredient]
Cyclic AMIDES formed from aminocarboxylic acids by the elimination of water. Lactims are the enol forms of lactams.
Cyclic esters of hydroxy carboxylic acids, containing a 1-oxacycloalkan-2-one structure. Large cyclic lactones of over a dozen atoms are MACROLIDES.
A broad class of substances containing carbon and its derivatives. Many of these chemicals will frequently contain hydrogen with or without oxygen, nitrogen, sulfur, phosphorus, and other elements. They exist in either carbon chain or carbon ring form.
Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed)
Organic compounds that contain phosphorus as an integral part of the molecule. Included under this heading is broad array of synthetic compounds that are used as PESTICIDES and DRUGS.
Organophosphorus Compounds [Chemical/Ingredient]
Inorganic acids that contain phosphorus as an integral part of the molecule.
Inorganic compounds derived from hydrochloric acid that contain the Cl- ion.
A general class of ortho-dihydroxyphenylalkylamines derived from tyrosine.
A group of polycyclic compounds closely related biochemically to TERPENES. They include cholesterol, numerous hormones, precursors of certain vitamins, bile acids, alcohols (STEROLS), and certain natural drugs and poisons. Steroids have a common nucleus, a fused, reduced 17-carbon atom ring system, cyclopentanoperhydrophenanthrene. Most steroids also have two methyl groups and an aliphatic side-chain attached to the nucleus. (From Hawley's Condensed Chemical Dictionary, 11th ed)
A simple organophosphorus compound that inhibits DNA polymerase, especially in viruses and is used as an antiviral agent.
Phosphonoacetic Acid [Chemical/Ingredient]
A group of naturally occurring amines derived by enzymatic decarboxylation of the natural amino acids. Many have powerful physiological effects (e.g., histamine, serotonin, epinephrine, tyramine). Those derived from aromatic amino acids, and also their synthetic analogs (e.g., amphetamine), are of use in pharmacology.
Steroids with a hydroxyl group at C-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain. (IUPAC Steroid Nomenclature, 1987)
Steroids with methyl groups at C-10 and C-13 and a branched 8-carbon chain at C-17. Members include compounds with any degree of unsaturation; however, CHOLESTADIENES is available for derivatives containing two double bonds.
Inorganic compounds that contain chlorine as an integral part of the molecule.
Chlorine Compounds [Chemical/Ingredient]
Inorganic compounds that contain calcium as an integral part of the molecule.
Inorganic compounds that contain magnesium as an integral part of the molecule.
Magnesium Compounds [Chemical/Ingredient]
Two-ring crystalline hydrocarbons isolated from coal tar. They are used as intermediates in chemical synthesis, as insect repellents, fungicides, lubricants, preservatives, and, formerly, as topical antiseptics.
A class of saturated compounds consisting of two rings only, having two or more atoms in common, containing at least one hetero atom, and that take the name of an open chain hydrocarbon containing the same total number of atoms. (From Riguady et al., Nomenclature of Organic Chemistry, 1979, p31)
Bicyclo Compounds, Heterocyclic [Chemical/Ingredient]
Naphthalene rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.
Lipids, predominantly phospholipids, cholesterol and small amounts of glycolipids found in membranes including cellular and intracellular membranes. These lipids may be arranged in bilayers in the membranes with integral proteins between the layers and peripheral proteins attached to the outside. Membrane lipids are required for active transport, several enzymatic activities and membrane formation.
Amino acids and chains of amino acids connected by peptide linkages.
Amino Acids, Peptides, and Proteins [Chemical/Ingredient]
Inorganic compounds that contain sodium as an integral part of the molecule.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Any compound that contains a constituent sugar, in which the hydroxyl group attached to the first carbon is substituted by an alcoholic, phenolic, or other group. They are named specifically for the sugar contained, such as glucoside (glucose), pentoside (pentose), fructoside (fructose), etc. Upon hydrolysis, a sugar and nonsugar component (aglycone) are formed. (From Dorland, 28th ed; From Miall's Dictionary of Chemistry, 5th ed)
Substances that comprise all matter. Each element is made up of atoms that are identical in number of electrons and protons and in nuclear charge, but may differ in mass or number of neutrons.
Endogenous substances, usually proteins, that are involved in the blood coagulation process.
Blood Coagulation Factors [Chemical/Ingredient]
Steroids in which fission of one or more ring structures and concomitant addition of a hydrogen atom at each terminal group has occurred.
Multi-subunit proteins which function in IMMUNITY. They are produced by B LYMPHOCYTES from the IMMUNOGLOBULIN GENES. They are comprised of two heavy (IMMUNOGLOBULIN HEAVY CHAINS) and two light chains (IMMUNOGLOBULIN LIGHT CHAINS) with additional ancillary polypeptide chains depending on their isoforms. The variety of isoforms include monomeric or polymeric forms, and transmembrane forms (B-CELL ANTIGEN RECEPTORS) or secreted forms (ANTIBODIES). They are divided by the amino acid sequence of their heavy chains into five classes (IMMUNOGLOBULIN A; IMMUNOGLOBULIN D; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M) and various subclasses.
Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.
A class of compounds composed of repeating 5-carbon units of HEMITERPENES.
Proteins prepared by recombinant DNA technology.
Recombinant Proteins [Chemical/Ingredient]
A group of compounds with the heterocyclic ring structure of benzo(c)pyridine. The ring structure is characteristic of the group of opium alkaloids such as papaverine. (From Stedman, 25th ed)
Organic compounds containing both the hydroxyl and carboxyl radicals.
Hydroxy analogs of vitamin D 3; (CHOLECALCIFEROL); including CALCIFEDIOL; CALCITRIOL; and 24,25-DIHYDROXYVITAMIN D 3.
Hydroxycholecalciferols [Chemical/Ingredient]
Metals that constitute the group 2 (formerly group IIa) of the periodic table.
Metals, Alkaline Earth [Chemical/Ingredient]
Metals with low specific gravity, typically smaller than 5, characterized by a single valence (1, 2, or 3), a simple spectrum, strong electromotive force (positive), and colorless compounds. (From Grant & Hackh's Chemical Dictionary, 5th ed)
A group of compounds that contain the structure SO2NH2. Members of this group, also known as sulfa drugs, are derivatives of sulfanilamide, which competitively inhibit folic acid synthesis in microorganisms, and are bacteriostatic. They have been largely supplanted by more effective and less toxic antibiotics. (From Dorland, 28th ed)
Ring compounds having atoms other than carbon in their nuclei. (Grant & Hackh's Chemical Dictionary, 5th ed)
Heterocyclic Compounds [Chemical/Ingredient]
Acetic acid and its derivatives which may be formed by substitution reactions. Mono- and di-substituted, as well as halogenated compounds have been synthesized.
Organic compounds containing the carboxy group (-COOH). This group of compounds includes amino acids and fatty acids. Carboxylic acids can be saturated, unsaturated, or aromatic.
Cyclic hydrocarbons that contain multiple rings and share one or more atoms.
Inorganic compounds that contain phosphorus as an integral part of the molecule.
Phosphorus Compounds [Chemical/Ingredient]
A major group of unsaturated cyclic hydrocarbons containing two or more rings. The vast number of compounds of this important group, derived chiefly from petroleum and coal tar, are rather highly reactive and chemically versatile. The name is due to the strong and not unpleasant odor characteristic of most substances of this nature. (From Hawley's Condensed Chemical Dictionary, 12th ed, p96)
Polycyclic Hydrocarbons, Aromatic [Chemical/Ingredient]
A group of compounds derived from ammonia by substituting organic radicals for the hydrogens. (From Grant & Hackh's Chemical Dictionary, 5th ed)
Short-chain fatty acids of up to six carbon atoms in length. They are the major end products of microbial fermentation in the ruminant digestive tract and have also been implicated in the causation of neurological diseases in humans.
Fatty Acids, Volatile [Chemical/Ingredient]
Inorganic or organic derivatives of phosphonic acid with the general formula ROP(OH)2 or RP(=O)(OH)2. The tautomeric form of this compound (P(OH)3) is PHOSPHOROUS ACIDS. Nucleoside phosphonates have a phosphate-carbon bond that is more resistant to enzymatic cleavage than the normal phosphate-oxygen bond.
Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.
Derivatives of the saturated steroid cholestane with methyl groups at C-18 and C-19 and an iso-octyl side chain at C-17.
An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.
Twenty-carbon compounds derived from MEVALONIC ACID or deoxyxylulose phosphate.
Partial immunoglobulin molecules resulting from selective cleavage by proteolytic enzymes or generated through PROTEIN ENGINEERING techniques.
Immunoglobulin Fragments [Chemical/Ingredient]
Blood proteins whose activities affect or play a role in the functioning of the immune system.
Organic compounds containing carbon and hydrogen in the form of an unsaturated, usually hexagonal ring structure. The compounds can be single ring, or double, triple, or multiple fused rings.
Hydrocarbons, Aromatic [Chemical/Ingredient]
Electropositive chemical elements characterized by ductility, malleability, luster, and conductance of heat and electricity. They can replace the hydrogen of an acid and form bases with hydroxyl radicals. (Grant & Hackh's Chemical Dictionary, 5th ed)
All blood proteins except albumin ( = SERUM ALBUMIN, which is not a globulin) and FIBRINOGEN (which is not in the serum). The serum globulins are subdivided into ALPHA-GLOBULINS; BETA-GLOBULINS; and GAMMA-GLOBULINS on the basis of their electrophoretic mobilities. (From Dorland, 28th ed)
Inorganic or organic compounds that contain sulfur as an integral part of the molecule.
Simple sugars, carbohydrates which cannot be decomposed by hydrolysis. They are colorless crystalline substances with a sweet taste and have the same general formula CnH2nOn. (From Dorland, 28th ed)
A broad class of substances encompassing all those that do not include carbon and its derivatives as their principal elements. However, carbides, carbonates, cyanides, cyanates, and carbon disulfide are included in this class.
Inorganic Chemicals [Chemical/Ingredient]
A class of organic compounds which contain two rings that share a pair of bridgehead carbon atoms.
Heterocyclic Compounds, Bridged-Ring [Chemical/Ingredient]
A class of organic compounds containing a ring structure made up of more than one kind of atom, usually carbon plus another atom. The ring structure can be aromatic or nonaromatic.
Heterocyclic Compounds, 1-Ring [Chemical/Ingredient]
A class of organic compounds containing two ring structures, one of which is made up of more than one kind of atom, usually carbon plus another atom. The heterocycle may be either aromatic or nonaromatic.
Heterocyclic Compounds, 2-Ring [Chemical/Ingredient]
Substances that dissociate into two or more ions, to some extent, in water. Solutions of electrolytes thus conduct an electric current and can be decomposed by it (ELECTROLYSIS). (Grant & Hackh's Chemical Dictionary, 5th ed)
Organic compounds composed exclusively of carbon and hydrogen forming a closed ring that may be either alicyclic or aromatic.
Hydrocarbons, Cyclic [Chemical/Ingredient]
Alveolar Surface Tension Alteration [PE]
Blood & Lymphatic Fluid Function Alteration
Blood & Lymphatic Fluid Function Alteration [PE]
Cellular Synthetic Activity Alteration [PE]
Coagulation Factor Activity Alteration [PE]
Decreased Immunologically Active Molecule Activity
Decreased Immunologically Active Molecule Activity [PE]
Decreased Immunologically Active Molecule Production
Decreased Immunologically Active Molecule Production [PE]
Decreased Lymphocyte Cell Production [PE]
Decreased Respiratory Secretion Viscosity
Decreased Respiratory Secretion Viscosity [PE]
Decreased Striated Muscle Contraction [PE]
Hematological Cell Quantity Alteration [PE]
Hemic/Lymphatic Activity Alteration [PE]
Immunologically Active Molecule Activity Alteration
Immunologically Active Molecule Activity Alteration [PE]
Immunologically Active Molecule Production Alteration
Immunologically Active Molecule Production Alteration [PE]
Increased Cardiac Muscle Organized Electrical Activity
Increased Cardiac Muscle Organized Electrical Activity [PE]
Increased Coagulation Factor Activity [PE]
Increased Distal Tubule H+ Excretion [PE]
Increased Distal Tubule K+ Excretion [PE]
Increased Distal Tubule Na+ Excretion [PE]
Increased Loop of Henle Ca++ Excretion [PE]
Increased Loop of Henle Cl- Excretion [PE]
Increased Loop of Henle K+ Excretion [PE]
Increased Loop of Henle Mg++ Excretion [PE]
Increased Loop of Henle Na+ Excretion [PE]
Increased Muscular System Organized Electrical Activity
Increased Muscular System Organized Electrical Activity [PE]
Increased Organized Electrical Activity [PE]
Musculoskeletal Activity Alteration [PE]
Nucleic Acid Replication Alteration [PE]
Organized Electrical Activity Alteration
Organized Electrical Activity Alteration [PE]
Renal/Urological Activity Alteration [PE]
Respiratory Secretion Viscosity Alteration
Respiratory Secretion Viscosity Alteration [PE]
Respiratory/Pulmonary Activity Alteration
Respiratory/Pulmonary Activity Alteration [PE]
Striated Muscle Metabolic Alteration [PE]
Striated Muscle Anabolism Alteration [PE]
Striated Muscle Contraction Alteration [PE]
Unknown Cellular or Molecular Interaction
Unknown Cellular or Molecular Interaction [MoA]
Interleukin 2 Receptor Interactions [MoA]
Interleukin 2 Receptor Antagonists [MoA]
Drug Products by Generic Ingredient Combinations
Hemorrhagic and thrombotic disorders that occur as a consequence of inherited abnormalities in blood coagulation.
Blood Coagulation Disorders, Inherited [Disease/Finding]
An imbalanced nutritional status resulted from insufficient intake of nutrients to meet normal physiological requirement.
Diseases that are caused by genetic mutations present during embryo or fetal development, although they may be observed later in life. The mutations may be inherited from a parent's genome or they may be acquired in utero.
Genetic Diseases, Inborn [Disease/Finding]
Pathological conditions in which the BLOOD GLUCOSE cannot be maintained within the normal range, such as in HYPOGLYCEMIA and HYPERGLYCEMIA. Etiology of these disorders varies. Plasma glucose concentration is critical to survival for it is the predominant fuel for the CENTRAL NERVOUS SYSTEM.
Glucose Metabolism Disorders [Disease/Finding]
Four-membered cyclic AMIDES, best known for the PENICILLINS based on a bicyclo-thiazolidine, as well as the CEPHALOSPORINS based on a bicyclo-thiazine, and including monocyclic MONOBACTAMS. The BETA-LACTAMASES hydrolyze the beta lactam ring, accounting for BETA-LACTAM RESISTANCE of infective bacteria.
Antibodies produced by a single clone of cells.
Antibodies, Monoclonal [Chemical/Ingredient]
Immunoglobulin molecules having a specific amino acid sequence by virtue of which they interact only with the ANTIGEN (or a very similar shape) that induced their synthesis in cells of the lymphoid series (especially PLASMA CELLS).
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Recombinant Fusion Proteins [Chemical/Ingredient]
A group of antibiotics that contain 6-aminopenicillanic acid with a side chain attached to the 6-amino group. The penicillin nucleus is the chief structural requirement for biological activity. The side-chain structure determines many of the antibacterial and pharmacological characteristics. (Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th ed, p1065)
Endogenously-synthesized compounds that may influence biological phenomena or represent quantifiable biomarkers. Biological factors are a variety of extracellular substances that are not otherwise classified under ENZYMES; HORMONES or HORMONE ANTAGONISTS
Biological Factors [Chemical/Ingredient]
Cyclic compounds with a ring size of approximately 1-4 dozen atoms.
Macrocyclic Compounds [Chemical/Ingredient]
Compounds consisting of two or more fused ring structures.
Polycyclic Compounds [Chemical/Ingredient]
ISOQUINOLINES with a benzyl substituent.
Benzylisoquinolines [Chemical/Ingredient]
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
Polysaccharide Metabolism Alteration [PE]
NOTE: Combination products containing two or more active ingredients from the same subclassification are classified in that subclassification (e.g.,triple sulfas in AM650). Products containing two or more active ingredients from different subclassifications are classified under "anti-infectives, other" (e.g., tetracycline and amphotericin B (AM900). Products containing probenecid or clavulanic acid are classified under the subclassification of the antimicrobial agent. Beta-lactam antibiotics not classified under penicillins or cephalosporins are classified (AM130). Excludes topical anti-infectives (DE100), topical anti- infective/anti-inflammatory combinations (DE250), ophthalmic anti-infectives (OP200), ophthalmic anti- infective/anti-inflammatory combinations (OP350), otic anti-infectives (OT100), otic anti-infective/anti- inflammatory combinations (OT250); vaginal anti- infectives (GU300).
NOTE: Excludes 50% dimethyl sulfoxide (GU900).
Heterocyclic compounds with SULFUR and NITROGEN in the ring. This term commonly refers to the BENZOTHIADIAZINES that inhibit SODIUM-POTASSIUM-CHLORIDE SYMPORTERS and are used as DIURETICS.
Univalent antigen-binding fragments composed of one entire IMMUNOGLOBULIN LIGHT CHAIN and the amino terminal end of one of the IMMUNOGLOBULIN HEAVY CHAINS from the hinge region, linked to each other by disulfide bonds. Fab contains the IMMUNOGLOBULIN VARIABLE REGIONS, which are part of the antigen-binding site, and the first IMMUNOGLOBULIN CONSTANT REGIONS. This fragment can be obtained by digestion of immunoglobulins with the proteolytic enzyme PAPAIN.
Immunoglobulin Fab Fragments [Chemical/Ingredient]
Conditions in which the KIDNEYS perform below the normal level in the ability to remove wastes, concentrate URINE, and maintain ELECTROLYTE BALANCE; BLOOD PRESSURE; and CALCIUM metabolism. Renal insufficiency can be classified by the degree of kidney damage (as measured by the level of PROTEINURIA) and reduction in GLOMERULAR FILTRATION RATE.
Conditions in which the KIDNEYS perform below the normal level for more than three months. Chronic kidney insufficiency is classified by five stages according to the decline in GLOMERULAR FILTRATION RATE and the degree of kidney damage (as measured by the level of PROTEINURIA). The most severe form is the end-stage renal disease (CHRONIC KIDNEY FAILURE). (Kidney Foundation: Kidney Disease Outcome Quality Initiative, 2002)
Renal Insufficiency, Chronic [Disease/Finding]
Chemicals with two conjoined aromatic rings incorporating two nitrogen atoms and one of the carbons oxidized with a keto oxygen.
Increased Diuresis at Loop of Henle [PE]
Competitive Cholinergic Nicotinic Antagonists
Competitive Cholinergic Nicotinic Antagonists [MoA]
Cholinergic Neuromuscular Nicotinic Antagonists
Cholinergic Neuromuscular Nicotinic Antagonists [MoA]
Bicyclic bridged compounds that contain a nitrogen which has three bonds. The nomenclature indicates the number of atoms in each path around the rings, such as [2.2.2] for three equal length paths. Some members are TROPANES and BETA LACTAMS.
Azabicyclo Compounds [Chemical/Ingredient]
Dopamine Hydrochloride [Chemical/Ingredient]
digoxin antibodies Fab fragments [Chemical/Ingredient]
Formation of stones in any part of the URINARY TRACT, usually in the KIDNEY; URINARY BLADDER; or the URETER.
Pathological processes of the female URINARY TRACT and the reproductive system (GENITALIA, FEMALE).
Female Urogenital Diseases [Disease/Finding]
Abrupt reduction in kidney function defined as an absolute increase in serum CREATININE of more than or equal to 0.3. mg/dl, a percentage increase in serum creatinine of more than or equal to 50%, or a reduction in urine output. Acute kidney injury encompasses the entire spectrum of the syndrome including acute kidney failure; ACUTE KIDNEY TUBULAR NECROSIS; and other less severe conditions.
entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocitosis and exocitosis
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
anatomical entity
connected anatomical structure
material anatomical entity
multi-cell-part structure
neuron projection bundle
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3.
A cardiovascular drug that tends to raise reduced blood pressure.
Any compound that can disrupt the functions of the endocrine (hormone) system
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety.
An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups.
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
A peptide containing ten or more amino acid residues.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells.
A naturally occurring polypeptide synthesized at the ribosome.
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001.
An aldehyde resulting from the formal oxidation of methanol.
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
Any polysaccharide containing a substantial proportion of aminomonosaccharide residues.
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
An iron group element atom that has atomic number 26.
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
Any compound that produces a peak used to reference an NMR spectrum during data pre-processing.
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring.
A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
A defined linked collection of atoms or a single atom within a molecular entity.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds.
A compound consisting of carbon and hydrogen only.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A molecular entity that contains no carbon.
A molecular entity having a net electric charge.
Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
Any organic ion with a net negative charge.
An oxide is a chemical compound of oxygen with other chemical elements.
Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides.
Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.
A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity.
A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it.
A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups.
A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell.
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
A cobalt group element atom that has atomic number 27.
A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria.
An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring.
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
An onium cation obtained by protonation of ammonia.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
A cobalt-corrinoid hexaamide that is cobalamin with the oxidation state of the central cobalt atom unspecified.
A heme is any tetrapyrrolic chelate of iron.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
An acene that consists of four ortho-fused benzene rings in a rectilinear arrangement.
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A biochemical role played by any micronutrient that is an organic compound. Vitamins are present in foods in small amounts and are essential to normal metabolism and biochemical functions, usually as coenzymes. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines.
Intended use of the molecular entity or part thereof by humans.
A particle not known to have substructure.
An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands).
An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.
Any substituent group which does not contain carbon.
Any substituent group or skeleton containing carbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Heavy nuclear particle: proton or neutron.
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
An anion consisting of more than one atom.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A substance (or active part thereof) that kills or slows the growth of bacteria.
A nutrient is a food component that an organism uses to survive and grow.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life.
Any material that can be ingested by an organism.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
A molecular entity containing one or more atoms of a transition element.
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
Any main group element atom belonging to the p-block of the periodic table.
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
An oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
Any molecule that consists of a series of atoms joined together to form a ring.
A cyclic compound having as ring members atoms of the same element only.
A homocyclic compound in which all of the ring members are carbon atoms.
A molecule that features two fused rings.
A polycyclic compound in which two rings have two, and only two, atoms in common. Such compounds have n common faces and 2n common atoms.
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
Any monocyclic or polycyclic aromatic hydrocarbon.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.
A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
A macromolecule formed by a living organism.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A carboxylic acid containing one or more amino groups.
An amino-acid residue derived from an alpha-amino acid.
An organic compound having at least one hydroxy group attached to a carbon atom.
Any organic molecule that consists of atoms connected in the form of a ring.
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
polymer
transition element coordination entities
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
A derivative of the corrin nucleus, which contains four reduced or partly reduced pyrrole rings joined in a macrocycle by three =C- groups and one direct carbon-carbon bond linking alpha positions.
Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
Conjugated proteins containing heme as the prosthetic group.
A substance that diminishes the rate of a chemical reaction.
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
A polyclic compound in which all of the ring members are carbon atoms.
A polycyclic aromatic hydrocarbon consisting of fused benzene rings in a rectilinear arrangement.
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene, so may be considered as triterpenoids.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
A substance used in the prophylaxis or therapy of infectious diseases.
A substance used to treat or prevent parasitic infections.
A beta-lactam is a lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
Any antimicrobial drug which is used to treat or prevent protozoal infections.
Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified.
A drug used to treat or prevent microbial infections.
A drug used to treat or prevent bacterial infections.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
A cyclic compound in which a carbonyl group in a ring is bonded to one or two skeletal heteroatoms.
Any of a class of steroid hormones that are produced in the adrenal cortex.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid.
An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
A compound composed of two or more pyrrole units.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
A compound, usually an anti-bacterial agent or a toxin, which inhibits the synthesis of a protein.
Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
A product in capsule, tablet or liquid form that provide essential nutrients, such as a vitamin, an essential mineral, a protein, an herb, or similar nutritional substance.
A natural or synthetic analogue of the hormones secreted by the adrenal gland.
Any molecular entity that contains carbon.
A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities.
A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy.
A role is particular behaviour which a material entity may exhibit.
A poison that interferes with the functions of the nervous system.
A drug that modulates the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites.
A role played by the molecular entity or part thereof within a chemical context.
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
Polycyclic aromatic hydrocarbons consisting of fused benzene rings in a rectilinear arrangement and their substitution derivatives.
Compounds containing a tetracene skeleton.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
A biological role played by the molecular entity or part thereof within a biochemical context.
A role played by the molecular entity or part thereof which causes the development of a pathological process.
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group.
An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom.
A polymer carrying multiple negative charges.
A macromolecule containing ionic groups.
A cyclic compound having as ring members atoms of at least two different elements.
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc..
An ionic polymer is a polymer, composed of ionic macromolecules.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.
A polymer, composed of polyanion macromolecules.
Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.
A carbohydrate derivative that is formally obtained from a carbohydrate acid.
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative.
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
A carbohydrate derivative that is any derivative of a polysaccharide.
An organic anion that is the conjugate base of tetracycline obtained by deprotonation of the two enolic hydroxy groups and protonation of the tertiary amino group.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment.
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
Any animal metabolite produced during a metabolic reaction in mammals.
A role played by any of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B). The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such). B vitamins play important roles in cell metabolism.
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
Saccharomyces cerevisiae secondary metabolites
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor
EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor
EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor
non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
An enzyme inhibitor that interferes with one or more steps in a metabolic pathway.
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
A zwitterion obtained by transfer of a proton from the 2-hydroxy group to the 1-amino group of tetracycline. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.
Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.
carbohydrates and carbohydrate derivatives
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
Any metal which causes the onset of an allergic reaction.
A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors.
cell line cell
细胞系细胞
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分
immortal cell line cell
永生细胞系细胞
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。
cell line
细胞系
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。
培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。
immortal cell line
A cell line that is expected to be capable of indefinite propagation in an vitro culture.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
A cell found in the embryo before the formation of all the gem layers is complete.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’.
A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.
Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.
A progenitor cell committed to the erythroid lineage.
A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.
Originally this term had some plant germ line cell children.
A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.
Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.
A stem cell that can give rise to multiple lineages of cells.
A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.
colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte
This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).
A progenitor cell committed to the megakaryocyte and erythroid lineages.
colony forming unit erythroid megakaryocyte
MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.
A oligopotent progenitor cell committed to the lymphoid lineage.
CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative.
A stem cell from which all cells of the body can form.
A precursor cell with a limited number of potential fates.
define using PATO mulit-potent or oligopotent?
A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
A cell that has a filiform extrusion of the cell surface.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
An epithelial cell that is part of a duct.
An endothelial cell that lines the vasculature.
cuboidal endothelial cell of vascular tree
A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube.
A flattened epithelial cell of mesenchymal origin that lines the serous cavity.
A cell found predominately in the blood.
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive.
Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.
A leukocyte with abundant granules in the cytoplasm.
A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive.
Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)).
A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5.
A vertebrate phagocyte with a single nucleus.
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].
A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.
Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571
A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.
Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.
An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes.
Cultured human fibrocytes are MHCI-positive, MHCII-positive, CD1a-negative, CD3-negative, CD4-negative, CD8-negative, CD10-negative, CD11b-positive, CD13-positive, CD14-negative, CD16-negative, CD18-positive, CD19-negative, CD25-negative, CD29-positive, CD32-positive, CD33-negative, CD34-positive, CD38-negative, CD40-positive, CD44-negative, CD45RO-positive, CD49a-positive, CD49b-positive, CD49c-negative, CD49d-negative, CD49e-positive, CD49f-negative, CD56-negative, CD58-positive, CD61-positive, CD64-positive, CD70-negative, CD71-positive, CD80-positive, CD83-negative, CD86-positive, CD103-negative, CD105-positive, CD181-positive, CD182-negative, CD183-positive, CD184-positive, CD185-negative, CD186-negative, CD191-positive, CD192-negative, CD193-positive, CD194-positive, CD195-positive, CD196-negative, CD197-positive, CD199-positive, desmin-negative, F4/80-positive, Gr1-positive, LSP-1-positive, MHCI-positive, MHCII-positive, alpha-SMA-negative, TCRab-negative, TCRgd-negative, and vimentin-positive. Fibrocytes are also capable of secreting angiogenin, bFGF, CCL2, CCL3, CCL4, CCL8, CXCL1, type I collagen, type III collagen, CTGF, fibronectin, GM-CSF, IL-1a, IL-6, IL-8, IL-10, M-CSF, MMP-9, PDGF-A, TGF-alpha, TGF-beta1, TNF-alpha, and VEGF-A.
A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.
Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells.
A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.
A cell that specializes in controlled release of one or more substances.
A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.
An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.
A cell that secretes insulin and is located towards the center of the islets of Langerhans.
Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.
A cell whose primary function is to shorten.
An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell.
Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha.
A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.
A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast).
A cell whose function is determined by the generation or the reception of an electric signal.
A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.
A cell whose primary function is to prevent the transport of stuff across compartments.
A cell that moves by its own activities.
A cell of the outer of the three germ layers of the embryo.
A cell of the middle germ layer of the embryo.
A cell of the inner of the three germ layers of the embryo.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.
Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF.
Any cell capable of ingesting particulate matter via phagocytosis.
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.
A lymphocyte of B lineage that is capable of B cell mediated immunity.
A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium.
Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid.
A cell that is specialised to accumulate a particular substance(s).
A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.
A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.
A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation.
A smooth muscle cell associated with the vasculature.
Diploid cell produced by the fusion of sperm cell nucleus and egg cell.
A cell whose function is determined by its response to an electric signal.
A cell that initiates an electrical signal and passes that signal to another cell.
A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids.
A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).
A cell type that secretes 5-Hydroxytryptamine (serotonin).
A cell whose primary function is to protect the organism.
A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere.
A precursor cell destined to differentiate into smooth muscle myocytes.
A phagocyte in vertebrates that is able to phagocytosis.
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.
A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.
A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.
The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.
The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).
Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.
A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.
A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release.
Megakaryocytes are reportedly CD181-positive and CD182-positive.
A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.
colony forming unit granulocyte macrophage
Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.
An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules.
Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.
A mesenchymal stem cell capable of developing into blood vessel endothelium.
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
The reproductive cell in multicellular organisms.
A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells.
A cell whose primary function is to support other cell types.
A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation.
A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries.
Do all of these cells really develop from some mesenchymal stem cell?
A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes.
epithelial cell of visceral layer of glomerular capsule
An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells.
Pericytes are CD10-positive, CD13-positive, CD31-negative, CD45-negative, CD106-positive, CD117-negative, CD140-positive, CD144-negative, CD146-positive, CD271-positive, CD325-positive, NG2-positive, RGS5-positive, SMA-positive, and desmin-positive. A subpopulation is CD248-positive. They are also capable of producing angiopoietin 1, CXCL12, TGF-beta, and VEGF-A.
A non-terminally differentiated cell that is capable of developing into a muscle cell.
A stem cell that can give rise to cell types of the body other than those of the germ-line.
A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria.
A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria.
transitional epithelial cell of urinary bladder
urinary tract transitional epithelial cell
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
A immature or mature cell in the lineage leading to and including erythrocytes.
Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes.
A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers.
A cell of the monocyte, granulocyte, or mast cell lineage.
Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive.
Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
A dendritic cell of the myeloid lineage.
These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8).
A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen.
Mature B cells are also reportedly CD10-negative, CD19-positive, CD22-positive, CD34-negative, CD48-positive, CD79a-positive, CD84-positive, CD127-negative, CD352-positive, RAG-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Transcription factors expressed: Pax5-positive.
A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
Plasma cells develop in the spleen and migrate to the bone marrow. Plasma cells are also reportedly CD5-negative, CD10-negative, CD19-positive, CD20-negative, CD21-negative, CD22-negative, CD23-negative, CD24-negative, CD25-negative, CD27-positive, CD34-negative, CD38-positive, CD40-positive, CD43-positive, CD45-positive, CD48-positive, CD53-low, CD80-negative, CD81-positive, CD86-positive, CD95-positive, CD196-negative, CD229-positive, CD270-positive, CD352-positive, CD361-positive, and IgD-negative. Transcription factors: BLIMP1-positive, IRF4-positive, PAX5-negative, SpiB-negative, Ets1-negative, and XBP1-positive.
A T cell that expresses an alpha-beta T cell receptor complex.
An alpha-beta T cell that has an immature phenotype and has not completed T cell selection.
A alpha-beta T cell that has a mature phenotype.
A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive.
Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages.
A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive.
Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains. Also, there is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.
A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain.
There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.
A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive.
Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'.
A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors.
double-positive, alpha-beta immature T lymphocyte
Thymocytes of this stage are undergoing positive and negative selection.
A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation.
Immature B cells are also reportedly CD5-positive, CD10-positive, CD19-positive, CD20-positive, CD21-positive, CD22-positive, CD24-positive, CD25-negative, CD27-negative, CD34-negative, CD38-positive, CD40-positive, CD43-negative, CD45-positive, CD48-positive, CD53-positive, CD79a-positive, CD80-negative, CD81-positive, CD86-negative, CD95-negative, CD127-negative, CD138-negative, CD185-positive, CD196-positive, MHCII/HLA-DR-positive, RAG-positive, TdT-negative, Vpre-B-negative, and preBCR-negative. Transcription factors expressed: Pax5-positive.
A precursor B cell is a B cell with the phenotype CD10-positive.
An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen.
This cell type is compatible with the HIPC Lyoplate markers for 'transitional B cell'.
A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative.
Most markers only described for human pro NK cells.
A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs.
Human pro-B cells are reportedly CD10-positive, CD22-positive, CD34-positive, CD38-positive, CD45-low, CD48-positive, CD79a-positive, CD127-positive, CD184-positive, RAG-positive, TdT-positive, Vpre-B-positive, pre-BCR-negative, IgD-negative, and IgM-negative. Transcription factors expressed: Pax5-positive, EBF-positive, E2A-negative, Ikaros-negative, and PU.1-negative.
A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage.
A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative.
MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa.
A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans.
hematopoietic multipotent progenitor cell
A progenitor cell restricted to the lymphoid lineage.
Note that this is a class of cell types, not an identified single cell type.
lymphoid lineage restricted progenitor cell
A progenitor cell restricted to the myeloid lineage.
myeloid lineage restricted progenitor cell
A leukocyte with a single non-segmented nucleus in the mature form.
A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes.
Markers: CCR2+CXCCR1<low> (human, mouse, rat).
A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive.
Markers: CD11b+, CD68+; Mouse: F4/80+; role or process: immune, inflammation (inflammatory response).
A macrophage that suppresses immune responses.
An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity.
Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response).
A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling.
A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions.
An immature T cell located in the thymus.
A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative.
An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers.
A lymphocyte of B lineage with the commitment to express an immunoglobulin complex.
Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex).
A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin.
A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes.
Small pre-B-II cells are also reportedly CD10-positive, CD19-positive, CD34-negative, CD79a-positive, CD127-negative, TdT-negative, Vpre-B-negative, sIgM-negative, and sIgD-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive.
A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain.
pre-B-II cell are also reportedly CD19-positive, CD22-positive, CD38-positive, CD45-positive, and CD48-positive.
An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative.
CD27-positive, CD38-positive, CD20-negative B cell
This cell type is compatible with the HIPC Lyoplate markers for 'plasmablast'. Plasmablasts are also reportedly CD48-positive, CD63-positive, CD229-positive, CD270-positive, CD319-positive, CD352-positive, CD361-positive, and IgD-negative.
Conventional dendritic cell is a dendritic cell that is CD11c-high.
Originally described in the dendritic cell ontology (DC_CL:0000003)(PMID:19243617) These cells are also CD20-negative, MHCII-positive.
CD71-positive common myeloid precursor OR CD7-negative lymphoid precursor OR CD7-positive lymphoid
Originally described in the dendritic cell ontology (DC_CL:1100000)(PMID:19243617).
CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor
Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive.
Originally described in the dendritic cell ontology (DC_CL:0000020)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10).
Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID:19243617).
CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor
A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive.
CD10-positive common lymphocyte precursor
CD10-positive common lymphocyte progenitor
These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID:19243617).
CD34-positive, CD38-positive common lymphoid progenitor
CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive.
Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID:19243617).
CD34-positive, CD38-negative hematopoietic stem cell
A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative.
Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617).
CD34-positive, CD38-positive common myeloid progenitor
CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative.
These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID:19243617).
A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1.
CMP are reportedly CD16-positive, CD32-positive, CD38-positive, CD45RA-negative, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.
common myeloid progenitor, CD34-positive
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers.
hematopoietic oligopotent progenitor cell, lineage-negative
A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses.
An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines.
A lymphocyte of B lineage that is CD19-positive.
A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages.
A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa
There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low.
A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells.
hematopoietic lineage restricted progenitor cell
A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities.
This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060).
hematopoietic oligopotent progenitor cell
A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell.
A CD24-low, CD44-negative, NK1.1-negative NK T cell.
NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org.
A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell.
A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell.
A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative.
Cell markers are associated with human hematopoietic multipotent progenitor cells.
CD34-positive, CD38-negative multipotent progenitor cell
An epithelial cell derived from endoderm.
An epithelial cell derived from ectoderm.
Epithelial cell derived from mesoderm or mesenchyme.
A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells.
MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense.
An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels.
cubodial endothelial cell of vascular tree
These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive.
An endothelial cell found in capillaries.
A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells.
An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate.
A cell involved in the formation of a granulocyte.
A cell involved in the formation of a monocyte (monopoiesis).
A renal intercalated cell that secretes base and reabsorbs acid in the distal segments of the kidney tubule to maintain acid/base balance.
An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies.
An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH.
An epithelial cell of the proximal tubule of the kidney.
A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow.
brush border cell of the proximal tubule
A cell that is part of the nervous system.
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1.
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
A T cell that expresses a T cell receptor complex and has completed T cell selection.
A T cell that has not completed T cell selection.
A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive.
ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative.
A conventional dendritic cell that expresses CD11b (ITGAM).
A thymocyte that lacks expression of CD4 and CD8.
These are precursors to mature T cells; normally, they do not circulate, but are found in the thymus and they have not undergone rearrangement of the alpha and beta T cell receptor genes.
A cell located in the heart, including both muscle and non muscle cells.
From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.
An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type.
A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both.
A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros.
mesonephric glomerular visceral epithelial cell
A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the metanephros.
metanephric glomerular visceral epithelial cell
An endothelial cell that is part of the vein.
An endothelial progenitor cell that participates in angiogenesis during development.
embryonic blood vessel endothelial progenitor cell
A glial cell that myelinates or ensheathes axons in the peripheral nervous system.
A myelinating Schwann cell wraps around a single axon. Myelination occurs in larger diameter axons, while a process called ensheathment occurs on smaller diameter axons in which a single cell wraps around multiple small, unmyelinated axons separating them with a thin layer of cytoplasm. The structure formed is called a Remak bundle.
An epithelial cell of the kidney cortex.
A cell that is part of a cortex of kidney.
A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system.
A cuboidal epithelial cell of the kidney that regulates acid/base balance.
Intercalated cells are also called “mitochondria-rich cells”, reflecting the high levels of round mitochondria at their apical pole, or in their cytoplasm, a distribution that is quite different from that of other kidney tubule cells, which accumulated mitochondria around the basolateral membrane. These cells also have numerous irregular apical microvilli compared with the surrounding segment-specific cells. Intercalated cells lack a central cilium, at least in the cortex, which also differentiates them from the adjacent principal cells.
A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance.
Type A intercalated cells are the more abundant type of intercalated cell in the outer stripe of the outer medulla in most mammalian species.
Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized).
Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)
Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells.
Any muscle cell in which the fibers are not organised into sarcomeres.
Any hematopoietic cell that is a precursor of some other hematopoietic cell type.
A muscle cell that is part of some visceral muscle
visceral muscle cell
A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration.
An endocrine cell that is part of the pancreas.
Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation.
mural cell
microcirculation associated smooth muscle cell
A kidney cortical cell that is part of the nephrogenic zone.
zygote
A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.
A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses.
A cell that, by division or terminal differentiation, can give rise to other cell types.
Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.
Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain.
Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain.
Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions.
Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions.
Heterochromatin that is arranged in a carthwheel pattern.
A smooth muscle cell that is part of any blood vessel.
blood vessel smooth muscle cell
mesonephric nephron tubule epithelial cell
pronephric nephron tubule epithelial cell
metanephric nephron tubule epithelial cell
An endothelial cell that is part of the arteriole.
A blood vessel endothelial cell that is part of an arterial endothelium.
An epithelial cell that is part of the nephron.
An epithelial cell that is part of the glomerular capsule.
An epithelial cell that is part of the glomerular parietal epithelium.
epithelial cell of parietal layer of glomerular capsule
An epithelial cell that is part of the intermediate tubule.
An epithelial cell that is part of the collecting duct of renal tubule.
epithelial cell of renal collecting tubule
An epithelial cell that is part of a nephron tubule.
This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON.
A cell that is part of kidney interstitium.
A cell that is part of a nephron tubule.
An epithelial cell that is part of a renal medulla collecting duct.
kidney medulla collecting duct epithelial cell
An epithelial cell that is part of some inner medullary collecting duct.
kidney inner medulla collecting duct epithelial cell
An epithelial cell that is part of an outer medullary collecting duct.
kidney outer medulla collecting duct epithelial cell
An epithelial cell that is part of a cortical collecting duct.
kidney cortex collecting duct epithelial cell
kidney papillary duct principal epithelial cell
A cell that is part of a tip of a renal papilla.
kidney interstitial alternatively activated macrophage
kidney interstitial inflammatory macrophage
kidney interstitial suppressor macrophage
A tissue-resident macrophage that is part of some kidney.
kidney cortex collecting duct principal cell
kidney cortex collecting duct intercalated cell
Principal cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may express the epithelial sodium channel (ENaC).
kidney outer medulla collecting duct principal cell
Intercalated cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may contribute in the maintenance of acid/base homeostasis.
kidney outer medulla collecting duct intercalated cell
kidney inner medulla collecting duct principal cell
kidney inner medulla collecting duct intercalated cell
A mesangial cell located among the glomerular capillaries in a renal corpuscle.
Like smooth muscle, a glomerular mesangial cell is contractile and possesses the filaments actin and myosin. The contractile mechanism is also similar to that of smooth muscle, with Ca2+/calmodulin-activated myosin light-chain kinase instigating myosin-actin cross-bridge cycling. Mesangial cell phagocytosis of apoptotic neutrophils involves a novel CD36-independent, alpha(v)beta3/TSP-mediated mechanism that is uncoupled from chemokine secretion, emphasizing the injury-limiting potential of mesangial cell phagocytosis of apoptotic cells.
kidney connecting tubule epithelial cell
kidney proximal convoluted tubule epithelial cell
kidney proximal straight tubule epithelial cell
kidney distal convoluted tubule epithelial cell
kidney loop of Henle ascending limb epithelial cell
kidney loop of Henle descending limb epithelial cell
An endothelial cell that is part of some peritubular capillary.
Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure.
Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure.
Note that the source of this term is KUPO:0001068 (venous system smooth muscle cell), which we believe actually denotes the kidney specific structure.
kidney afferent arteriole endothelial cell
kidney afferent arteriole smooth muscle cell
kidney efferent arteriole endothelial cell
kidney efferent arteriole smooth muscle cell
An epithelial cell that is part of some loop of Henle thick ascending limb. It is known in some mammalian species that this cell may express the Na+-K+-2Cl− cotransporter (NKCC2) apically.
kidney loop of Henle thick ascending limb epithelial cell
An epithelial cell that is part of some loop of Henle thin ascending limb.
kidney loop of Henle thin ascending limb epithelial cell
An epithelial cell that is part of some loop of Henle thick ascending limb segment located in the renal medulla.
kidney loop of Henle medullary thick ascending limb epithelial cell
An epithelial cell that is part of some loop of Henle thick ascending limb segment located in the renal cortex.
kidney loop of Henle cortical thick ascending limb epithelial cell
An epithelial cell that is part of some loop of Henle thin descending limb.
kidney loop of Henle thin descending limb epithelial cell
kidney outer medulla peritubular capillary cell
kidney cortex peritubular capillary cell
A cell that is part of some vasa recta ascending limb.
It is known in some mammalian species that this cell may express PV-1, a component of the fenestral diaphragm.
inner medulla vasa recta ascending limb cell
outer medulla vasa recta ascending limb cell
A cell that is part of a collecting duct of renal tubule.
A cell that is part of some vasa recta descending limb.
It is known in some mammalian species that this cell may express the urea transporter B.
inner medulla vasa recta descending limb cell
outer medulla vasa recta descending limb cell
A pericyte cell located in the kidney interstitium.
kidney collecting duct intercalated cell
Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes.
Any blood vessel endothelial cell that is part of a microvascular endothelium.
A neuron that is part of a peripheral nervous system.
A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type.
kidney collecting duct intercalated cell type B
kidney collecting duct beta-intercalated cell
A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros.
pronephric glomerular visceral epithelial cell
Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium.
epithelial cell of segment 1 of proximal tubule
epithelial cell of proximal tubule segment 1
Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium.
epithelial cell of segment 2 of proximal tubule
epithelial cell of proximal tubule segment 2
Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium.
epithelial cell of segment 3 of proximal tubule
epithelial cell of proximal tubule segment 3
Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2.
epithelial cell of the descending thin limb of the short loop of Henle
kidney loop of Henle short descending thin limb epithelial cell
Epithelial cell of the descending thin limb of the long loop (juxtamedullary) nephron that spans the outer medulla (inner stripe). It is known in some mammalian species that the long descending limb of the loop of Henle in the outer medulla selectively expresses the secreted activin-antagonist protein follistatin (Fst), the GPI-linked adhesion protein Cdh13, and the protein kinase Stk32a.
epithelial cell of the outer medulla of the long descending limb of the loop of Henle
kidney loop of Henle long descending thin limb outer medulla epithelial cell
Epithelial cell of the descending thin limb of the long loop (juxtamedullary) nephron that spans the inner medulla. It is known in some mammalian species that the long descending limb of the loop of Henle in the inner medulla selectively expresses the nuclear receptor Nr2e3, the Ig kappa chain Igkc, and the secreted protein dermokine (Dmkn). SLC14A2, which expresses a urea transporter, is also expressed in the inner medulla.
epithelial cell of the inner medulla of the long descending limb of the loop of Henle
kidney loop of Henle long descending thin limb inner medulla epithelial cell
A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule.
kidney collecting duct intercalated cell type A
kidney collecting duct alpha-intercalated cell
An epithelial cell located in the early distal convoluted tubule.
epithelial cell of early distal convoluted tubule
An epithelial cell located in the late distal convoluted tubule.
Although mineralocorticoid receptors are expressed throughout the entire [distal convoluted tubule], the DCT2 is sensitive to the actions of aldosterone, because it expresses an enzyme called 11-β hydroxysteroid dehydrogenase 2 (11-βHSD2)
epithelial cell of late distal convoluted tubule
A renal principal cell located in the connecting tubule.
A renal intercalated cell that is part of the renal connecting tubule.
kidney connecting tubule intercalated cell
A renal alpha-intercalated cell that is part of the renal connecting tubule.
kidney connecting tubule intercalated cell type A
kidney connecting tubule alpha-intercalated cell
A renal beta-intercalated cell that is part of the renal connecting tubule.
kidney connecting tubule intercalated cell type B
kidney connecting tubule beta-intercalated cell
A fibroblast that is located in the renal medulla interstitium.
It has been noted that inner medullary fibroblasts are involved in the regulation of water and electrolyte homeostasis.
A fibroblast that is located in the renal cortical interstitium.
Renal cortical fibroblasts have key roles in mediating intercellular communication with neighboring/infiltrating cells and extracellular matrix and maintenance of renal tissue architecture. They additionally have an endocrine function in the production of epoetin.
Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. "Interstitial cell" is a morphological term and refers to a variety of cells with differing origins and phenotypes.
A CD24-positive, CD-133-positive, vimentin-positive cell found scattered throughout a renal proximal tubule and that may participate in tubular regeneration. Compared to other proximal tubular cell types, this cell contains less cytoplasm, fewer mitochondria and no brush border.
After acute tubular injury, this cell type becomes more numerous. In healthy rat kidneys, this cell is not detectable, whereas after unilateral ureteral obstruction (renal injury), it may appear de novo, arguing against the notion that this cell type represents a pre-existing progenitor cell population. In at least one study, data indicate that this cell type represents transiently dedifferentiated tubular cells involved in regeneration.
CD24-positive, CD-133-positive, vimentin-positive proximal tubular cell
An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion.
A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics.
A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
The number of contractions of the cardiac ventricles per unit of time.
Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
The maximum arterial pressure within the cardiac cycle, i.e. at the point at which the heart is in its maximal state of contraction. This is the time when the blood is forced from the ventricles of the heart into the pulmonary artery and the aorta.
The minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
The minimum pressure in the heart left ventricle, usually at the point at which the heart is in a state of relaxation and expansion and the ventricles fill with blood.
left ventricular diastolic blood pressure
Measurement of the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta.
left ventricular systolic blood pressure
A blood pressure measurement which has been normalized or adjusted by a mathematical process or computation. Blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
The average blood pressure within an artery over a specified period of time. It is often calculated using the formula of one third systolic pressure plus two thirds diastolic pressure, or alternatively, using the formula diastolic pressure plus 1/3 of the difference between systolic pressure and diastolic pressure (i.e. 1/3 pulse pressure).
A calculated value for the difference between the systolic blood pressure and the diastolic blood pressure at a given point in time when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
A measurement of the physical form or structure of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system.
This is the term which was just "heart measurement". Since it was under body morphological measurement it seemed to clearly refer to a morphological measurement. I made this term more specific so that another term for "heart measurement" could be added to the ontology above it which would also be a parent to other non-morphological heart-related terms. JRS 2-15-2012.
The heaviness of the heart (the central cardiac muscle which maintains the circulation of the blood) or the degree to which it is drawn to the earth by gravity.
A calculated measurement of the difference between the systolic pressure and the diastolic pressure in the heart left ventricle at a given point in time in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
Measurement of the structure or forms of the entire body or parts of the body of an organism.
A quantification of a parameter of the chemical composition of blood.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of one or more of the various, specific types of leukocytes present in a sample of blood for which a total white blood cell count was taken, usually 1 cubic mm of peripheral venous blood.
calculated blood differential leukocyte count
calculated differential white blood cell count
The amount of hemoglobin in a specific volume of blood, expressed as grams per deciliter of whole blood in humans.
The number of white blood cells in a specified volume of blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood.
The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood.
A measurement of the blood, it's contents, cells or other factors contained within the blood.
A value resulting from the quantification of a morphological or physiological parameter of blood cells, i.e. cells native to the circulation, including those of erythroid, lymphoid, myeloid and monocytic lineages. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
The level of urea in the blood in terms of nitrogen content; converted to urea concentration by multiplying by 60/28 or 2.14. Urea is the chief nitrogenous end product of protein metabolism in whole blood. Urea is formed in the liver from amino acids and from ammonia compounds and can be found in urine, blood, and lymph.
Any value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipid, any of a structurally diverse group of organic compounds found in blood that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure.
Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them.
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in high-density lipoprotein (HDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. HDL is the smallest of the major lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The HDL class of lipoproteins, specifically the subtypes of HDL2 and HDL3, have densities between 1.063 and 1.210 g/ml.
Values for density ranges of the lipoprotein classes are approximate. The classes may be defined differently by different researchers, in part because class definitions depend on the number of subclasses into which the lipoprotein fractions are divided.
blood high density lipoprotein cholesterol level
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in low-density lipoprotein (LDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. LDL constitute a class of relatively large, heterogeneous lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The LDL class of lipoproteins has a density between 1.019 and 1.063 g/ml. In some animal species, such as canine and rodents, this may overlap with the HDL1 class and be designated LDL/HDL1.
blood low density lipoprotein cholesterol level
Measurement of the total amount of all proteins, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, found in a specific volume of plasma, the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended.
A quantification of one or more mineral salts found in the blood in the form of electrically charged ions.
Any quantitation of the catalytic effect exerted by an enzyme in a specified sample of blood. An enzyme is a protein that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reaction(s).
A measurement of the physical form and structure of an organ.
This is the term which used to be just "organ measurement". Since it was under body morphological measurement, it clearly referred to a morphological measurement. Because a term for organ measurement was needed that was not morphological, and since this one already had annotations, I changed the term while keeping the ID and location in the ontology the same. JRS 2-15-2012.
The weight of the heart after removal from the body but without desiccation.
The weight of the heart after desiccation.
The weight of the lower left chamber of the heart, which pumps oxygenated blood through the aorta into the systemic arteries, after removal from the body and separation from the rest of the heart but without desiccation.
The weight of the lower right chamber of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, after removal from the body and separation from the rest of the heart but without desiccation.
A calculated value in which the weight of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system, is divided by the total weight of the body, and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
A calculated value in which the weight of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system, is presented as percentage of the total weight of the body, thus normalizing it to body weight.
heart weight as percentage of body weight
The weight of the aorta, the main trunk from which the arterial system proceeds. Weight is the heaviness or degree to which a body is drawn to the earth by gravity.
Any quantification of a morphological or physiological parameter of one or more blood vessels, the network of muscular tubes that carry blood through the body.
The weight of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The weight of the right kidney, the organ which lies on the right side of the body from the perspective of the subject and functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight of the left kidney, the organ which lies on the left side of the body from the perspective of the subject and functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight of a single kidney, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight of both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
Measurement of the physical form or structure of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated value which compares the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, with the weight of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body, and presents it as a ratio.
heart right ventricle weight to left ventricle weight ratio
The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
The amount of lipoproteins, any of a group of conjugated proteins that have at least one lipid component, in a specific volume of blood.
Measurement of the amount of creatinine in a specified sample of urine, the fluid waste product excreted by the kidneys. Creatinine is a nitrogenous compound formed in muscle as the end product of creatine metabolism. Blood and urine tests for creatinine are used as diagnostic indicators of kidney function and muscle mass.
Any measurement of the physical form or structure of the skeletal, smooth and/or heart muscles of the body.
The amount of albumin in a specified volume of urine. Urine albumin levels which are above normal but not detectable with routine protein testing are referred to as microalbuminuria.
A calculated measurement in which the weight after removal from the body but without desiccation of both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a percentage, thus normalizing it to body weight.
both kidneys wet weight as percentage of body weight
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of one or both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The weight of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight after desiccation of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at either the inner surface or outer surface of the blood vessel wall.
Percentage of blood pumped out of the left ventricle with each heart beat.
Volume of blood left in a ventricle at end of contraction.
Any measurement of the movement of blood through the heart and blood vessels.
The volume of blood flowing through a vessel or organ per unit of time.
The volume of blood pumped from the right or left ventricle per minute, also used to calculate - stroke volume X heart rate.
The volume of blood flowing through an artery per unit time.
The volume of blood passing through a vein per unit time.
Movement of blood along the solid wall of a vessel, often represented by the Hagen-Poiseuille equation.
The time needed for plasma to form a fibrin clot after the addition of calcium and a phospholipid reagent. It is used to evaluate the intrinsic clotting system.
lumen diameter at maximum dilation expressed as percent of baseline
lumen diameter at maximum constriction expressed as percent of baseline
Resistance to blood flow by blood vessels throughout the body, the degree to which the blood vessels impede the flow of blood, often calculated as SVR equal to the difference between mean arterial blood pressure(MAP) and central venous pressure(CVP) divided by cardiac output(CO).
Volume of blood in ventricle immediately before a contraction.
Volume of blood pumped from one ventricle of the heart with each beat, calculated by subtracting the volume of blood in the ventricle at the end of a beat (end-systolic volume) from the volume of blood just prior to the beat (end-diastolic volume).
Any quantification of a morphological or physiological parameter of one or more cells. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
Number of cells of muscular tissue in the heart in a specified sample size.
The enumeration, i.e. measurement of the total number, of the specialized liner cells that form an interface between the circulating blood and the rest of the vessel wall in a specified sample of blood vessel, any one of the network of muscular tubes that carry blood through the body.
Any measurement of components of the Electrical conduction system of the heart.The electrical conduction system of the heart transmits signals generated usually by the sinoatrial node to cause contraction of the heart muscle.
Interval between an R wave and the next R wave of successive heart beats, inverse of the heart rate.
Time between the beginning of the P wave to the beginning of the QRS complex, reflects the time the electrical impulse takes to travel from the sinus node through the AVE node and entering the ventricles, used as an estimate of AV node function.
The time between the J point ( the point at which the QRS complex finishes and the ST segment begins) to the end of the T wave.
An interval measured from the onset of the QRS wave complex to the offset of the T wave.
The depth of the wall of the aorta, the main trunk from which the arterial system proceeds.
The thickness or depth of the dorsal/posterior wall of the heart. The dorsal wall is the portion of the heart muscle which is closest to the spine and farthest from the chest wall of the organism.
The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
heart left ventricle dorsal wall thickness
Note that "left" in this context refers to the perspective of the organism, not that of the observer.
heart left ventricle posterior wall thickness
The thickness or depth of the dorsal/posterior wall of the right ventricle of the heart. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism.
heart right ventricle dorsal wall thickness
heart right ventricle posterior wall thickness
Any measurement of urine, the fluid waste product excreted by the kidneys, or its components.
Measure of the concentration of particles in the urine.
The magnitude of the P wave, the initial deflection of the cardiac cycle representing excitation of the atria as presented in an electrocardiogram.
The time from start to finish of the P wave , in the electrocardiograph illustrating the initial deflection of the cardiac cycle, representing the excitation of the atria.
The distance to the lowest part of the Q wave which shows the initial downward deflection related to the initial phase of depolarization of the ventricular myocardium and the depolarization of the interventricular septum as measured by electrocardiograph.
The time from start to finish of the Q wave which illustrates the initial downward deflection related to the initial phase of depolarization of the ventricular myocardium and the depolarization of the interventricular septum as measured by an electrocardiograph.
The time from start to finish of the QRS interval as calculated from a set of measurements taken from the beginning of the QRS complex to the end of the QRS complex representing the time it takes for ventricles to depolarize.
The magnitude of the portion of the electrocardiograph comprising the Q, R, and S waves which together represent ventricular depolarization.
QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds.
The magnitude of the R wave, which is the initial upward deflection of the QRS complex following the Q wave representing early depolarization of the ventricles as illustrated by an electrocardiograph.
The time from start to finish of the R wave, the initial upward deflection of the QRS complex following the Q wave which represents early depolarization of the ventricles as illustrated in and electrocardiograph.
The magnitude of the S wave, the downward deflection of the QRS complex following the R wave representing late depolarization of the ventricles as illustrated in an electrocardiograph.
The time from start to finish of the S wave which is the downward deflection of the QRS complex following the R wave representing late depolarization as illustrated by an electrocardiograph.
The magnitude of the T wave, the deflection following the QRS complex representing repolarization of the ventricles as illustrated by and electrocardiograph.
An interval measured from the onset of the P wave in one PQRST wave complex to the onset of the P wave in the following PQRST wave complex.
The difference between systolic and diastolic blood pressures, i.e. the difference between the maximal arterial pressure and minimal arterial pressure during the cardiac cycle.
The count of the rhythmic contractions and expansions of an artery due to the surge of blood from the beat of the heart.
Measurement of the physical form or structure of either the right or the left upper chamber of the heart that receives blood from the veins and forces it into a ventricle.
The weight of the left atrium of the heart, the upper chamber on the left which empties into the lower chamber. Weight is the heaviness or degree to which a body is drawn toward the earth by gravity.
The weight of the right atrium, the upper right chamber of the heart which empties into the lower right chamber, i.e. the right ventricle. Weight is the heaviness or degree to which a body is drawn to the earth by gravity.
A measure of the capacity of the left heart atrium, the upper left chamber which empties into the lower heart chamber.
A measure of the three dimensional capacity of the right atrium of the heart, the upper right chamber which empties into the lower right chamber, i.e. the right ventricle.
Any measurement of the physical form or structure of one or both ventricles of the heart, that is, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body.
heart ventricle morphological measurement
A calculated measurement in which the weight after removal from the body but without desiccation of both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a ratio, fraction or quotient, thus normalizing it to body weight.
both kidneys wet weight to body weight ratio
The amount of triglycerides in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Triglycerides are any of a group of lipids that are esters formed from one molecule of glycerol and three molecules of one or more fatty acids, are widespread in adipose tissue, and commonly circulate in the blood in the form of lipoproteins.
Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter.
blood differential white blood cell count
A calculated measurement in which the number of all granulocytes (regardless of type) in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
granulocyte count as percentage of total white blood cells
granulocyte count to total WBC count ratio
granulocyte count to total white blood cell count ratio
blood granulocyte count to total leukocyte count ratio
A calculated measurement in which the number of eosinophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. An eosinophil is a granular leukocyte having a nucleus with two lobes connected by a thread of chromatin, and cytoplasm containing coarse, round granules of uniform size that stain readily with eosin and other acid dyes.
eosinophil count as percentage of total white blood cells
eosinophil count to total WBC count ratio
blood eosinophil count to total leukocyte count ratio
A calculated measurement in which the number of neutrophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. A neutrophil is, or is in the process of becoming, a granular leucocyte having a nucleus with three to five lobes connected by threads of chromatin, cytoplasm containing very fine granules, and which is readily stainable with neutral dyes.
neutrophil count as percentage of total white blood cells
neutrophil count to total WBC count ratio
blood neutrophil count to total leukocyte count ratio
A calculated measurement in which the number of lymphocytes in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
lymphocyte count as percentage of total white blood cells
lymphocyte count to total WBC count ratio
blood lymphocyte count to total leukocyte count ratio
The complete or entire amount of bilirubin in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Bilirubin is the bile pigment produced by breakdown of heme and reduction of biliverdin.
The amount of carbonic acid dissolved in carbon dioxide and carbonate ion found in a specified volume of serum.
The amount of chloride ions found in a specified volume of serum.
An estimation of the volume of blood filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time based on serum creatinine level, wieght and age of organism and other factors.
blood glomerular filtration rate, Diet in Renal Disease Formula (MDRD)
A calculated measurement which estimates the glomerular filtration rate (GFR), that is, the volume of fluid filtered from the renal capillaries per unit time, based on the serum creatinine level and adjusted for gender.
blood glomerular filtration rate, Chronic Kidney Disease Epidemiology Collaboration formula (CKE-EPI)
blood glomerular filtration rate, May Quadratic formula
blood glomerular filtration rate, Schwartz formula
Amount of potassium ions in a specified volume of serum.
The amount of sodium ions in a specified volume of serum.
The amount of calcium ions in a specified volume of serum.
Blood pressure measured in the pulmonary artery during diastole, that is, during dilation or relaxation of the heart ventricles.
pulmonary arterial diastolic blood pressure
Blood pressure measured in the pulmonary artery during systole, that is, during contraction of the heart ventricles.
pulmonary arterial systolic blood pressure
A calculated value in which the weight of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and by extension to the size of the organism.
heart left ventricle weight as a percentage of body weight
heart left ventricle weight to body weight ratio
The difference in mean arterial blood pressure between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign.
absolute change in mean arterial blood pressure
Absolute difference in heart rate between two points in time or two conditions.
The number of glomeruli in all or part of a kidney. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
The amount of phosphorus, measured as inorganic phosphate, in a specified sample of serum.
Measurement of the amount of glucose, the monosaccharide sugar, C6H12O6, occurring widely in plant and animal tissues which is one of the three dietary monosaccharides that are absorbed directly into the bloodstream during digestion, is the end product of carbohydrate metabolism, and is the chief source of energy for living organisms, in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
The amount of albumin in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
The amount of ezymatic activity of glutamic-pyruvate transaminase enzyme, commonly known as alanine transaminase or alanine aminotransferase (ALT), enzyme in a specified sample of serum. ALT catalyzes the reversible transamination between alanine and 2-oxoglutarate to generate pyruvate and glutamate. Serum ALT level is used as an enzymatic marker for liver disease or damage.
serum alanine transaminase activity level
serum glutamic-pyruvate transaminase activity level
serum alanine aminotransferase activity level
Quantitation of the catalytic effect exerted by alkaline phosphatase (AP) in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. AP is an enzyme that catalyzes the cleavage of orthophosphate from orthophosphoric monoesters under alkaline conditions.
serum alkaline phosphatase activity level
The amount of enzymatic activity of glutamic-oxaloacetic transaminase enzyme, commonly known as aspartate transaminase or aspartate aminotransferase (AST), in a specified sample of serum. AST catalyzes the reversible transfer of an amine group from l-glutamic acid to oxaloacetic acid, forming alpha-ketoglutaric acid and l-aspartic acid. Serum AST level is used as an enzymatic marker for liver disease or damage.
serum aspartate transaminase activity level
serum glutamic-oxaloacetic transaminase activity level
serum aspartate aminotransferase activity level
Measurement of the pressure within the heart left ventricle at the end of systole, the period of contraction of the heart when the blood is forced from the ventricles into the pulmonary artery (right ventricle) and the aorta (left ventricle).
left ventricular end-systolic blood pressure
The pressure in the heart left ventricle at the end of diastole, the period when the heart is in a state of relaxation and expansion and the ventricles fill with blood.
left ventricular end-diastolic blood pressure
Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity.
absolute change in systolic blood pressure
Calculated measurement of a difference in diastolic blood pressure between two points or two conditions expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
absolute change in diastolic blood pressure
A calculated measurement in which the weight after removal from the body but without desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a ratio, fraction or quotient, thus normalizing it to body weight.
individual kidney wet weight to body weight ratio
single kidney wet weight to body weight ratio
A calculated measurement in which the weight after removal from the body but without desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a percentage, thus normalizing it to body weight.
individual kidney wet weight as percentage of body weight
single kidney wet weight as percentage of body weight
Any measurement of components of the periodic tightening and loosening of the heart muscle.
Measure of the time from the relaxation of the heart muscle to the beginning of the tightening of the heart muscle during contraction.
Measurement of the time from the beginning of heart muscle contraction to the maximum contracted state.
Pressure exerted by the heart muscle in its maximally contracted state.
Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function.
This is not the same term as the original "heart measurement". That term is now "heart morphological measurement".
A measurement made on a fluid flowing out of the heart.
The volume of a fluid flowing out of the heart.
The volume of a fluid flowing out of the heart during a specified amount of time.
The amount of an enzyme in a specified volume of fluid flowing out of the heart.
The amount of lactate dehydrogenase activity measured in a specified volume of fluid flowing out of the heart.
heart effluent lactate dehydrogenase activity level
Measurement of a lesion in an organ. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
A measurement of any lesion of the heart. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
Measurement of an area of necrotic tissue resulting from a reduction or obstruction of the oxygen supplied to that tissue.
Measurement of an area of necrotic tissue in the heart resulting from a reduction or obstruction of the oxygen supply.
Measurement of an area of necrotic tissue in the left ventricle of the heart resulting from a reduction or obstruction of the oxygen supply to the heart.
heart left ventricle infarction measurement
Measurement of the area, volume or weight of necrotic tissue resulting from a reduction or obstruction of the oxygen supplied to that tissue.
Measurement of the area, volume or weight of necrotic tissue in the heart resulting from a reduction or obstruction of the oxygen supply to the heart.
Measurement of the area, volume or weight of necrotic tissue in the heart left ventricle resulting from a reduction or obstruction of the oxygen supply to the heart.
calculated heart left ventricle infarction size
heart left ventricle infarction size as percentage of total heart left ventricle size
The heaviness of one or both ventricles of the heart, that is, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body, or the degree to which one or both ventricles of the heart are drawn toward the earth by gravity.
calculated heart left ventricle infarction area
calculated heart left ventricle infarction weight
heart left ventricle infarction weight as percentage of total heart left ventricle weight
The difference in body temperature between two different points in time or between two different conditions.
Measurement of the amount of resistance in a blood vessel to the flow of blood or other fluid through it.
Resistance to blood flow by blood vessels in the lung.
Measurement of vascular resistance in lung blood vessels calculated from other indirect measurements.
calculated pulmonary vascular resistance
calculated pulmonary vascular resistance normalized to body weight
Measurement made on the endothelial tissue or endothelial cells lining a blood vessel.
calculated blood vessel endothelium measurement
methylene blue metabolism-surface area product without auto-oxidation
methylene blue metabolism-surface area product after auto-oxidation
Ratio of the methylene blue metabolism-surface area product without auto-oxidation to the FAPGG metabolism-surface area product.
methylene blue to FAPGG metabolism-surface area product ratio
Any measurement of the energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
blood vessel contractile force measurement
Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
blood vessel maximum contractility measurement
maximum contractile force per wet weight of vessel
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to a drug or other chemical stimulus.
chemical response/sensitivity measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
calculated blood vessel contractile force measurement
A calculated value for the concentration of phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of PE is halfway between the baseline value and the highest achievable value of such PE-induced contractile energy.
phenylephrine half maximal effective concentration (EC50)
concentration of phenylephrine at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of PE is halfway between the baseline value and the highest achievable value of such PE-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
phenylephrine Log half maximal effective concentration (Log EC50)
logarithm of the concentration of phenylephrine at which the force of blood vessel contraction is half the maximum value (Log EC50)
Measurement of the reduction in force during dilation of a blood vessel via calculations from direct measurements rather than expressing the direct measurements themselves.
calculated blood vessel dilation force reduction measurement
A calculated value for the concentration of acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of ACh is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during ACh-induced relaxation of the vessel wall (i.e. the maximum effect of Ach which is the minimum contractile energy).
acetylcholine half maximal effective concentration (EC50)
concentration of acetylcholine at which the reduction in force during dilation of a blood vessel is half the maximum value (EC50)
A calculated value for logarithm of the concentration of acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of ACh is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during ACh-induced relaxation of the vessel wall (i.e. the maximum effect of Ach which is the minimum contractile energy). The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
acetylcholine Log half maximal effective concentration (Log EC50)
logarithm of the concentration of acetylcholine at which the reduction in force during dilation of a blood vessel is half the maximum value (Log EC50)
A calculated value for the concentration of sodium nitroprusside (SNP), the red-colored inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of SNP is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during SNP-induced relaxation of the vessel wall (i.e. the maximum effect of SNP which is the minimum contractile energy).
sodium nitroprusside half maximal effective concentration (EC50)
concentration of sodium nitroprusside at which the reduction in force during dilation of a blood vessel is half the maximum value (EC50)
A calculated value for logarithm of the concentration of sodium nitroprusside (SNP), the red-coloured inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of SNP is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during SNP-induced relaxation of the vessel wall (i.e. the maximum effect of SNP which is the minimum contractile energy).
sodium nitroprusside Log half maximal effective concentration (Log EC50)
logarithm of the concentration of sodium nitroprusside at which the reduction in force during dilation of a blood vessel is half the maximum value (Log EC50)
maximum contractile force per wet weight of aorta
Measurement of the reduction in force during blood vessel dilation.
blood vessel dilation force reduction measurement
blood vessel dilation expressed as percent of force at maximum constriction
acetylcholine-induced blood vessel dilation expressed as percent of phenylephrine-induced vasoconstriction
acetylcholine-induced blood vessel dilation expressed as percent of force at maximum constriction
sodium nitroprusside-induced blood vessel dilation expressed as percent of phenylephrine-induced vasoconstriction
sodium nitroprusside-induced blood vessel dilation expressed as percent of force at maximum constriction
hypoxia-induced blood vessel dilation expressed as percent of force at maximum constriction
slope measurement of phenylephrine-induced contraction
slope measurement of drug-induced contraction
slope measurement of chemical-induced contraction
fast-slope measurement of phenylephrine-induced contraction
fast-slope measurement of drug-induced contraction
fast-slope measurement of chemical-induced contraction
slow-slope measurement of phenylephrine-induced contraction
slow-slope measurement of drug-induced contraction
slow-slope measurement of chemical-induced contraction
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter.
acetylcholine response/sensitivity measurement
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor.
phenylephrine response/sensitivity measurement
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to sodium nitroprusside (SNP), the red-colored inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator.
sodium nitroprusside response/sensitivity measurement
Calculation of a difference between representations of blood pressure in a treated versus untreated state or over time, after the original values have been normalized or adjusted by a mathematical process or computation. Blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
A calculated measurement of the difference in developed blood pressure between a treated state and a control state. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
A calculated measurement of the difference in developed blood pressure between a treated state and a control state, expressed as a percentage. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
percent change in developed blood pressure
Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions.
The relative difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions expressed as a percentage.
percent change in systolic blood pressure
percent change in arterial blood flow rate
absolute change in arterial blood flow rate
A calculated measurement of the difference in developed pressure measured in the heart left ventricle between a treated state and a control state, expressed as a percentage. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
percent change in left ventricular developed pressure
A calculated measurement of the difference in developed pressure measured in the heart left ventricle between a treated state and a control state. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
change in left ventricular developed pressure
Difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions.
change in left ventricular systolic blood pressure
The relative difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions expressed as a percentage.
percent change in left ventricular systolic blood pressure
The activity level of LDH in effluent expressed relative to the weight of the heart; calculated as LDH activity divided by heart wet weight.
heart effluent lactate dehydrogenase activity level normalized to heart weight
The average blood pressure within the pulmonary artery over a specified period of time, or technically over a complete cycle of one heartbeat.
Measurement of blood pressure in the pulmonary artery.
pulmonary artery (PA) blood pressure measurement
pulmonary arterial blood pressure measurement
Measurement of an organ lesion which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells.
Measurement of an organ lesion which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc.
Measurement of a heart lesion which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc.
Measurement of a lesion of the heart which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells.
Any measurement, morphological or physiological, involving the kidney or any part thereof.
Renal blood flow (RBF) is the volume of blood delivered to or exiting from the kidneys per unit time.
Arterial renal blood flow (RBFa) is the volume of blood delivered to the kidneys per unit time via the renal arteries.
Venous renal blood flow (RBFv) is the volume of blood exiting from the kidneys per unit time via the renal veins.
A calculated value in which the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is divided by the total weight of the body and presented as a ratio thus normalizing it to body weight.
heart right ventricle weight to body weight ratio
A calculated value in which the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is presented as percentage of the total weight of the body thus normalizing it to body weight.
heart right ventricle weight as a percentage of body weight
Any measurement of the physical form or structure of the left ventricle of the heart. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
Note, "left" in this context refers to the perspective of the organism, not that of the nobserver.
heart left ventricle morphological measurement
Any measurement of the physical form or structure of the right ventricle of the heart. The right ventricle is the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
heart right ventricle morphological measurement
Measurement of a localized pathological change in structure of a blood vessel due to injury or disease; especially one that is circumscribed and well defined.
A measurement of blood vessel diameter which has been normalized or adjusted by a mathematical process or computation.
calculated blood vessel diameter measurement
A measurement of the depth of the wall of a blood vessel which has been normalized or adjusted by a mathematical process or computation.
calculated blood vessel wall thickness measurement
A measurement of the depth of the wall of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
A measurement of the depth of the wall of an artery which has been normalized or adjusted by a mathematical process or computation. An artery is one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
calculated artery wall thickness measurement
The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at the inner surface of the blood vessel wall.
The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at the outer surface of the blood vessel wall.
The length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall.
The length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall.
Measurement of the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at either the inner surface or outer surface of the blood vessel wall, which has been normalized or adjusted by a mathematical process or computation.
Any measurement of one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
Measurement of any localized pathological change in structure of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues, due to injury or disease; especially one that is circumscribed and well defined.
Measurement which has been normalized or adjusted by a mathematical process or computation of any localized pathological change in structure of an artery due to injury or disease; especially one that is circumscribed and well defined.
Measurement which has been normalized or adjusted by a mathematical process or computation of any localized pathological change in structure of a blood vessel due to injury or disease; especially one that is circumscribed and well defined.
calculated blood vessel lesion measurement
A calculated measurement in which the ratio of the wall thickness (WT) of a blood vessel is divided by the inner diameter (ID) of that vessel at that location, and the result presented as a ratio, fraction, quotient or percentage, for example, WT/ID x 100. This measurement is often used to assess stenosis, a pathological narrowing of a blood vessel.
blood vessel wall thickness as percentage of blood vessel lumen diameter
blood vessel wall thickness as percentage of blood vessel inner diameter
blood vessel wall thickness to blood vessel inner diameter ratio
Ratio of the wall thickness (WT) of an artery to inner diameter (ID) of that artery at that location, usually expressed as a percentage, i.e. WT/ID x 100, but could also be expressed as a ratio, fraction or quotient. This measurement can be used to assess stenosis, a pathological narrowing of a blood vessel.
artery wall thickness as percentage of artery inner diameter
artery wall thickness as percentage of artery lumen diameter
artery wall thickness to artery inner diameter ratio
A measurement of the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. An artery is a blood vessel that carries blood away from the heart.
calculated artery inner diameter measurement
Any measurement of components of the periodic tightening and loosening of the muscles of a ventricle of the heart.
The diameter across the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed, and usually corresponds to its largest diameter.
left ventricular end-diastolic dimension
heart left ventricular end-diastolic diameter
The diameter across the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted, and usually corresponds to its smallest diameter.
heart left ventricle end-systolic diameter
A measurement of the physical form or structure of the left ventricle of the heart which has been normalized or adjusted by a mathematical process or computation. The heart left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated heart left ventricle morphological measurement
A calculated measurement corresponding to the ratio or percent reduction in left ventricular diameter between end-diastole and end-systole. Can be calculated as the left ventricle end-diastolic diameter (LVDd) minus the left ventricle end-systolic diameter (LVSd) divided by the left ventricle end-diastolic diameter (LVDd) with the quotient multiplied by 100, i.e. FS = [(LVDd-LVSd)/LVDd] x 100.
heart left ventricle fractional shortening
The thickness or depth of the ventral/anterior wall of the left ventricle of the heart. The ventral/anterior wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism.
heart left ventricle ventral wall thickness
heart left ventricle anterior wall thickness
The thickness or depth of the septal wall of the heart ventricles. The septal wall is the portion of the heart left ventricle ventral/anterior wall and right ventricle dorsal/posterior wall which is shared between the ventricles.
A calculated measurement of left ventricular geometry and is calculated by dividing the end-diastolic diameter into 2x the posterior wall thickness, 2x the septal wall thickness or the sum of the posterior and septal wall thicknesses. It represents a measure of the wall thickness normalized to the size of the ventricle lumen.
heart left ventricle relative wall thickness
A calculated measurement of left ventricular geometry and is calculated by dividing the end-diastolic diameter into 2x the posterior wall thickness at end-diastole, 2x the septal wall thickness at end-diastole or the sum of the posterior and septal wall thicknesses at end-diastole. It represents a measure of the wall thickness normalized to the size of the ventricle lumen.
heart left ventricle end-diastolic relative wall thickness
The thickness or depth of the ventral/anterior wall of the heart. The ventral wall is the portion of the heart muscle which is farthest from the spine and closest to the chest wall of the organism.
calculated heart wall thickness measurement
The extent of shortening of the minor internal circumference (at the midpoint of the long axis) between end-diastole and end-systole, divided by the time required for shortening.
mean circumferential fiber shortening rate
mean velocity of circumferential fiber shortening
The thickness or depth of the ventral/anterior wall of the right ventricle of the heart. The ventral wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism.
heart right ventricle ventral wall thickness
heart right ventricle anterior wall thickness
Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis, and directly in contact with the surface of the kidney, i.e. the renal capsule. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
count of superficial glomeruli directly contacting the kidney surface
Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis but without any direct contact with the surface of the kidney, i.e. the renal capsule. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
count of superficial glomeruli not directly contacting the kidney surface
Measurement of any change or difference in the diastolic blood pressure between two points or two conditions. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
The relative difference in the diastolic blood pressure between two points or two conditions, expressed as a percentage. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
percent change in diastolic blood pressure
Calculated measurement of a difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in left ventricular systolic blood pressure
Temperature measured at the surface of or within the head of an experimental subject. Because the temperature of the head/brain can influence neurological measurements, head temperature is or can be considered to be distinct from core body temperature.
The temperature of the internal tissues and organs of the body.
A measurement which has been normalized or adjusted by a mathematical process or computation of the weight of the left ventricle of the heart, that is, its the heaviness or degree to which it is drawn toward the earth by gravity. The heart left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated heart right ventricle morphological measurement
The length of a line which crosses a transverse view of a cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The cerebral arteries are those which supply blood to the brain, more specifically, to the cerebrum.
The length of a line which crosses a transverse view of an anterior cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The anterior cerebral artery (ACA) is one of a pair of arteries that supply oxygenated blood to the most medial portions of the frontal lobes and superior medial parietal lobes of the brain.
The length of a line which crosses a transverse view of a middle cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The middle cerebral arteries are the largest of the cerebral arteries and supply blood to the lateral cerebral cortex, anterior temporal lobes and insular cortices of the brain.
The length of a line which crosses a transverse view of a posterior cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The posterior cerebral artery (PCA) is one of a pair of blood vessels that supply blood to the posterior aspect, i.e. the occipital lobe, of the brain.
posterior cerebral artery lumen diameter
posterior cerebral artery inner diameter
Measurement of a lesion in kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
Measurement of a lesion in the kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc.
Measurement of a lesion in the kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells.
Any measurement of lesions resulting from fibrosis, scarring or hyaline deposits within a kidney glomerulus, a tuft of capillaries situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney, that filters waste products from the blood and thus initiates urine formation.
renal glomerulosclerotic lesion measurement
kidney glomerulosclerotic lesion measurement
A measurement of lesions resulting from fibrosis, scarring or hyaline deposits within one or more kidney glomeruli which has been normalized, adjusted or derived by a mathematical process or computation.
calculated kidney glomerulosclerosis measurement
calculated renal glomerulosclerosis measurement
calculated renal glomerulosclerotic lesion measurement
calculated kidney glomerulosclerotic lesion measurement
A measurement of lesions resulting from fibrosis, scarring or hyaline deposits within kidney glomeruli which is derived from a combination of multiple measurements and/or objective or subjective severity scores according to a specified formula or set of criteria.
Any measurement, morphological or physiological of a muscle or a group of muscles. Muscles are organs or tissues composed of bundles of fibers that have the power to contract and hence to produce movement.
Measurement of the physical form or structure of one or more glomeruli in the kidney. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
kidney glomerulus morphological measurement
The length of a straight line passing through the center of a kidney glomerulus and connecting opposite points on its circumference.
A measurement of the volume of blood delivered to or exiting from the kidneys per unit time, which has been normalized, adjusted or derived by a mathematical process or computation.
The difference in the volume of blood delivered to or exiting from the kidneys per unit time between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in renal blood flow rate
The number of kidney glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits, or the number of such lesions in a specified sample.
Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins (complex high molecular weight organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) or peptides (low molecular weight compounds composed of at least two amino acids joined by peptide linkages) in kidney.
kidney tissue protein/peptide composition measurement
kidney protein/peptide composition measurement
Any measurement, morphological or physiological of the outer part of the kidney, composed mainly of glomeruli and convoluted tubules.
Any measurement, morphological or physiological, of the renal medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in kidney medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in renal cortex, the outer part of the kidney, composed mainly of glomeruli and convoluted tubules.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the composition, that is, the absolute amount, relative amount or type, of protein (the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) in kidney.
calculated renal protein composition measurement
calculated kidney protein composition measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation involving the amount, composition or type of protein in the kidney cortex, the outer part of the kidney, composed mainly of glomeruli and convoluted tubules.
calculated kidney cortex protein composition measurement
calculated renal cortex protein composition measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation involving the amount, composition or type of protein in the renal medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood.
calculated kidney medulla protein composition measurement
calculated renal medulla protein composition measurement
A calculated value in which the amount of TRPV4 protein in a specified sample of kidney is divided by the amount of beta-actin protein in the same or a corresponding sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level.
renal TRPV4 protein level to beta-actin protein level ratio
kidney TRPV4 protein level to beta-actin protein level ratio
A calculated value in which the amount of TRPV4 protein in a specified sample of renal cortex is divided by the amount of beta-actin protein in the same or a corresponding sample of renal cortex and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level.
kidney cortex TRPV4 protein level to beta-actin protein level ratio
renal cortex TRPV4 protein level to beta-actin protein level ratio
A calculated value in which the amount of TRPV4 protein in a specified sample of renal medulla is divided by the amount of beta-actin protein in the same or a corresponding sample of renal medulla and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level.
kidney medulla TRPV4 protein level to beta-actin protein level ratio
renal medulla TRPV4 protein level to beta-actin protein level ratio
The length of a line which crosses a transverse view of a cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. The cerebral arteries are those which supply blood to the brain, more specifically, to the cerebrum.
calculated cerebral artery inner diameter measurement
The length of a line which crosses a transverse view of a middle cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. The middle cerebral arteries are the largest of the cerebral arteries and supply blood to the lateral cerebral cortex, anterior temporal lobes and insular cortices of the brain.
calculated middle cerebral artery inner diameter measurement
A calculated measurement of the relative difference in the middle cerebral artery inner diameter between a treated state and a control state or between two points in time, expressed as a percentage.
percent change in middle cerebral artery inner diameter
A measurement of the extent of a two-dimensional plane through the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed, and usually corresponds to its largest diameter.
A measurement of the extent of a two-dimensional plane through the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted, and usually corresponds to its smallest diameter.
A calculated value in which the weight of the heart, the chambered, muscular organ that maintains the circulation of the blood, is divided by the length of the tibia, the inner and larger bone of the lower leg or hindlimb, and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the length of the leg and, by extension, to the length of the body.
A calculated value in which the total weight after removal from the body but without desiccation of both kidneys is divided by the length of the tibia, the inner and larger bone of the lower leg or hindlimb, and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the length of the leg and, by extension, to the length of the body.
both kidneys wet weight to tibia length ratio
A calculated measurement of the ratio between the change in mean arterial blood pressure and the concentration of sodium infused directly into the ventricle(s) of the brain; calculated as the slope of the curve of mean arterial blood pressure versus intracerebroventricular-infused sodium concentration.
change in mean arterial blood pressure to change in intracerebroventricular sodium concentration ratio
A calculated measurement of the ratio between the change in heart rate and the concentration of sodium infused directly into the ventricle(s) of the brain; calculated as the slope of the curve of heart rate versus intracerebroventricular-infused sodium concentration.
change in heart rate to change in intracerebroventricular sodium concentration ratio
A value calculated by dividing the proportionate change in renal blood flow (RBF) by the proportionate change in renal perfusion pressure (RPP), i.e. (RBF2 - RBF1)/RBF1 divided by (RPP2 - RPP1)/RPP1.
ratio of renal blood flow change to renal perfusion pressure change
ratio of change in renal blood flow to change in renal perfusion pressure
Any measurement of a lesion in the kidney characterized by an abnormal proliferation of fibrous connective tissue. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
Any measurement of the physical dimensions, proportions, magnitude, or extent of a lesion in the kidney characterized by an abnormal proliferation of fibrous connective tissue. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
A measurement of the extent of a two-dimensional surface of or plane through a single kidney fibrotic lesion, or a measurement of the total area occupied by fibrotic lesions in a cross-section of the kidney.
A measurement of the extent of a two-dimensional surface of or plane through a single kidney fibrotic lesion, or a measurement of the total area occupied by fibrotic lesions in a cross-section of the kidney, when that value has been normalized, adjusted or derived by a mathematical process or computation.
calculated kidney fibrotic lesion area measurement
A calculated value in which the extent of the two-dimensional surface occupied by fibrotic lesions is divided by the total extent of the two-dimensional surface of the kidney and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the size of the kidney.
kidney fibrotic lesion area to total kidney area ratio
A calculated value in which the number of glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits is divided by the total number of glomeruli in a specified sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli.
sclerotic glomeruli to total glomeruli ratio
kidney glomerulosclerotic lesion count to total glomeruli count ratio
kidney sclerotic glomeruli count to total glomeruli count ratio
The combined weight of both ventricles of the heart, that is, their heaviness or the degree to which they are drawn toward the earth by gravity. The ventricles are the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body.
A measurement of the combined weight of both heart ventricles that has been normalized, adjusted or derived by a mathematical process or computation.
A calculated value in which the combined weight of both the left and right ventricles, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body, is presented as percentage of the total weight of the body thus normalizing it to body weight.
total heart ventricle weight as a percentage of body weight
Any measurement of the cavity or channel within an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
A measurement of the two-dimensional extent of the enclosed cavity or channel in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
Any measurement of the fibrous and muscular structure of one of the large blood vessels carrying blood in a direction away from the heart to the tissues. The wall of an artery is composed of three layers: the tunica intima, the inner coat; the tunica media, the middle coat; and the tunica adventitia, the outer coat.
Any measurement of the tunica media, or middle coat, of the wall of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
A direct measurement of two dimensional extent of the tunica media, the middle coat of the arterial wall, in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. The total area of the tunica media gives an indication of the thickness of the arterial wall.
A calculated measurement of the average width of the tunica media, the middle coat of the arterial wall. Can be calculated using the media area and the length of the internal elastic lamina.
A measurement of the extent of a two-dimensional surface of or plane through a single hyperplastic lesion of the tunica intima, that is, the inner coat of the arterial wall, or a measurement of the total area occupied by hyperplastic lesions of the tunica intima in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. A hyperplastic lesion is a localized pathological increase in the number of cells of an organ or tissue resulting from an increased rate of cellular division due to injury or disease; especially one that is circumscribed and well defined.
artery neointimal hyperplastic lesion area
Any measurement of one or more hyperplastic lesions of the arterial tunica intima which has been normalized, adjusted or derived by a mathematical process.
calculated arterial intima hyperplasia area
calculated artery neointimal hyperplastic lesion area
A calculated measurement in which the area of the arterial tunica intima occupied by one or more hyperplastic lesions is divided by the total cross-sectional area of the artery wall and presented as a ratio, fraction, quotient or percentage.
ratio of neointimal hyperplasia area to total wall area of artery
artery neointimal hyperplastic lesion area to total wall area ratio
The area of the arterial lumen remaining when the luminal space is restricted by a pathological process, e.g. hyperplasia.
The weight after desiccation of both kidneys, the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The weight after desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
Any measurement of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
Any quantification of the physical form or structure of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
The speed at which the blood flows through the circulatory system or through a specific segment of a vein or artery, expressed as distance per unit of time.
The speed at which the blood flows through an artery, expressed as distance per unit of time.
The speed at which the blood flows through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds, expressed as distance per unit of time.
Any measurement of the movement of blood through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds.
The volume of blood flowing through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds, per unit of time.
The maximum speed at which the blood flows through the aorta during the cardiac cycle, expressed as distance per unit of time.
The length of time in the cardiac cycle between the closing of the aortic and pulmonic/pulmonary semilunar valves and opening of the atrioventricular (AV) valves marking the beginning of ventricular filling. Used as an indicator of diastolic dysfunction.
Measurement of the physical form or structure of the left upper chamber of the heart that receives blood from the veins and forces it into the left ventricle.
heart left atrium morphological measurement
Measurement of the physical form or structure of the right upper chamber of the heart that receives blood from the veins and forces it into the right ventricle.
heart right atrium morphological measurement
The distance between two specified opposite points on the periphery of the left atrium of the heart at the end of systole, that is, when the left ventricle is maximally contracted, and usually corresponds to the left atrium's largest diameter.
The distance between two specified opposite points on the periphery of the left atrium of the heart at the end of diastole, that is, when the left ventricle is maximally dilated, and usually corresponds to the left atrium's smallest diameter.
heart left atrium end-diastolic diameter
A measurement of the physical form or structure of the left atrium, the left upper chamber of the heart that receives blood from the veins and forces it into the left ventricle, which has been normalized, adjusted or derived by a mathematical process or computation.
calculated heart left atrium morphological measurement
A calculated measurement corresponding to the ratio or percent reduction in left atrial diameter between end-systole and end-diastole. It is calculated as the left atrium end-systolic diameter (LADs) minus the left atrium end-diastolic diameter (LADd) divided by the left atrium end-systolic diameter (LADs).
Measurement of the number of white blood cells, including lymphocytes and monocytes, with a single round or oval nucleus in a specified volume of blood.
A measurement of the movement of blood through one or more vessels or organs in the body which has been normalized, adjusted or derived by a mathematical process or computation.
Any measurement of the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall.
The volume of fluid flowing into, out of or through the blood vessels and microvasculature of the myocardium, the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall, per unit time.
Measurement of the amount of radioactive or other tracer is lost from the myocardium, the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall, per unit time.
A value resulting from the quantification of a morphological or physiological parameter of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body.
Any quantification of the physical form or structure of the layered tissue which encloses and constitutes the structural component of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
Measurement of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
Measurement of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body.
calculated vascular smooth muscle cell count
calculated blood vessel smooth muscle cell count
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
calculated aortic smooth muscle cell count
calculated aorta smooth muscle cell count
A calculated value in which the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds, is divided by the length of the smooth muscle section in which that number is determined.
aortic smooth muscle cell count per unit vessel length
aorta smooth muscle cell count per unit vessel length
The amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body.
heart left ventricle deoxyribonucleic acid content
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated heart left ventricle DNA content
calculated heart left ventricle deoxyribonucleic acid content
A calculated measurement in which amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body, is divided by the total weight or heaviness of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
heart LV DNA content to body weight ratio
heart left ventricle DNA content to BW ratio
heart left ventricle DNA content to body weight ratio
heart left ventricle deoxyribonucleic acid content to body weight ratio
The amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
heart right ventricle deoxyribonucleic acid content
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
calculated heart right ventricle DNA content
calculated heart right ventricle deoxyribonucleic acid content
A calculated measurement in which amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is divided by the total weight or heaviness of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
heart RV DNA content to body weight ratio
heart right ventricle DNA content to BW ratio
heart right ventricle DNA content to body weight ratio
heart right ventricle deoxyribonucleic acid content to body weight ratio
Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel which does not involve the action of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect.
blood vessel receptor-independent maximum contractility
receptor-independent blood vessel maximum contractile force
Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel which is instigated by the activation of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect.
blood vessel receptor-dependent maximum contractility
receptor-dependent blood vessel maximum contractile force
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
calculated blood vessel maximum contractile force measurement
A calculated measurement in which the receptor-dependent maximum contractile force of a blood vessel is divided by the receptor-independent maximum contractile force of a blood vessel and presented as a ratio, fraction, quotient or percentage. The maximum contractile force of a blood vessel is the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel. Receptor-dependent refers to such a contraction which is instigated by the activation of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect. Receptor-independent denotes such a contraction that does not involve the action of a receptor.
blood vessel receptor-dependent contractility to receptor-independent contractility ratio
receptor-dependent blood vessel maximum contractile force exoressed as a percentage of receptor-independent blood vessel maximum contractile force
receptor-dependent blood vessel maximum contractile force to receptor-independent blood vessel maximum contractile force ratio
A calculated value for the concentration of angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of AngII is halfway between the baseline value and the highest achievable value of such AngII-induced contractile energy.
Ang2 half maximal effective concentration
AngII half maximal effective concentration
angiotensin 2 half maximal effective concentration
angiotensin II half maximal effective concentration (EC50)
concentration of angiotensin II at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of AngII is halfway between the baseline value and the highest achievable value of such AngII-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
Ang2 Log half maximal effective concentration
AngII Log half maximal effective concentration
angiotensin 2 Log half maximal effective concentration
angiotensin II Log half maximal effective concentration (EC50)
logarithm of the concentration of angiotensin II at which the force of blood vessel contraction is half the maximum value (Log EC50)
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion.
angiotensin II response/sensitivity measurement
The difference in left ventricular diastolic blood pressure between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in left ventricular diastolic blood pressure
Any measurement of the blood pressure in the left ventricle of the heart which has been normalized or adjusted by a mathematical process or computation. Left ventricular blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated left ventricular blood pressure
A calculated measurement that is used as an index to characterize the contractile ability of the heart. It is believed that maximum dP/dt is a reasonable index of the initial velocity of myocardial contraction.
rate of maximum positive change in left ventricular blood pressure
maximum rate of positive change in left ventricular blood pressure
A calculated hemodynamic measurement related to the ability of the heart left ventricle to relax. The point at which the negative pressure fall velocity reaches its peak is taken to be the onset of isovolumic relaxation of the left ventricle.
rate of maximum negative change in left ventricular blood pressure
maximum rate of negative change in left ventricular blood pressure
A calculated hemodynamic value related to the ability of the heart left ventricle to relax. Tau is calculated as an exponential function of the change in intraventricular pressure during the diastolic isovolumic left ventricular pressure decrease.
time constant of left ventricular relaxation
time constant of left ventricular pressure decay
The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
end-systolic heart left ventricle posterior wall thickness
heart left ventricle end-systolic posterior wall thickness
Any quantification of the amounts or proportions of proteins, lipids, minerals, nutrients, gases, or other substances ina specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
kidney molecular composition measurement
Quanitification of one or more lipids in a specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. A lipid is any of a structurally diverse group of organic compounds that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure.
The amount of 20-hydroxyeicosatetraenoic acid, a vasoconstrictor that consists of arachidonic acid (a C20, polyunsaturated fatty acid having four (Z)-double bonds at positions 5, 8, 11 and 14) bearing a hydroxy substituent at position 20, in a specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
kidney 20-hydroxyeicosatetraenoic acid level
The number of immune cells in a specified sample. An immune cell is any cell involved in the immune system, a complex set of interconnected and interdependent cellular and molecular components having the primary functions of distinguishing self from not self and of defense against foreign organisms or substances. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
The difference in the pulse pressure of an individual between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. Pulse pressure is the difference between systolic and diastolic blood pressures, i.e. the difference between the maximal arterial pressure and minimal arterial pressure during the cardiac cycle.
A calculated measurement of the degree to which a change in the size of the remaining kidney after surgical removal of the other kidney can be attributed to compensatory growth, calculated as the ratio of the normalized weight of a single kidney at the time of surgical removal divided by the similarly normalized weight of the single remaining kidney at a specified period of time after removal. The normalized kidney weight is the weight of the kidney corrected for body weight using an empirically determined allometric scaling factor (i.e., an exponential factor which adjusts for the normal increase in kidney weight due to normal growth and development of the individual). Compensatory growth is the phenomenon in which the impaired function of one organ in a paired organ system or of part of an organ in a single organ system is followed by enlargement of the surviving organ or tissue so that functional capacity is maintained. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated measurement in which the difference in the volume of blood delivered to and/or exiting from the kidneys per unit time between two points in time or two conditions is divided by the weight (heaviness or degree to which a body is drawn toward the earth by gravity) of one or both kidneys, and presented as a ratio, fraction, quotient or percentage. The kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
ratio of change in renal blood flow rate to kidney weight
A measurement of the degree to which the blood vessels of the kidneys impede the flow of blood through them. Renal vascular resistance is calculated as the renal blood flow rate divided by the mean arterial pressure.
A measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The difference in renal vascular resistance between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. Renal vascular resistance is the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
absolute change in kidney vascular resistance
absolute change in renal vascular resistance
A calculated measurement of the slope, the ratio of vertical change to horizontal change, of the line of a graph designating the change in renal vascular resistance in response to a drug or other condition which causes constriction or reduction of the interior diameter of blood vessels. Renal vascular resistance is the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
slope of constriction-induced renal vascular resistance curve
slope of contraction-induced kidney vascular resistance curve
slope of contraction-induced renal vascular resistance curve
The enumeration, i.e. measurement of the total number, of defects or lesions of the internal elastic lamina which are not hyperplastic or neoplastic in origin in a specified sample of artery. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. The internal elastic lamina (IEL) is a fenestrated (perforated) layer of elastic tissue, i.e., one having the property of returning to the original shape after being distorted, that is the outermost part of the intima (innermost layer) of an artery. The IEL is the elastic layer that is situated between the tunica intima (inner layers) and tunica media (middle layers) of artery walls. An artery is any one of the branching system of muscular, elastic blood vessels that carry blood away from the heart.
artery internal elastic lamina defect count
artery internal elastic lamina non-tumorous lesion count
The amount of plasma that perfuses the kidneys per unit time. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated measurement in which the effective renal plasma flow rate (eRPF) is divided by weight (i.e. the heaviness or the degree to which an object is drawn toward the earth by gravity) of both kidneys and presented as a ratio, fraction, quotient or percentage. The eRPF is the amount of plasma that perfuses the renal tubules per unit time, derived by measurement of the clearance rate of a non-metabolizable solute such as para-aminohippurate (PAH). Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
effective renal plasma flow rate to both kidney weight ratio
ratio of the effective renal plasma flow to the weight of both kidneys
A calculated measurement of the amount of plasma that perfuses the renal tubules per unit time, derived by measurement of the clearance rate of a non-metabolizable solute such as para-aminohippurate (PAH). The effective RPF is approximately 10% less than the actual RPF. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of plasma that perfuses the kidneys per unit time. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of only one of the kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of both (the complete set of two) of the kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated measurement in which the weight after removal from the body but without desiccation of only the single right kidney is divided by the total weight of the body and presented as a ratio, fraction, quotient or percent, thus normalizing it to body weight and by extension to the size of the organism. The right kidney is the organ which lies on the right side of the body from the perspective of the subject.
individual right kidney wet weight to body weight ratio
right kidney wet weight to body weight ratio
A calculated measurement in which the weight after removal from the body but without desiccation of only the left kidney is divided by the total weight of the body and presented as a ratio, fraction, quotient or percent, thus normalizing it to body weight and, by extension, to the size of the organism. The left kidney is the organ which lies on the left side of the body from the perspective of the subject.
individual left kidney wet weight to body weight ratio
left kidney wet weight to body weight ratio
A calculated measurement in which the value for the volume of blood delivered to and/or exiting from the kidneys per unit time is divided by the weight (heaviness or degree to which an object is drawn toward the earth by gravity) of one or both kidneys, and presented as a ratio, fraction, quotient or percentage.
renal blood flow rate to kidney weight ratio
A calculated measurement in which difference in the mean arterial blood pressure between two or more dosages of a drug or chemical which reduces the interior diameter of blood vessels is divided by difference in the logarithm of the applied dosages and presented as a ratio, fraction, quotient or percentage. The value is calculated as the slope of the curve of the mean arterial blood pressure versus log of the vasoconstrictor dose [VC] graph, given by the equation (log[VC]2 - log[VC]1)/(MAP at [VC]2 - MAP at [VC]1). A logarithm is the power to which a base, such as 10, must be raised to produce a given number.
change in MAP to change in log[vasoconstrictor] ratio
change in mean arterial blood pressure to change in the logarithm of the vasoconstrictor dose ratio
Measurement of the length of a straight line passing through the center and connecting opposite points on the circumference of a circle delineating the outer limits of a glomerulosclerotic lesion.
kidney glomerulosclerotic lesion diameter
A calculated measurement in which the diameter of kidney glomerular injury is divided by the value of the mean arterial blood pressure and presented as a ratio, fraction, quotient or percentage, for example to give an index of kidney damage relative to the level of hypertension.
kidney glomerulosclerotic lesion diameter to mean arterial blood pressure ratio
Measurement of the physical form or structure of one or more blood vessels, the network of muscular tubes that carry blood through the body.
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of the aorta, the layered tissue which encloses and constitutes the structural component of the great artery arising from the left ventricle from which the systemic arterial system proceeds. A molecule is an aggregation of atoms, specifically a chemical combination of two or more atoms forming a specific chemical substance.
aortic wall molecular composition measurement
aorta wall molecular composition measurement
The amount of elastin in a specified sample of aorta wall tissue. Elastin is an elastic, fibrous mucoprotein, similar to collagen, and the major connective tissue protein of elastic fibers, such as those in arterial walls.
The amount of collagen in a specified sample of aorta wall tissue. Collagen refers to any of a family of extracellular, closely related proteins occurring as a major component of connective tissue, giving it strength and flexibility.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of the aorta.
calculated aortic wall molecular composition measurement
calculated aorta wall molecular composition measurement
A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of aorta wall is divided by the total weight after dessication of that sample of aorta wall, and the result presented as a ratio, fraction, quotient or percentage.
aortic wall elastin dry weight to total aortic wall dry weight ratio
aorta wall extracellular elastin dry weight to aorta wall dry weight ratio
A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of aorta wall is divided by the weight of extracellular collagen in that sample of aorta wall, and the result presented as a ratio, fraction, quotient or percentage.
aortic wall elastin dry weight to aortic wall collagen weight ratio
aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio
The total amount of protein extracted from within the cells of the aortic wall in a specified sample of aorta. Protein is any of a group of complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages.
aorta wall total intracellular protein level
The difference in mean arterial blood pressure between two points in time or two conditions expressed as a percentage (the proportion or rate per hundred parts).
percent change in mean arterial blood pressure
Average slope of the line defined by the change in heart rate (the number of contractions of the cardiac ventricles per unit of time) relative to the change in mean arterial blood pressure (the average force the blood exerts on an artery wall) over time and/or in response to a change in conditions.
change in heart rate to change in mean arterial blood pressure ratio
Maximum, largest or steepest slope of the line defined by the change in heart rate (the number of contractions of the cardiac ventricles per unit of time) relative to the change in mean arterial blood pressure (the average blood pressure within an artery over a specified period of time) over time and/or in response to a change in conditions.
maximum change in heart rate to change in mean arterial blood pressure ratio
The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of blood.
The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of a specified tissue or set of tissues.
tissue molecular composition measurement
Determination of the number of mononuclear cells, i.e. leukocytes such as lymphocytes and monocytes with a single round or oval nucleus (including but not limited to such cells found in blood, lymph or spleen) found in a specified sample.
A calculated measurement in which .the number of kidney glomeruli displaying an abnormal (i.e., pathogenic) crescentic morphology is divided by the number of kidney glomeruli displaying normal morphology, and the result presented as a ratio, fraction, quotient or percentage.
kidney crescentic glomeruli count to kidney normal glomeruli count ratio
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of heart rate, the number of contractions of the cardiac ventricles per unit of time.
The difference between two points in time or two conditions in heart rate expressed as the ratio of the low frequency R-R interval component of the power spectrum analysis to the high frequency R-R interval component of the power spectrum analysis, expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in heart rate variability
absolute change in electrocardiographic low frequency R-R interval to high frequency R-R interval ratio
absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the tissue(s) of the heart left ventricle. A molecule is an aggregation of atoms, specifically a chemical combination of two or more atoms forming a specific chemical substance.
heart left ventricle molecular composition measurement
The amount in a specified sample of tissue from the heart left ventricle, of natriuretic peptide A (NPPA), a powerful vasodilator and peptide hormone secreted mainly by heart muscle cells and involved in control of extracellular fluid volume and electrolyte homeostasis.
heart left ventricle atrial natriuretic factor level
heart left ventricle natriuretic peptide A protein level
heart left ventricle natriuretic peptide A level
The amount of renin in a specified sample of kidney tissue. Renin, an aspartyl protease, catalyzes the cleavage of angiotensinogen to form angiotensin I, the first step in the activation pathway of angiotensinogen--a cascade that can result in aldosterone release,vasoconstriction, and increase in blood pressure.
Any quantification of the ability of a protein of the kidney to accomplish an effect, e.g. take part in a chemical reaction or carry out a specified molecular function.
Any quantification of the ability of a kidney enzyme, i.e. a protein located in the kidney that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions, to carry out its specified molecular function.
A calculated measurement in which the level of catalase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Catalase converts the reactive oxygen species hydrogen peroxide to water and oxygen.
kidney catalase activity to total protein level ratio
A calculated measurement in which the level of glucose-6-phosphate dehydrogenase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glucose-6-phosphate dehydrogenase catalizes the conversion of D-glucose 6-phosphate + NADP+ to 6-phospho-D-glucono-1,5-lactone + NADPH.
kidney G6PD activity to total protein level ratio
kidney glucose-6-phosphate dehydrogenase activity to total protein level ratio
A calculated measurement in which the level of glutathione reductase (GSR) enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. GSR reduces oxidized glutathione disulfide (GSSG) to the sulfhydryl form GSH.
kidney GSR activity to total protein level ratio
kidney glutathione reductase activity to total protein level ratio
A calculated measurement in which the level of glutathione peroxidase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glutathione peroxidases constitute a family of proteins that reduce lipid hydroperoxides to their corresponding alcohols and reduce free hydrogen peroxide to water.
kidney glutathione peroxidase activity to total protein level ratio
A calculated measurement in which the level of glutathione-S-transferase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glutathione-S-transferase refers to any of a family of proteins with the ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification.
kidney glutathione-S-transferase activity to total protein level ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. superoxide dismutases constitute a family of proteins that convert naturally-occuring but harmful superoxide radicals to molecular oxygen and hydrogen peroxide.
kidney superoxide dismutase activity to total protein level ratio
A calculated measurement in which the level of paraoxonase 1 enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Paraoxonase 1 is an arylesterase that mainly hydrolyzes paroxon, an organophosphorus anticholinesterase compound, to produce p-nitrophenol.
kidney paraoxonase-1 activity to total protein level ratio
kidney paraoxonase1 activity to total protein level ratio
A calculated measurement in which the level of glutathione peroxidase enzyme activity in a specified sample of kidney is divided by the level of glutathione reductase enzyme activity in that same sample.
kidney glutathione peroxidase activity to glutathione reductase activity ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of catalase enzyme activity in that same sample.
kidney superoxide dismutase to catalase activity ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of glutathione peroxidase enzyme activity in that same sample.
kidney superoxide dismutase to glutathione peroxidase ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of paraoxonase 1 enzyme activity in that same sample.
kidney superoxide dismutase to paraoxonase-1 activity ratio
kidney superoxide dismutase to paraoxonase1 activity ratio
The amount of glutathione in a specified sample of kidney tissue. Glutathione (GSH/GSSG) is an antioxidant tripeptide with a gamma peptide linkage between the amine group of cysteine (which is attached by normal peptide linkage to a glycine) and the carboxyl group of the glutamate side-chain.
The amount of malondialdehyde in a specified sample of kidney tissue. Malondialdehyde is an organic compound with the formula CH2(CHO)2. It is a reactive species which occurs naturally, is generally found in the enol form (HOCH=CH-CHO), and is a marker for oxidative stress.
A calculated measurement in which the level of protein carbonyl (PCO) derivatives in a specified sample of kidney is divided by the total amount of protein in the sample. Protein carbonyl (PCO) derivatives are produced by the oxidation of amino acids and can be used as a marker of oxidative stress.
kidney protein carbonyl level to total protein level ratio
The amount of platinum, the chemical element with atomic number 78, in a specified sample of kidney tissue.
The amount of enzymatic activity of creatine kinase (CK) enzyme in a specified sample of serum. CK catalyses the reversible transfer of phosphate between ATP and various phosphogens such as creatine phosphate. Serum CK level is used as an enzymatic marker for myocardial infarction, rhabdomyolysis and acute renal failure.
serum creatine phosphokinase activity level
The amount of lipid peroxidation end products in a specified sample of kidney tissue. Lipid peroxidation is the oxidative degradation of lipids.
Measurement of the size of the three dimensional space occupied by a single kidney glomerulus.
Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time, one during the day and the other at night, expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity.
absolute circadian change in systolic blood pressure
absolute diurnal change in systolic blood pressure
The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of blood. Cholesterol in the blood is generally associated with various lipoproteins.
The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Cholesterol in the serum is associated with various lipoproteins.
A calculated measurement in which difference in the mean arterial blood pressure between two or more dosages of a drug or chemical which reduces or increases the interior diameter of blood vessels is divided by difference the applied dosages and presented as a ratio, fraction, quotient or percentage. The value is calculated as the slope of the curve of the mean arterial blood pressure versus the chemical dose graph.
beta coefficient of mean arterial blood pressure change
change in MAP to change in [vasoactive chemical] ratio
slope of the change in mean arterial blood pressure
change in mean arterial blood pressure to change in vasoactive chemical dose ratio
Ratio of the wall thickness (WT) of an artery to outer diameter (OD) of that artery at that location, usually expressed as a percentage, i.e. WT/OD x 100, but could also be expressed as a ratio, fraction or quotient. This measurement can be used to assess stenosis, a pathological narrowing of a blood vessel.
artery wall thickness as percentage of artery outer diameter
artery wall thickness as percentage of artery total diameter
artery wall thickness to artery total diameter ratio
Any value resulting from the quantification of a morphological or physiological parameter of leukocytes, largely colorless blood corpuscles capable of ameboid movement, whose chief function is to protect the body against microorganisms and other disease-causing entities.
A calculated measurement in which the number of white blood cells of one or more specific types in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
blood differential leukocyte count to total WBC count ratio
blood differential leukocyte count as percentage of total white blood cells
differential white blood cell percentage
blood differential leukocyte count to total leukocyte count ratio
Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of a morphological or physiological parameter of non-neoplastic lesions in the kidney.
calculated renal non-tumorous lesion measurement
calculated kidney non-tumorous lesion measurement
A calculated measurement in which the area occupied by renal protein casts is divided by the total, combined area of the outer stripe of the kidney outer medulla and the kidney cortex, and the result presented as a ratio, fraction, quotient or percentage. Renal protein casts are gelled proteins precipitated in the renal tubules and molded to the tubular lumen. The medulla outer stripe is the section of the renal medula adjacent to the renal cortex and contains portions of the nephron, including the straight proximal tubules, and portions of the loops of henle and outer medullary collecting ducts.
ratio of the area occupied by protein casts to the total area of the kidney outer medulla outer stripe and cortex
A calculated value in which the weight of the heart after removal from the body but without dessication is divided by the total weight of the body, and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
heart wet weight as a percentage of body weight
A calculated measurement in which the difference between the contractile force of a blood vessel in response to a vasoconstrictor and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls.
vasoconstrictor-induced blood vessel contractile force expressed as percent of force at baseline
A calculated measurement in which the difference between the contractile force of a blood vessel in response to a specified dosage of phenylephrine and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. Phenylephrine is an adrenergic drug that is a powerful vasoconstrictor.
phenylephrine-induced blood vessel constriction expressed as percent of force at baseline
phenylephrine-induced blood vessel contractile force expressed as percent of force at baseline
A calculated measurement in which the difference between the contractile force of a blood vessel in response to a specified dosage of potassium chloride and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. Potassium chloride is the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). It is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels.
KCl-induced blood vessel constriction expressed as percent of force at baseline
potassium chloride-induced blood vessel contractile force expressed as percent of force at baseline
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to potassium chloride, the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). Potassium chloride is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels.
potassium chloride response/sensitivity measurement
A calculated value for the concentration of potassium chloride (KCl) at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of KCl is halfway between the baseline value and the highest achievable value of such KCl-induced contractile energy. Potassium chloride is the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). It is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels.
potassium chloride half maximal effective concentration (EC50)
KCl half maximal effective concentration (EC50)
concentration of potassium chloride at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of potassium chloride (KCl) at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of KCl is halfway between the baseline value and the highest achievable value of such KCl-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
potassium chloride Log half maximal effective concentration (Log EC50)
KCl Log half maximal effective concentration (Log EC50)
logarithm of the concentration of potassium chloride at which the force of blood vessel contraction is half the maximum value (Log EC50)
A calculated value for the concentration of a vasoconstrictor at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of the stimulus is halfway between the baseline value and the highest achievable value of such stimulus-induced contractile energy. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls.
vasoconstrictor half maximal effective concentration (EC50)
concentration of vasoconstrictor at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of a vasoconstrictor at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of the stimulus is halfway between the baseline value and the highest achievable value of such stimulus-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls.
vasoconstrictor Log half maximal effective concentration (Log EC50)
logarithm of the concentration of vasoconstrictor at which the force of blood vessel contraction is half the maximum value (Log EC50)
The thickness or depth of the ventral/anterior wall of the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed. The ventral/anterior wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism.
heart left ventricle end-diastolic ventral wall thickness
heart left ventricle end-diastolic anterior wall thickness
A calculated measurement in which the weight of the left ventricle of the heart is divided by its area at end-diastole, that is, when the heart muscle is maximally relaxed, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle weight to heart left ventricle end-diastolic area ratio
Any measurement of the movement of blood into, through or out of the heart.
Measurement of the speed at which blood flows into the ventricle during passive filling, that is, during the period when the blood flows from the atrium to the ventricle due to gravity rather than as a result of active contraction of the atrium.
An echocardiographic measurement of the amount of time between the maximum 'E point', that is, the maximum velocity of passive blood flow from the atrium to the ventricle, and the return to baseline at the end of early mitral flow.
Measurement of the decrease in transmitral blood flow velocity per unit time or the rate at which the velocity of passive blood flow from the atrium to the ventricle decreases over time as the ventricle fills and the atrium empties, calculated as the slope of transmitral velocity vs time.
Any measurement of the physical form or structure of a muscle fiber, any of the cells of skeletal or cardiac muscle tissue. Each cell is one fiber of the muscle.
Any measurementof the physical form or structure of a skeletal muscle fiber, a cylindrical multinucleate cell of skeletal muscle tissue containing contracting myofibrils and across which run transverse striations.
skeletal muscle fiber morphological measurement
The average number of capillaries associated with and/or surrounding an individual skeletal muscle fiber, a cylindrical multinucleate cell of skeletal muscle tissue containing contracting myofibrils and across which run transverse striations. Capillaries are the minute vessels connecting arterioles and venules, the walls of which act as a semipermeable membrane for interchange of various substances between the blood and tissue fluid.
number of capillaries per skeletal muscle cell
number of capillaries per skeletal muscle fiber
Any measurement, morphological or physiological of the minute vessels connecting arterioles and venules, the walls of which act as a semipermeable membrane for interchange of various substances between the blood and tissue fluid.
The length of time in the cardiac cycle between the end of left ventricular relaxation and the start of left ventricular filling. This represents the time in the cardiac cycle between closure of the aortic valve and opening of the mitral valve.
left ventricular isovolumetric relaxation time
The time interval from the completion of the mitral valve closure to the beginning of the aortic valve opening, that is, the period of contraction during which both the mitral and aortic valves are closed so that the volume of the ventricular space doesn't change.
left ventricular isovolumetric contraction time
The length of time in the cardiac cycle between the end of right ventricular relaxation and the start of right ventricular filling.
right ventricular isovolumetric relaxation time
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the length of time in the cardiac cycle between the end of left ventricular relaxation and the start of left ventricular filling.
calculated left ventricular isovolumetric relaxation time
A calculated measurement in which the value of the left ventricular isovolumetric relaxation time is corrected by the square root of the R-R interval [IVRT/(RR)1/2] on a simultaneously-recorded ECG.
heart rate-corrected left ventricular isovolumetric relaxation time
Measurement of the length of time between the closing of the mitral valve (the dual-flap valve in the heart that controls blood flow between the left atrium and the left ventricle) at the end of ventricular filling (that is, after atrial contraction) and its opening at the beginning of the next round of ventricular filling.
The time interval from the opening to the closing of the aortic valve (mechanical systole).
A calculated measurement comprised of the sum of left ventricular isovolumetric contraction time and isovolumetric relaxation time divided by the left ventricular ejection time.
Any measurement of the degree to which the presentation of any cardiovascular disease state, causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof.
cardiovascular disease severity measurement
Any measurement related to a deviation from or interruption of the normal structure or function of the cardiovascular system that is manifested by a characteristic set of symptoms and signs.
Any measurement of the degree to which the presentation of an arterial disease state, causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof. Arterial disease is a deviation from or interruption of the normal structure or function of one or more arteries, the vessels in which blood flows away from the heart carrying oxygenated blood, that is manifested by a characteristic set of symptoms and signs.
Measurement of the degree to which a tear or break in the continuity or configuration of the aorta (the great artery arising from the left ventricle and from which the systemic arterial system proceeds) causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof.
The value or quantity determined by count of tears or breaks in the continuity or configuration of the fenestrated layer of elastic tissue that is the outermost part of the intima of an artery.
number of ruptures of internal elastic lamina in arteries
number of ruptures of internal elastic laminae in arteries
number of ruptures of arterial internal elastic lamina
The value or quantity determined by count of tears or breaks in the continuity or configuration of the internal elastic lamina (IEL) of the abdominal aorta and iliac arteries, that is, the distal segment of the descending aorta and the large arteries that originate from it.
number of RIEL in abdominal aorta and iliac arteries
number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries
The value or quantity determined by count of tears or breaks in the continuity or configuration of the internal elastic lamina (IEL) of the renal arteries, that is, the ateries which arise from the side of the abdominal aorta and which supply the kidneys with blood.
number of ruptures of the internal elastic lamina of the renal arteries
A measurement of the severity of tears or breaks in the arterial internal elastic lamina (IEL) which is derived from a combination of multiple measurements and/or objective or subjective severity scores according to a specified formula or set of criteria. The IEL is the fenestrated layer of elastic tissue that is the outermost part of the intima of an artery.
arterial internal elastic lamina rupture composite score
A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of the wall of the aorta is divided by the length (that is, the distance between the two ends) of that segment, and the result presented as a ratio, fraction, quotient or percentage.
aorta wall extracellular elastin dry weight to aorta length ratio
A measurement of the existance and severity of a patent ductus arteriosus (PDA) when such a measurement is derived from a combination of multiple measurements and/or an objective or subjective ranking or rating system according to a specified formula or set of criteria. PDA is the abnormal persistence of an open lumen in the ductus arteriosus, between the aorta and the pulmonary artery, after birth.
Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins (complex high molecular weight organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) or peptides (low molecular weight compounds composed of at least two amino acids joined by peptide linkages) in a specified tissue or set of tissues.
tissue protein/peptide composition measurement
Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins or peptides in a specified sample of tissue from the wall of the aorta.
aortic wall protein/peptide composition measurement
aorta wall protein/peptide composition measurement
A calculated parameter derived from a a sequence of blood pressure measurements taken sequentially and ordered in time. A parameter is a mathematical and statistical variable in a model system that partially or completely characterises the mathematical model.
blood pressure time series calculated parameter
A mathematical and statistical variable in a model system that partially or completely characterises the baroreceptor response in a blood pressure time series calculation. The baroreceptor response is the system whereby specific nerve terminals that stabilize moment to moment blood pressure variability in the carotid sinus and aortic arch sense deviations from the baseline pressure and initiate signals that dampens such deviations.
blood pressure time series baroreceptor response calculation parameter
The first order coefficient parameter derived from a blood pressure time series moving average (also known as a rolling average, running average, moving mean, or rolling mean) calculation.
blood pressure time series first order moving average coefficient
The fractal parameter derived from a blood pressure time series calculation based on a autoregressive fractionally integrated moving average time series model (ARFIMA, FARIMA, or fARIMA).
blood pressure time series fractal parameter
The experimental set point parameter of the blood pressure time series baroreceptor response calculation.
blood pressure time series experimental set point of the baroreceptor response
The average exponential scaling factor parameter of the blood pressure time series baroreceptor response calculation.
blood pressure time series average exponential scaling factor of the baroreceptor response
A parameter based on a blood pressure time series calculation using a first order mechanistic model.
blood pressure time series linear term first order parameter
A parameter based on a blood pressure time series calculation using a second order mechanistic model.
blood pressure time series linear term second order parameter
The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism.
end-diastolic heart left ventricle posterior wall thickness
heart left ventricle end-diastolic posterior wall thickness
A value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipoprotein, any of a class of complex molecules found in blood that consist of a protein membrane surrounding a core of lipids.
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in lipoprotein molecules in a specified volume of blood. Lipoprotein particles are complex molecules that consist of a protein membrane surrounding a core of lipids.
The distance between the two ends, that is, of the extent of the longest dimension, of the aorta, the main trunk from which the arterial system proceeds.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the physical form or structure of the aorta, the main trunk from which the arterial system proceeds.
calculated aorta morphological measurement
A calculated measurement in which the weight of the aorta is divided by its length and the resulting quantity is divided by the total body weight of the organism.
aorta mass to aorta length to body mass ratio
aorta weight to aorta length to body weight ratio
A calculated measurement of the relative difference in pulse pressure between a treated state and a control state or between two points in time, expressed as a percentage.
Any quantification of the ability of a protein of the heart to accomplish an effect, e.g. take part in a chemical reaction or carry out a specified molecular function.
Any quantification of the ability of a heart enzyme, i.e. a protein located in the heart that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions, to carry out its specified molecular function.
Quantitation of the catalytic effect exerted by angiotensin I converting enzyme 2 (ACE2) in a specified sample of heart tissue. ACE2, an ACE homolog, is a zinc-dependent peptidase of the M2-metalloprotease family that is sensitive to chloride ion concentration, is a membrane-bound enzyme that acts as a monocarboxypeptidase, and is an essential regulator of heart function.
heart angiotensin II converting enzyme activity level
heart angiotensin I converting enzyme 2 activity level
Quantitation of the catalytic effect exerted by angiotensin I converting enzyme (ACE) in a specified sample of heart tissue. ACE is one of the enzymes of the renin-angiotensin system, and catalyzes the conversion of angiotensin I into a physiologically active vasoconstrictor peptide angiotensin II.
heart angiotensin I converting enzyme activity level
Quantitation of the catalytic effect exerted by angiotensin converting enzyme2 (ACE2) in a specified sample of kidney. ACE2, an ACE homolog, is a zinc-dependent peptidase of the M2-metalloprotease family that is sensitive to chloride ion concentration, and is a membrane-bound enzyme that acts as a monocarboxypeptidase and is an essential regulator of heart function.
kidney angiotensin II converting enzyme activity level
kidney angiotensin I converting enzyme 2 activity level
Quantitation of the catalytic effect exerted by angiotensin I converting enzyme (ACE) in a specified sample of kidney tissue. ACE is one of the enzymes of the renin-angiotensin system, and catalyzes the conversion of angiotensin I into a physiologically active vasoconstrictor peptide angiotensin II.
kidney angiotensin I converting enzyme activity level
Any measurement of the physical form or structure of a cardiac muscle fiber, a striated cardiac muscle cell (cardiomyocyte) that is responsible for heart contraction.
cardiac muscle cell morphological measurement
cardiac myocyte morphological measurement
heart muscle cell morphological measurement
cardiac muscle fiber morphological measurement
The length of a straight line passing through a cardiac muscle fiber, that is a cardiomyocyte, for instance through the center of its nucleus, and connecting opposite points on its periphery.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of plasma that perfuses the kidneys per unit time per amount of body weight.
A calculated measurement in which glomerular filtration rate, an estimate of the volume of fluid filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time, is divided by the total weight of the body and the result is presented as a ratio, fraction, quotient or percentage.
glomerular filtration rate to body weight ratio
A calculated value in which the volume of glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits is divided by the total volume of glomeruli in a specified sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total volume of glomeruli.
kidney sclerotic glomerular volume to total kidney glomerular volume ratio
A calculated value in which the weight of the heart left ventricle is divided by the length of the tibia (the medial and larger of the two bones of the lower leg of bipeds or hindlimb of quadrupeds which articulates with the femur, fibula, and talus), and the result is presented as a ratio, fraction, quotient or percentage,thus normalizing it to the length of the leg and, by extension, to the size of the body.
heart left ventricle weight to tibia length ratio
Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the movement of blood into, through or out of the heart.
A calculated measurement in which the value of the E wave (that is, the velocity of the blood flow across the mitral valve during passive filling of the left ventricle in early diastole) is divided by the value of the A wave (that is, the velocity of the blood flow across the mitral valve during active filling of the left ventricle caused by atrial contraction in late diastole).
A calculated measurement in which the average width of the tunica media is divided by the inner diameter (that is, the diameter of the lumen) of the artery and the result is presented as a ratio, fraction, quotient or percentage.
artery tunica media width to artery inner diameter ratio
The thickness, width or depth of the septal wall of the heart ventricles (that is, the portion of the wall between the left and right ventricles that is shared between the two) at the end of diastole when the heart muscle is maximally relaxed.
heart intraventricular septum end-diastolic thickness
heart intraventricular end-diastolic wall thickness
The thickness, width or depth of the septal wall of the heart ventricles (that is, the portion of the wall between the left and right ventricles that is shared between the two) at the end of systole when the heart muscle is maximally contracted.
heart intraventricular septum end-systolic thickness
heart intraventricular end-systolic wall thickness
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour systolic blood pressure measurements.
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour diastolic blood pressure measurements.
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour mean arterial blood pressure measurements.
mean arterial blood pressure variability
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour heart rate measurements.
A calculated value in which the number of glomeruli with microaneurysm (focal dilation of arteriocapillary junctions), is divided by the total number of glomeruli in the kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli.
ratio of number of glomeruli with microaneurysms to number of total glomeruli
A calculated value in which the area of glomeruli with activated mesangial cells (determined by the expression of α-smooth muscle actin), is divided by the total area of glomeruli counted in the kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli.
ratio of glomerular area occupied by activated mesangial cells to total glomerular area
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the glomeruli of one or both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
calculated kidney glomerulus morphological measurement
calculated kidney glomerulus measurement
Any measurement of the physical form or structure of one or more of the mesenteric arteries, which arise from the anterior surface of the abdominal aorta, just inferior to the origin of the celiac trunk, and supplies blood to the intestine from the lower part of the duodenum through two-thirds of the transverse colon, as well as the pancreas.
mesenteric artery morphological measurement
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of one or more of the mesenteric arteries.
mesenteric artery molecular composition measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the physical form or structure of any of the mesenteric arteries.
calculated mesenteric artery wall molecular composition measurement
calculated mesenteric artery molecular composition measurement
A calculated measurement in which mesenteric artery phosphorylated eNOS protein level is divided by aorta wall total eNOS protein level and presented as a ratio, fraction, quotient or percentage. Phosphorylation of eNOS is a mechanism that catylzes a structural change of the enzyme to an activated form.
mesenteric artery phosphylated eNOS protein level to total eNOS protein level ratio
mesenteric artery wall phosphylated eNOS level to total eNOS level ratio
mesenteric artery phosphylated eNOS level to total eNOS level ratio
A calculated measurement in which aorta wall phosphorylated eNOS protein level is divided by aorta wall total eNOS protein level and presented as a ratio, fraction, quotient or percentage. Phosphorylation of eNOS is a mechanism that catylzes a structural change of the enzyme to an activated form.
aorta wall phosphylated eNOS protein level to total eNOS protein level ratio
aorta wall phosphylated eNOS level to total eNOS level ratio
Monophasic action potentials (MAPs) are recorded using contact electrode catheters. The recordings provide local information about the actual cellular depolarization and repolarization process of myocardial tissue. They are different from body surface electrocardiographic (ECG) recordings or standard endocardial electrograms, which produce a summative or derivative view of the heart's electrical activity
Conduction velocity is calculated as the distance from pacing electrode to the monophasic action potential recording electrode across the epicardial surface, divided by the conduction time, the time from the pacing spike to monophasic action potential onset.
The E/E' is a ratio of peak velocity of early diastolic trans-mitral flow (E) to the peak velocity of early diastolic mitral annular motion (E')
E wave velocity to E' wave velocity ratio
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the tissue(s) of the heart.
cardiac molecular composition measurement
Measurement of the amount of free fatty acids within the heart.
Measurement of the amount of triglycerides within the heart.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the end-systolic heart left ventricle posterior wall thickness.
calculated heart left ventricle end-systolic posterior wall thickness
A calculated measurement in which the heart left ventricle end-systolic posterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-systolic posterior wall index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart left ventricle end-systolic internal diameter.
calculated heart left ventricle end-systolic internal dimension
calculated heart left ventricle end-systolic internal diameter
A calculated measurement in which the heart left ventricle end-systolic internal diameter is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-systolic internal dimension index
heart left ventricle end-systolic internal diameter index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart ventricle end-systolic septal wall thickness.
calculated heart end-systolic intraventricular wall thickness
calculated heart ventricle end-systolic septal wall thickness
A calculated measurement in which the heart ventricle end-systolic septal wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart ventricle end-systolic septal wall index
Peak velocity of late atrial diastolic trans-mitral flow (A).
E' wave velocity is the peak velocity of early mitral annular diastolic motion.
A' wave velocity (A') is the peak velocity of late (atrial) diastolic mitral annular motion.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of cardiac output.
A calculated measurement in which the cardiac output is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of cardiac stroke volume.
A calculated measurement in which the cardiac stroke volume is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the left ventricular end-systolic blood pressure.
calculated left ventricular end-systolic blood pressure
Effective arterial elastance (Ea), defined as the ratio of left ventricular (LV) end-systolic pressure and stroke volume, lumps the steady and pulsatile components of the arterial load in a concise way.
Defined as the work performed by the left or right ventricle to eject the stroke volume into the aorta or pulmonary artery, respectively.
Defined as the work performed by the left ventricle to eject the stroke volume into the aorta.
Preload recruitable stroke work (PRSW) is determined by the linear regression of stroke work with the end-diastolic volume. The slope of the PRSW relationship is a highly linear index of myocardial contractility that is insensitive to preload and afterload.
preload recruitable left ventricle stroke work
A calculated measurement in which the maximum rate of positive change in left ventricular blood pressure is divided by the left ventricular end-diastolic volume, and the result presented as a ratio, fraction, quotient or percentage.
maximum rate of positive change in left ventricular blood pressure to left ventricular end-diastolic volume ratio
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the end-diastolic heart left ventricle posterior wall thickness.
calculated heart left ventricle end-diastolic posterior wall thickness
A calculated measurement in which the heart left ventricle end-diastolic posterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-diastolic posterior wall index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart left ventricle end-diastolic anterior wall thickness.
calculated heart left ventricle end-diastolic anterior wall thickness
A calculated measurement in which the heart left ventricle end-diastolic anterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-diastolic anterior wall index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart ventricle end-diastolic septal wall thickness.
calculated heart ventricle end-diastolic septal wall thickness
A calculated measurement in which the heart ventricle end-diastolic septal wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart ventricle end-diastolic septal wall index
Renal medullary blood flow (MBF) is the volume of blood delivered to or exiting from the renal medulla per unit time.
Left ventricle end-diastolic elastance (Eed) is the estimate of the slope of the line Ped=Eed(Ved-V0), which is based on linear regression of points determined by iterative calculation of the LV end-diastolic pressurevolume relationship.
heart left ventricle end-diastolic elastance
Left ventricle end-systolic elastance (Ees) is the estimate of the slope of the line Pes=Ees(Ves-V0), which is based on linear regression of points determined by iterative calculation of the LV end-systolic pressurevolume relationship.
heart left ventricle end-systolic elastance
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of components of the periodic tightening and loosening of the muscles of a ventricle of the heart.
calculated ventricle contraction measurement
Left ventricle diastolic volume-axis intercept (V0) is determined by the line Ped=Eed(Ved-V0), which is based on linear regression of points determined by interative calculation of the LV end-diastolic pressurevolume relationship.
Heart left ventricle diastolic volume-axis intercept (V0)
Left ventricle systolic volume-axis intercept (V0) is determined by the line Pes=Ees(Ves-V0), which is based on linear regression of points determined by iterative calculation of the LV end-diastolic pressurevolume relationship.
Heart left ventricle systolic volume-axis intercept (V0)
A measurement of the volume of blood in ventricle immediately before a contraction which has been normalized or adjusted by a mathematical process or computation. .
A measurement of the volume of blood in a ventricle at the end of a contraction which has been normalized or adjusted by a mathematical process or computation.
The amount of adrenomedullin in a specified sample of kidney tissue.
The amount of adrenomedullin in a specified sample of medullary kidney tissue.
The amount of adrenomedullin in a specified sample of cortical kidney tissue.
Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the volume of fluid filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time based on serum creatinine level, wieght and age of organism and other factors.
Any quantification of a morphological or physiological parameter of one or more nucleic acids in the heart. Nucleic acids are high-molecular-weight polymeric compounds composed of nucleotides, each consisting of a purine or pyrimidine base, a ribose or deoxyribose sugar, and a phosphate group, and are involved in the determination and transmission of genetic characteristics.
Any measurement of the absolute or relative amount(s) of one or more of the ribonucleic acids (RNAs) of which the heart is formed or composed.
heart ribonucleic acid composition measurement
heart insulin-like growth factor 1 mRNA level
Any measurement of the absolute or relative amount(s) of one or more of the ribonucleic acids (RNAs) of which the heart left ventricle is formed or composed.
heart left ventricle ribonucleic acid content
heart right ventricle insulin-like growth factor 1 mRNA level
The amount of ribonucleic acid (DNA), the molecule composed of the sugar ribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or uracil , extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
heart right ventricle ribonucleic acid content
heart right ventricle molecular composition measurement
heart left ventricle insulin-like growth factor 1 mRNA level
heart insulin-like growth factor 1 receptor mRNA level
heart right ventricle insulin-like growth factor 1 receptor mRNA level
heart left ventricle insulin-like growth factor 1 receptor mRNA level
Filtration fraction is the ratio of the glomerular filtration rate (GFR) to the renal plasma flow (RPF). Filtration Fraction, FF = GFR/RPF. The filtration fraction, therefore, represents the proportion of the fluid reaching the kidneys which passes into the renal tubules.
glomerular filtration rate to kidney weight ratio
A calculated measurement to determine the volume of fluid filtered from the renal (kidney) glomerular capillaries of a single nephron into Bowman's capsule per unit time.
single nephron glomerular filtration rate
A calculated measurement to determine the ratio of the single nephron glomerular filtration rate (SNGFR) to the renal plasma flow (RPF). Single nephron filtration Fraction, SNFF = SNGFR/RPF. The single nephron filtration fraction, therefore, represents the proportion of the fluid reaching the kidneys which passes into the renal tubules from a single nephron.
calculated kidney morphological measurement
""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]
A calculated value in which the weight of the left atrium, the upper chamber on the left side of the heart which empties into the lower left chamber, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight.
heart left atrium weight to body weight ratio
A measurement of the physical form or structure of the right atrium, the right upper chamber of the heart that receives blood from the vena cava and forces it into the right ventricle, which has been normalized, adjusted or derived by a mathematical process or computation.
calculated heart right atrium morphological measurement
A calculated value in which the weight of the right atrium, the upper chamber on the right side of the heart which empties into the lower right left chamber, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight.
heart right atrium weight to body weight ratio
The weight of the septum of the heart, which is the portion of the heart left ventricle ventral/anterior wall and right ventricle dorsal/posterior wall which is shared between the ventricles, after removal from the body and separation from the rest of the heart.
The average number of podocytes in the kidney glomeruli.
number of podocytes per kidney glomerulus
A calculated measurement in which the average number of podocytes is divided by the average volume of kidney glomeruli.
number of podocytes to glomerular volume ratio
The average number of nucleated cells in the kidney glomeruli.
number of nucleated cells per kidney glomerulus
An injury score obtained by multiplying the degree of glomerular damage (0 to 4) with the percentage of the glomeruli with that type of injury (i.e., increase in mesangial matrix material or glomerulosclerosis).
Volume of blood plasma delivered to a single glomerulus per unit time
Force exerted on the luminal capillary wall from fluid flowing through the capillary.
Any measurement of one of the small blood vessels carrying blood between arteries and capillaries.
Resistance that must be overcome to push blood through arterioles to create flow.
Resistance to blood flow measured within the efferent arteriole proximal to a glomerular capillary network.
efferent glomerular arteriolar resistance
Resistance to blood flow measured within the afferent arteriole distal to a glomerular capillary network.
afferent glomerular arteriolar resistance
Total resistance to blood flow measured within the afferent arteriole proximal and distal to a glomerular capillary network (Rt = Ra + Re).
Rt; total glomerular arteriolar resistance
Measurement of the total amount of all proteins found in a specific volume of afferent arteriolar plasma.
afferent arteriolar plasma protein concentration
Measurement of the total amount of all proteins found in a specific volume of efferent arteriolar plasma.
efferent arteriolar plasma protein concentration
A form of osmotic pressure exerted by proteins, notably albumin, in the afferent arteriole's plasma that tends to pull water into the circulatory system. It is the opposing force to hydrostatic pressure. It has a major effect on the pressure across the glomerular filter.
A form of osmotic pressure exerted by proteins, notably albumin, in the efferent arteriole's plasma that tends to pull water into the circulatory system. It is the opposing force to hydrostatic pressure. It has a major effect on the pressure across the glomerular filter
A measure of a membrane's permeability to water; specifically, the volume of fluid filtered in unit time through a unit area of membrane per unit pressure difference, and it is defined as the glomerular filtration rate (GFR) for both kidneys per millimeter of mercury (mmHg) of filtration pressure.
glomerular capillary ultrafiltration coefficient
A calculated measurement in which the area occupied by renal cysts is divided by the total the kidney, and the result presented as a ratio, fraction, quotient or percentage.
ratio of the area occupied by cysts to the total area of the kidney
Force exerted on the luminal surface of the proximal tubule from fluid flowing through the tubule.
mean proximal tubular hydraulic pressure
Force exerted on the luminal vessel wall from fluid flowing through the efferent arteriole.
efferent glomerular arteriolar hydraulic pressure
The difference between the force exerted on the luminal glomerular capillary wall and the force exerted on the luminal proximal tubular membrane (Pgc - Pt = delta P).
glomerular transcapillary hydraulic pressure gradient
calculated left ventricular end-diastolic blood pressure measurement
A calculated measurement in which the pressure in the heart left ventricle at the end of diastole, the period when the heart is in a state of relaxation and expansion and the ventricles fill with blood, divided by the diameter across the left ventricle of the heart at the end of diastole and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricular end-diastolic blood pressure to heart left ventricular end-diastolic diameter ratio
Rate-pressure product is defined as the product of the heart rate (the number of contractions of the cardiac ventricles per unit of time) and mean arterial blood pressure (the average force the blood exerts on an artery wall).
A calculated measurement of the average width of the tunica media (the middle coat of the arterial wall) divided by the artery total diameter (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall).
artery tunica media to artery total diameter ratio
A calculated measurement of the average width of the artery lumen (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall) divided by the artery total diameter (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall).
artery lumen to artery total diameter ratio
A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell.
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
clinical drug role
a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
William Hogan
drug product
active ingredient role
a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism
William R. Hogan
active ingredient
role of a scattered molecular aggregate
a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes
role of scattered molecular aggregate
administration of a drug product to an organism
a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism
drug administration
A exposure event involving the interaction of an exposure receptor to radiation.
A exposure event involving the interaction of an exposure receptor to electromagnetic radiation.
An exposure to organic molecular entity.
A exposure event involving the interaction of an exposure receptor to environmental system process.
exposure to environmental system process
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
A political association with effective dominion over a geographic area.
Place or area with clustered or scattered buildings and a permanent human population.
A feature that has been constructed by deliberate human effort.
"constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
A permanent walled and roofed construction.
A geographical region whose affairs and population are administered by an authority.
An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance.
This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter.
physical object of mesoscopic geological size
A material entity which determines an environmental system.
A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
anthropogenic abiotic mesoscopic feature
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
environmental
Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
A system which has the disposition to environ one or more material entities.
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
A building part is a construction which is part of a building.
Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
outer space
A settlement with a high density of buildings and inhabitants.
See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx
The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.
dense settlement
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
human dwelling
A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement.
This class may be split. "urban village" doesn't sit well and prevents relations to village biomes.
village
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.
astronomical object
A material part of an astronomical body.
astronomical body part
A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
A process during which a natural environmental system is altered by human action.
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body.
An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body.
technosphere
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.
manufacturing process
An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
The nature of "structures" must be further specified.
construction process
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
radiation
A radiation process during which waves (or their quanta, photons) of the electromagnetic field propagate (radiate) through space carrying electromagnetic energy.
electromagnetic radiation
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
geodiversity
A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective.
Umweltmaßnahme
active ecosystem management process
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
planned environmental usage process
A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans.
This class does not include environments which are primarily used for commerce or industry.
usage of an environment for residential activity
A building which is primarily used for the long-term habitation of humans.
domestic building
A process during which one entity loses energy to another entity.
energy transfer process
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process.
Relabel the obo foundry unique label to be generic process
anthropogenic modulatory intervention process
An environmental process which is driven by the action of humans.
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
Experimental class for structural purposes not recommended for annotation.
material transport process
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure.
Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products.
food product
foodon product type
A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component.
food component
food product component
Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience
food
foodstuff
nourishment
sustenance
food material
A food product type is a class of food products that is differentiated by its food composition, processing and/or consumption characteristics. This does not include brand name products but it may include generic food dish categories.
An agency food product type is a class of food product defined by an agency or consortium.
This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible.
agency food product type
food product type
Any chemical or chemical mixture that exists in a food material or was added to a food material.
chemical food component
food additive
Anatomical part of the plant or animal from which a food product or its major ingredient is derived.
part of organism
Bone, feathers, shell, skin or trim fat.
nonmeat part of animal
Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal.
animal body or body part
Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism.
part of animal
The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.
An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain an additional tiers: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell.
mitogen-activated protein kinase cascade
MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
microtubule cytoskeleton organization and biogenesis
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases.
The end of a linear chromosome, required for the integrity and maintenance of the end. A chromosome telomere usually includes a region of telomerase-encoded repeats the length of which rarely exceeds 20 bp each and that permits the formation of a telomeric loop (T-loop). The telomeric repeat region is usually preceded by a sub-telomeric region that is gene-poor but rich in repetitive elements. Some telomeres only consist of the latter part (for eg. D. melanogaster telomeres).
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation.
A dispersed and relatively uncompacted form of chromatin.
A compact and highly condensed form of chromatin that is refractory to transcription.
A compact and highly condensed form of chromatin.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form.
This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
blood vessel formation from pre-existing blood vessels
Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella.
ciliary or bacterial-type flagellar motility
cilium or flagellum-dependent cell motility
The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
A process that results in a parallel arrangement of microtubules.
The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure.
Interacting selectively and non-covalently with a G protein-coupled receptor.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
Note that this term should not be confused with 'response to anoxia ; GO:0034059'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%.
Cell migration that is accomplished by extension and retraction of a pseudopodium.
Note that this term refers to a mode of migration rather than to any particular cell type.
Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation ternary complex assembly
formation of translation initiation ternary complex
A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment.
The formation of the ectoderm, mesoderm and endoderm during gastrulation.
The formation of ectoderm during gastrulation.
The formation of the endoderm during gastrulation.
The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
Catalysis of the phosphorylation of a simple or complex lipid.
The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes.
The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell.
An inflammatory response resulting from recognition of immune complexes via complement or Fc receptors on effector cells leading to activation of neutrophils and other leukocytes and damage to bystander tissue.
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells.
The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems.
The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
The morphogenesis of an embryonic epithelium into a tube-shaped structure.
The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function.
The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism.
A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system.
renal blood volume control of blood pressure
renal system process involved in regulation of blood volume
The process in which hormones modulate the force with which blood passes through the circulatory system. A hormone is one of a group of substances formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which they have a specific regulatory action.
regulation of systemic arterial blood pressure by hormone
The process in which angiotensinogen metabolites in the bloodstream modulate the force with which blood passes through the circulatory system. The process begins when renin is released and cleaves angiotensinogen.
circulatory renin-angiotensin blood pressure regulation
circulatory renin-angiotensin regulation of blood pressure
circulatory renin-angiotensin control of blood pressure
control of blood pressure by circulatory renin-angiotensin
renin-angiotensin blood pressure control
regulation of systemic arterial blood pressure by circulatory renin-angiotensin
The physiological response of the kidneys to a decrease in blood flow.
renal response to blood flow during renin-angiotensin control of blood pressure
renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure
The regulated release of renin into the blood stream by juxtoglomerular cells.
The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences.
Note that this process covers somatic recombination, gene conversion, hypermutation, N-region addition, and alternate splicing processes of immune receptor diversification.
somatic diversification of immune receptors
The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response.
somatic recombination of antibody genes during immune response
somatic recombination of immunoglobulin genes during immune response
somatic recombination of immunoglobulin genes involved in immune response
The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response.
somatic diversification of antibodies during immune response
somatic diversification of immunoglobulins during immune response
somatic diversification of immunoglobulins involved in immune response
The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines.
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
response to bacteria associated molecule
response to bacterial associated molecule
response to bacterium associated molecule
response to molecule of bacterial origin
The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
haematopoietic progenitor cell differentiation
haemopoietic progenitor cell differentiation
hemopoietic progenitor cell differentiation
hematopoietic progenitor cell differentiation
An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
Any process of the immune system that can potentially contribute to an immune response.
Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation.
Any process that initiates an immune response.
The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response.
cell activation involved in immune response
A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand.
A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
lymphocyte activation during immune response
lymphocyte activation involved in immune response
The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
B cell activation during immune response
B lymphocyte activation during immune response
B-cell activation during immune response
B-lymphocyte activation during immune response
B cell activation involved in immune response
The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen.
Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
histamine production involved in acute inflammatory response
histamine production involved in inflammatory response
A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
immune cell activation during immune response
leucocyte activation during immune response
leukocyte activation during immune response
leukocyte activation involved in immune response
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels.
immunoglobulin production involved in immunoglobulin mediated immune response
immunoglobulin biosynthetic process involved in immune response
immunoglobulin secretion involved in immune response
antibody production during immune response
antibody secretion during immune response
immunoglobulin production during immune response
immunoglobulin production involved in immune response
immunoglobulin production involved in immunoglobulin-mediated immune response
An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
inflammatory response to antigenic stimulus
An acute inflammatory response to an antigenic stimulus. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
acute inflammatory response to antigenic stimulus
The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels.
production of cellular mediator of immune response
production of molecular mediator of immune response
Any process involved in the carrying out of an immune response by a leukocyte.
Any process involved in the carrying out of an immune response by a myeloid leukocyte.
myeloid leucocyte immune effector process
myeloid leukocyte immune effector process
Any process involved in the carrying out of an immune response by a lymphocyte.
Any process involved in the carrying out of an immune response by a T cell.
An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus.
adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation.
immune response-dependent tolerance induction
tolerance induction dependent upon immune response
Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues.
The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
peptide antigen processing and presentation via MHC class II
antigen processing and presentation of peptide antigen via MHC class II
The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
peptide or polysaccharide antigen processing and presentation of via MHC class II
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels.
production of molecular mediator involved in acute inflammatory response
production of cellular mediator of acute inflammation
production of molecular mediator involved in inflammatory response
A phase of elevated metabolic activity, during which oxygen consumption increases following a stimulus as part of an inflammatory response; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals, resulting in an increase in their intracellular or extracellular levels.
oxidative burst during acute inflammatory response
production of reactive oxygen species during acute inflammatory response
respiratory burst involved in acute inflammatory response
respiratory burst involved in inflammatory response
The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels.
arachidonic acid metabolite production involved in acute inflammatory response
production of arachidonic acid metabolites involved in acute inflammatory response
production of arachidonic acid metabolites involved in inflammatory response
arachidonic acid metabolite production involved in inflammatory response
The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
prostaglandin production involved in acute inflammatory response
prostaglandin production involved in inflammatory response
The movement of a monocyte in response to an external stimulus.
The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus.
somatic diversification of immune receptors via germline recombination within a single locus
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
Any process that modulates the frequency, rate, or extent of tolerance induction.
Any process that activates or increases the frequency, rate, or extent of tolerance induction.
positive regulation of tolerance induction
Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response.
regulation of immune response-dependent tolerance induction
regulation of tolerance induction dependent upon immune response
Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response.
positive regulation of immune response-dependent tolerance induction
up regulation of tolerance induction dependent upon immune response
up-regulation of tolerance induction dependent upon immune response
upregulation of tolerance induction dependent upon immune response
activation of tolerance induction dependent upon immune response
stimulation of tolerance induction dependent upon immune response
positive regulation of tolerance induction dependent upon immune response
Any process that modulates the frequency, rate, or extent of peripheral tolerance induction.
regulation of peripheral tolerance induction
Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction.
up regulation of peripheral tolerance induction
up-regulation of peripheral tolerance induction
upregulation of peripheral tolerance induction
activation of peripheral tolerance induction
stimulation of peripheral tolerance induction
positive regulation of peripheral tolerance induction
A phase of elevated metabolic activity, during which oxygen consumption increases made as part of a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
respiratory burst involved in defense response
Any process that modulates the frequency, rate, or extent of an immune system process.
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
down regulation of immune system process
down-regulation of immune system process
negative regulation of immune system process
Any process that activates or increases the frequency, rate, or extent of an immune system process.
positive regulation of immune system process
Any process that modulates the frequency, rate, or extent of leukocyte migration.
Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
positive regulation of immune cell migration
positive regulation of leucocyte migration
positive regulation of leukocyte migration
Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis.
Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
positive regulation of immune cell chemotaxis
positive regulation of leucocyte chemotaxis
positive regulation of leukocyte chemotaxis
Any process that modulates the frequency, rate, or extent of leukocyte activation.
Any process that activates or increases the frequency, rate, or extent of leukocyte activation.
positive regulation of immune cell activation
positive regulation of leucocyte activation
positive regulation of leukocyte activation
The controlled release of a peptide from a cell or a tissue.
Any process that modulates the frequency, rate, or extent of an adaptive immune response.
Any process that activates or increases the frequency, rate, or extent of an adaptive immune response.
up regulation of adaptive immune response
up-regulation of adaptive immune response
upregulation of adaptive immune response
positive regulation of adaptive immune response
Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata.
regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata.
positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
Any process that modulates the frequency, rate, or extent of a type 2 immune response.
regulation of T-helper 2 type immune response
Any process that activates or increases the frequency, rate, or extent of a type 2 immune response.
positive regulation of T-helper 2 type immune response
positive regulation of Th2 immune response
positive regulation of type 2 immune response
A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring.
developmental process involved in reproduction
A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective.
A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers.
A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange.
The regulation of blood pressure mediated by biochemical signaling: hormonal, autocrine or paracrine.
blood pressure regulation mediated by a chemical signal
regulation of systemic arterial blood pressure mediated by a chemical signal
Renal process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
renal regulation of systemic arterial blood pressure
renal system process involved in regulation of systemic arterial blood pressure
The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
regulation of systemic arterial blood pressure
The process in which renin-angiotensin modulates the force with which blood passes through the circulatory system.
blood pressure regulation by renin-angiotensin
regulation of systemic arterial blood pressure by renin-angiotensin
Renal process involved in the maintenance of an internal steady state of water in the body.
Any process that modulates the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process in which blood is filtered by the glomerulus into the renal tubule.
The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein.
The directed movement of water (H2O) by the renal system.
The process in which an amino acid is transported across a membrane.
The directed, self-propelled movement of a cilium.
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Interacting selectively and non-covalently with any nucleic acid.
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
orthophosphoric-monoester phosphohydrolase (alkaline optimum)
phosphate-monoester phosphohydrolase (alkaline optimum)
Catalysis of the reaction: D-glucopyranose 6-phosphate + H2O = D-glucose + phosphate. D-glucopyranose is also known as D-glucose 6-phosphate.
D-glucose-6-phosphate phosphohydrolase activity
glucose 6-phosphate phosphatase activity
Catalysis of the hydrolysis of any O-glycosyl bond.
hydrolase activity, hydrolyzing O-glycosyl compounds
Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
alpha-D-galactoside galactohydrolase activity
alpha-galactoside galactohydrolase activity
Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
Note that triphosphate is used as a phosphate donor by at least one kinase.
Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
ATP:protein-tyrosine O-phosphotransferase activity
ephrin-B3 receptor tyrosine kinase activity
insulin receptor protein-tyrosine kinase activity
neurite outgrowth regulating kinase activity
novel oncogene with kinase-domain activity
ATP:protein-L-tyrosine O-phosphotransferase (receptor-type) activity
receptor protein tyrosine kinase activity
receptor protein-tyrosine kinase activity
transmembrane receptor protein tyrosine kinase activity
Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+).
ribose-phosphate pyrophosphokinase activity
5-phosphoribose pyrophosphorylase activity
5-phosphoribosyl-1-pyrophosphate synthetase activity
5-phosphoribosyl-alpha-1-pyrophosphate synthetase activity
ATP:D-ribose-5-phosphate diphosphotransferase activity
phosphoribosyl diphosphate synthetase activity
phosphoribosyl pyrophosphate synthetase activity
phosphoribosyl-diphosphate synthetase activity
phosphoribosylpyrophosphate synthase activity
phosphoribosylpyrophosphate synthetase activity
pyrophosphoribosylphosphate synthetase activity
ribophosphate pyrophosphokinase activity
ribose-5-phosphate pyrophosphokinase activity
ribose-phosphate diphosphokinase activity
ribose phosphate diphosphokinase activity
Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
transmembrane signalling receptor activity
This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores.
transmembrane signaling receptor activity
Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
Epstein-Barr Virus-induced receptor activity
G-protein coupled receptor activity, unknown ligand
orphan G protein coupled receptor activity
orphan G-protein coupled receptor activity
super conserved receptor expressed in brain receptor activity
Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
Interacting selectively and non-covalently with a cytokine receptor.
hematopoietin/interferon-class (D200-domain) cytokine receptor binding
hematopoietin/interferon-class (D200-domain) cytokine receptor ligand
The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
The action characteristic of gonadotropin hormone-releasing hormone (GnRH), any of a family of decapeptide amide hormones that are released by the hypothalamus in response to neural and/or chemical stimuli. In at least mammals, upon receptor binding, GnRH causes the release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) by the anterior pituitary.
gonadotrophin hormone-releasing hormone activity
luteinizing hormone-releasing factor activity
luteinizing hormone-releasing hormone activity
luteinizing hormone/follicle-stimulating hormone releasing factor activity
gonadotropin hormone-releasing hormone activity
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
Enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage.
organic acid transmembrane transporter activity
Enables the transfer of water (H2O) from one side of a membrane to the other.
water transmembrane transporter activity
Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: inorganic anion A(out) + inorganic anion B(in) = inorganic anion A(in) + inorganic anion B(out).
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes.
A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer.
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
A lysosome before it has fused with a vesicle or vacuole.
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
The volume enclosed within the vacuolar membrane.
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
Note that this definition includes vesicles that are transiently associated with the Golgi.
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta.
The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects.
A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects.
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane.
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
multicellular organismal carbohydrate metabolic process
single-organism carbohydrate metabolic process
The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
multicellular organismal polysaccharide metabolic process
The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
generation of precursor metabolites and energy
The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase-containing compound metabolic process
The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
Any process in which DNA and associated proteins are formed into a compact, orderly structure.
The cellular synthesis of RNA on a template of DNA.
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
regulation of cellular transcription, DNA-dependent
regulation of transcription, DNA-dependent
regulation of gene-specific transcription
regulation of transcription, DNA-templated
Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
regulation of transcription from Pol II promoter
regulation of transcription from RNA polymerase II promoter
global transcription regulation from Pol II promoter
regulation of gene-specific transcription from RNA polymerase II promoter
regulation of global transcription from Pol II promoter
regulation of transcription from RNA polymerase II promoter, global
regulation of transcription by RNA polymerase II
The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
transcription from RNA polymerase II promoter
RNA polymerase II transcription factor activity
gene-specific transcription from RNA polymerase II promoter
general transcription from RNA polymerase II promoter
specific transcription from RNA polymerase II promoter
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
process resulting in protein modification
The process of introducing a phosphate group on to a protein.
A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the N4 atom of peptidyl-asparagine, the omega-N of arginine, or the N1' atom peptidyl-tryptophan.
protein amino acid N-linked glycosylation
A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan.
protein amino acid O-linked glycosylation
The covalent attachment of lipid groups to an amino acid in a protein.
The chemical reactions and pathways involving glycosylphosphatidylinositol anchors, molecular mechanisms for attaching membrane proteins to the lipid bilayer of cell membranes. Structurally they consist of a molecule of phosphatidylinositol to which is linked, via the C-6 hydroxyl of the inositol, a carbohydrate chain. This chain is in turn linked to the protein through an ethanolamine phosphate group, the amino group of which is in amide linkage with the C-terminal carboxyl of the protein chain, the phosphate group being esterified to the C-6 hydroxyl of the terminal mannose of the core carbohydrate chain.
glycosylphosphatidylinositol metabolic process
The chemical reactions and pathways resulting in the formation of a glycosylphosphatidylinositol (GPI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The phosphatidylinositol group is linked via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via an ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GPI anchors have variants on this canonical linkage.
glycosylphosphatidylinositol biosynthesis
glycosylphosphatidylinositol biosynthetic process
The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
cellular amino acid and derivative metabolic process
The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
The chemical reactions and pathways resulting in the breakdown of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
The chemical reactions and pathways involving membrane lipids, any lipid found in or associated with a biological membrane.
The chemical reactions and pathways involving phospholipids, any lipid containing phosphoric acid as a mono- or diester.
The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
phosphatidylinositol biosynthetic process
The chemical reactions and pathways involving glycolipids, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar group acylated by one or more fatty acids and the glycerol group may be absent.
The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
cellular aromatic compound metabolic process
The chemical reactions and pathways involving ubiquinone, a lipid-soluble electron-transporting coenzyme.
The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
The chemical reactions and pathways involving any phosphorylated nucleoside.
The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems.
The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water.
The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
porphyrin-containing compound metabolic process
The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
phosphate-containing compound metabolic process
The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
superoxide free radical metabolic process
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
di-, tri-valent inorganic cation transport
The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
mitochondrial sodium/calcium ion exchange
sodium channel auxiliary protein activity
The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems.
The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
Any process involved in the maintenance of an internal steady state of ions at the level of a cell.
Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell.
Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
Any process involved in maintaining the steady state of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell.
Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.
A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle.
A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
The evagination of a membrane, resulting in formation of a vesicle.
The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo.
Fusion of the membrane of a transport vesicle with its target membrane.
A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
cellular component disassembly involved in apoptotic process
cellular component disassembly involved in apoptosis
cellular component disassembly involved in execution phase of apoptosis
The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
Note that in GO cellular components include whole cells (cell is_a cellular component).
movement of cell or subcellular component
The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
An immune response mediated through a body fluid.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular response to DNA damage stimulus
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
mitochondrion organization and biogenesis
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cytoskeletal organization and biogenesis
cytoskeleton organization and biogenesis
Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
The directed movement of substances into, out of or within a vacuole.
The directed movement of substances into, out of or within a lysosome.
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell.
Note that this term should not be confused with 'abortive mitotic cell cycle ; GO:0033277'. Although abortive mitosis is sometimes called endomitosis, GO:0033277 refers to a process in which a mitotic spindle forms and chromosome separation begins.
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
The attachment of a leukocyte to another cell via adhesion molecules.
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
signal transduction by cis-phosphorylation
signal transduction by conformational transition
signal transduction by protein phosphorylation
signal transduction by trans-phosphorylation
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
cell surface receptor linked signal transduction
cell surface receptor linked signaling pathway
cell surface receptor linked signalling pathway
Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.
enzyme linked receptor protein signalling pathway
enzyme linked receptor protein signaling pathway
A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
transmembrane receptor protein tyrosine kinase signalling pathway
transmembrane receptor protein tyrosine kinase signaling pathway
The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane.
G protein coupled receptor protein signaling pathway
G protein coupled receptor protein signalling pathway
G-protein coupled receptor protein signal transduction
G-protein coupled receptor protein signaling pathway
G-protein coupled receptor signalling pathway
G-protein-coupled receptor protein signalling pathway
G-protein coupled receptor signaling pathway via GPCR dimer
dimeric G-protein coupled receptor signaling pathway
dimeric G-protein coupled receptor signalling pathway
G protein-coupled receptor signaling pathway
Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
small GTPase-mediated signal transduction
small GTPase mediated signal transduction
A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
Note that this term was 'developmental process'.
The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.
The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure.
The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
The establishment of the sex of an organism by physical differentiation.
The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
Attachment of the blastocyst to the uterine lining.
A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
respiratory gaseous exchange by respiratory system
The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
Also consider annotating to 'receptor agonist activity ; GO:0048018'.
Any process in which a protein is transported to, or maintained in, a specific location.
establishment and maintenance of asymmetric protein localization
establishment and maintenance of protein localization
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
Any process that stops, prevents or reduces the rate or extent of cell proliferation.
negative regulation of cell proliferation
negative regulation of cell population proliferation
The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
Any process that modulates the size of a cell.
Enables the transfer of a negatively charged ion from one side of a membrane to the other.
anion transmembrane transporter activity
The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
The process in which hexose is transported across a membrane. Hexoses are any aldoses with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
multicellular organismal catabolic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
multicellular organismal biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
aromatic amino acid family metabolic process
The chemical reactions and pathways resulting in the breakdown of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
aromatic amino acid family catabolic process
The chemical reactions and pathways involving glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
nucleoside triphosphate metabolic process
The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
nucleoside triphosphate biosynthetic process
The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar.
purine nucleoside triphosphate metabolism
purine nucleoside triphosphate metabolic process
The chemical reactions and pathways resulting in the formation of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar.
purine nucleoside triphosphate anabolism
purine nucleoside triphosphate biosynthesis
purine nucleoside triphosphate formation
purine nucleoside triphosphate synthesis
purine nucleoside triphosphate biosynthetic process
The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
purine ribonucleotide biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar.
ribonucleoside triphosphate metabolic process
The chemical reactions and pathways resulting in the formation of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar.
ribonucleoside triphosphate biosynthesis
ribonucleoside triphosphate biosynthetic process
The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar.
purine ribonucleoside triphosphate metabolism
purine ribonucleoside triphosphate metabolic process
The chemical reactions and pathways resulting in the formation of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar.
purine ribonucleoside triphosphate anabolism
purine ribonucleoside triphosphate biosynthesis
purine ribonucleoside triphosphate formation
purine ribonucleoside triphosphate synthesis
purine ribonucleoside triphosphate biosynthetic process
The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The chemical reactions and pathways resulting in the formation of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
The controlled release of proteins from a cell.
protein secretion during cell fate commitment
protein secretion resulting in cell fate commitment
The chemical reactions and pathways involving oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
multicellular organismal oligosaccharide metabolic process
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus.
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
embryo development ending in birth or egg hatching
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
positive regulation of biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
positive regulation of metabolic process
The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
Any process that modulates the frequency, rate or extent of signal transduction.
Any process that activates or increases the frequency, rate or extent of signal transduction.
positive regulation of signaling pathway
positive regulation of signalling pathway
positive regulation of signal transduction
The external part of the cell wall and/or plasma membrane.
Note that this term is intended to annotate gene products that are attached (integrated or loosely bound) to the plasma membrane or cell wall.
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
Any process involved in the maintenance of an internal steady state of water within a cell.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
process resulting in tolerance to organic substance
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule biosynthetic process
Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule biosynthetic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
positive regulation of phosphorus metabolic process
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
positive regulation of macromolecule metabolic process
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
positive regulation of cell communication
Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action.
Any process in which a lipid is transported to, or maintained in, a specific location.
The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity.
establishment of localization by movement along microtubule
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
The lipid bilayer surrounding any membrane-bounded vesicle in the cell.
The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell.
A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions.
phosphatidylinositol 3-kinase signal transduction
Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
regulation of phosphoinositide 3-kinase cascade
regulation of phosphatidylinositol 3-kinase cascade
regulation of phosphatidylinositol 3-kinase signaling
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
positive regulation of PI 3-kinase cascade
positive regulation of phosphoinositide 3-kinase cascade
up regulation of phosphatidylinositol 3-kinase cascade
up-regulation of phosphatidylinositol 3-kinase cascade
upregulation of phosphatidylinositol 3-kinase cascade
activation of phosphoinositide 3-kinase cascade
stimulation of phosphatidylinositol 3-kinase cascade
positive regulation of phosphatidylinositol 3-kinase cascade
positive regulation of phosphatidylinositol 3-kinase signaling
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of an ion from one side of a membrane to the other.
Enables the transfer of inorganic anions from one side of a membrane to the other. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage.
inorganic anion transmembrane transporter activity
Enables the transfer of carbohydrate from one side of a membrane to the other.
carbohydrate transmembrane transporter activity
Enables the transfer of glucose-6-phosphate from one side of a membrane to the other. Glucose-6-phosphate is a monophosphorylated derivative of glucose with the phosphate group attached to C-6.
glucose-6-phosphate transmembrane transporter activity
Enables the transfer of a polyol from one side of a membrane to the other. A polyol is any polyhydric alcohol.
polyol transmembrane transporter activity
Enables the transfer of glycerol from one side of a membrane to the other. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
glycerol transmembrane transporter activity
Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group.
amino acid/choline transmembrane transporter activity
hydroxy/aromatic amino acid permease activity
amino acid transmembrane transporter activity
Enables the transfer of urea from one side of a membrane to the other. Urea is the water soluble compound H2N-CO-NH2.
Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
Enables the facilitated diffusion of glycerol (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
Enables the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy, not direct ATP coupling. Secondary active transporters include symporters and antiporters.
electrochemical potential-driven transporter activity
energizer of outer membrane receptor-mediated transport activity
multidrug endosomal transmembrane transporter activity
galactose/glucose (methylgalactoside) porter activity
secondary active transmembrane transporter activity
Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion A(out) + anion B(in) = anion A(in) + anion B(out).
Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon.
inorganic solute uptake transmembrane transporter activity
inorganic molecular entity transmembrane transporter activity
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of magnesium (Mg) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of inorganic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Inorganic anions are atoms or small molecules with a negative charge which do not contain carbon in covalent linkage.
The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage.
The directed movement of hexose phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of bilirubin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organophosphate esters into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organophosphate esters are small organic molecules containing phosphate ester bonds.
The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
The directed movement of glucose-6-phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glucose-6-phosphate is a monophosphorylated derivative of glucose with the phosphate group attached to C-6.
The directed movement of polyols, any polyhydric alcohol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of glycerol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glycerol is 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
The directed movement of neutral amino acids, amino acids with no net charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of urea into, out of or within the cell. Urea is the water-soluble compound H2N-CO-NH2.
The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom.
Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative.
The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released.
energy derivation by oxidation of organic compounds
The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that provides energy for the synthesis of ATP or GTP.
energy coupled proton transport, down electrochemical gradient
The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
multicellular organism lipid catabolic process
multicellular organismal lipid catabolic process
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage.
An immune response mediated by immunoglobulins, whether cell-bound or in solution.
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
The region of the plasma membrane located at the apical end of the cell.
The process in which the anatomical structures of embryonic epithelia are generated and organized.
Recombination occurring within or between DNA molecules in somatic cells.
The somatic process that results in the generation of sequence diversity of immunoglobulins.
somatic diversification of immunoglobulins
The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus.
somatic recombination of antibody gene segments
somatic recombination of immunoglobulin gene segments
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues.
The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
oxidoreductase activity, acting on other substrates
Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
oxidoreductase activity, acting on the CH-CH group of donors, other acceptors
oxidoreductase activity, acting on the CH-CH group of donors
Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
phosphotransferase activity, alcohol group as acceptor
Catalysis of the transfer of a diphosphate group from one compound (donor) to a another (acceptor).
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
Catalysis of the hydrolysis of any ester bond.
hydrolase activity, acting on ester bonds
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
4-nitrophenylphosphate phosphohydrolase activity
p-nitrophenylphosphate phosphohydrolase activity
Catalysis of the hydrolysis of any glycosyl bond.
hydrolase activity, acting on glycosyl bonds
The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The alteration of an amino acid residue in a peptide.
The modification of a protein amino acid by phosphopantetheinylation.
protein amino acid phosphopantetheinylation
Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: a protein + ATP = a phosphoprotein + ADP.
transmembrane receptor protein kinase activity
Catalysis of the reaction: carbohydrate phosphate + H2O = carbohydrate + phosphate.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
regulation of nucleobase-containing compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission.
The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic hydrocarbon biosynthetic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
The chemical reactions and pathways involving a protein. Includes protein modification.
protein metabolic process and modification
multicellular organismal protein metabolic process
The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound.
The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.
Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells.
B lymphocyte mediated immune effector process
B-lymphocyte mediated immune effector process
Any process involved in the maintenance of an internal steady state at the level of the cell.
The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
The directed movement of one-carbon compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
B cell receptor accessory molecule complex
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
The accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.
The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
Any process that modulates the frequency, rate or extent of attachment of a cell to another cell.
Any process that activates or increases the rate or extent of cell adhesion to another cell.
positive regulation of cell-cell adhesion
A cellular process that results in the breakdown of a cellular component.
cellular component disassembly at cellular level
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis.
regulation of anatomical structure morphogenesis
The aggregation, arrangement and bonding together of a cellular component.
cellular component assembly at cellular level
The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.
ribonucleoprotein complex biogenesis and assembly
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged.
passive transmembrane transporter activity
Enables the transfer of a specific substance or related group of substances from one side of a membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction.
active transmembrane transporter activity
Enables the transfer of an ion from one side of a membrane to the other up the solute's concentration gradient. This is carried out by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction.
active ion transmembrane transporter activity
Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
substrate-specific transmembrane transporter activity
uptake transmembrane transporter activity
Binding to a major histocompatibility complex class Ib molecules.
Any process that modulates the frequency, rate or extent of a signaling process.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
positive regulation of signalling process
positive regulation of signaling process
The process in which a signal is secreted or discharged into the extracellular medium from a cellular source.
The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process involved in the maintenance of an internal steady state of cations at the level of a cell.
Any process involved in the maintenance of an internal steady state of monovalent inorganic cations at the level of a cell.
cellular monovalent inorganic cation homeostasis
Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cell projection organization and biogenesis
cell surface structure organization and biogenesis
Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins.
A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.
The regulated release of a peptide hormone from a cell.
The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
Any process involved in the maintenance of an internal steady state of water within an organism or cell.
Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.
constitutive secretory pathway transport vesicle
Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'secretory granule ; GO:0030141'.
A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'.
The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
cell adhesion receptor regulator activity
The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
extracellular matrix organization and biogenesis
The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
Note that the term 'thymocyte differentiation' was merged into this term because thymocytes are T cells, and thus the term was essentially redundant. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte.
The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
The covalent alteration of one or more fatty acids in a lipid, resulting in a change in the properties of the lipid.
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis.
The compaction of chromatin during apoptosis.
A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm.
sperm flagellum movement involved in flagellated sperm motility
sperm flagellum movement involved in flagellated sperm movement
The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract.
The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
Any process that modulates the frequency, rate or extent of cell migration.
Any process that activates or increases the frequency, rate or extent of cell migration.
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
The movement of a leukocyte in response to an external stimulus.
Any process involved in the maintenance of an internal equilibrium of hydrogen ions (protons) within a cell or between a cell and its external environment.
The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
cytoskeleton-dependent intracellular transport
Any chromosome other than a sex chromosome.
The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.
Note that we deem cilia and microtubule-based flagella to be equivalent.
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).
The volume enclosed by the membrane of the platelet alpha granule.
A developmental process involving two tissues in which one tissue (the inducer) produces a signal that directs cell fate commitment of cells in the second tissue (the responder).
A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.
The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane.
Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent.
The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement.
pseudopodium organization and biogenesis
The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B- or T cell receptor to augment B- or T cell activation.
The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
positive regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
regulation of cellular biosynthetic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
positive regulation of cellular anabolism
positive regulation of cellular biosynthesis
positive regulation of cellular formation
positive regulation of cellular synthesis
up regulation of cellular biosynthetic process
up-regulation of cellular biosynthetic process
upregulation of cellular biosynthetic process
activation of cellular biosynthetic process
stimulation of cellular biosynthetic process
positive regulation of cellular biosynthetic process
A vesicle found in the cytoplasm of a cell.
A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
establishment and maintenance of protein complex localization
cellular protein-containing complex localization
establishment and maintenance of cellular protein complex localization
The portion of the plasma membrane surrounding the brush border.
The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen.
The volume enclosed by the nuclear inner membrane.
Any small, fluid-filled, spherical organelle enclosed by membrane.
The volume enclosed by the membrane or protein that forms a vesicle.
A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses.
Any process that modulates the frequency, rate or extent of a response to an external stimulus.
regulation of response to external stimulus
Any process that activates, maintains or increases the rate of a response to an external stimulus.
up regulation of response to external stimulus
up-regulation of response to external stimulus
upregulation of response to external stimulus
activation of response to external stimulus
stimulation of response to external stimulus
positive regulation of response to external stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families.
Note that this term is intended for annotation of gene products that act as receptors for MHC class Ib protein complexes, not for components of the MHC class Ib protein complexes themselves.
An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
A process that modulates the size of a cellular component.
The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code.
The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
tumor necrosis factor biosynthetic process
Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). That this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication.
Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study.
All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection.
plasma membrane bounded cell projection cytoplasm
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
The controlled release of a substance by a cell.
The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form.
peripheral blood mononuclear cell proliferation
Any process that modulates the frequency, rate or extent of mononuclear cell proliferation.
regulation of peripheral blood mononuclear cell proliferation
regulation of mononuclear cell proliferation
The disaggregation of a protein-containing macromolecular complex into its constituent components.
cellular macromolecule complex disassembly
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
A macromolecular complex containing both protein and DNA molecules.
Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.
The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Any process in which a macromolecule is transported to, or maintained in, a specific location.
The deposition or aggregation of coloring matter in a cell.
The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined.
A process in which a protein is transported to, or maintained in, a location within an organelle.
A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
Any process of regulating the production and elimination of erythrocytes within an organism.
The process in which a carbohydrate is transported across a membrane.
Note that this term is not intended for use in annotating lateral movement within membranes.
A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
A process in which an ion is transported across a membrane.
ATP hydrolysis coupled ion transmembrane transport
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
cellular biopolymer biosynthetic process
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase, nucleoside, nucleotide and nucleic acid synthesis
nucleobase-containing compound biosynthetic process
The volume enclosed by the membrane of a secretory granule.
Catalysis of the reaction: ATP + a phosphatidylinositol = ADP + a phosphatidylinositol 3-phosphate. This reaction is the addition of a phosphate group to phosphatidylinositol or one of its phosphorylated derivatives at the 3' position of the inositol ring.
The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements.
Note that cilia and eukaryotic flagella are deemed to be equivalent.
Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow.
lumen formation in an anatomical structure
The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts.
An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
Despite its name, the pre-BCR is not a receptor complex, as it appears to provide a low level of signal not dependent on a ligand, but rather simply on correct assembly of the complex as a measure for correct Ig heavy chain recombination and folding. A significant proportion of pre-BCR complexes fail to reach the cell surface, and in some cases may provide their signaling function from the trans-Golgi network or lysosome.
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
intracellular signal transduction pathway
signal transmission via intracellular cascade
signal transduction via intracellular signaling cascade
The directed movement of a protein to a specific location within the extracellular region.
establishment of protein localisation in extracellular region
establishment of protein localization in extracellular region
establishment of protein localization to extracellular region
A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.
intraciliary transport involved in cilium morphogenesis
intraflagellar transport involved in cilium morphogenesis
intraciliary transport involved in cilium assembly
The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin, in response to a glucose stimulus.
insulin secretion involved in cellular response to glucose
insulin secretion involved in cellular response to glucose stimulus
A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm.
Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone.
The regulated release of any steroid that acts as a hormone into the circulatory system.
The regulated release of any corticosteroid hormone into the circulatory system.
The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism.
The regulated release of aldosterone into the circulatory system. Aldosterone is a pregnane-based steroid hormone produced by the outer-section (zona glomerulosa) of the adrenal cortex in the adrenal gland, and acts on the distal tubules and collecting ducts of the kidney to cause the conservation of sodium, secretion of potassium, increased water retention, and increased blood pressure. The overall effect of aldosterone is to increase reabsorption of ions and water in the kidney.
The regulated release of any glucocorticoid hormone into the circulatory system. Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood.
The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
A specialized cell-cell junction found between the cells of the excretory system, which provides a barrier for filtration of blood or hemolymph.
A specialized cell-cell junction found between the interdigitating foot processes of the glomerular epithelium (the podocytes) in the vertebrate kidney, which is adapted for facilitating glomerular filtration.
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen.
This term should be used when a decrease in oxygen levels is not considered a stress response. For a hypoxic stress response, consider instead 'response to hypoxia ; GO:0001666'.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen.
cellular response to lowered oxygen levels
This term should be used when a decrease in oxygen levels is not considered a stress response. For a hypoxic stress response, consider instead 'cellular response to hypoxia ; GO:0071456'.
cellular response to decreased oxygen levels
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
receptor activity involved in signal transduction
Self-propelled movement of a cell or organism from one location to another.
Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
The first few specialized divisions of an activated animal egg.
Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism.
The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The series of events that restore integrity to a damaged tissue, following an injury.
The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.
intraflagellar transport involved in cilium organization
intraflagellar transport involved in microtubule-based flagellum organisation
Note that we deem cilium and microtubule-based flagellum to be equivalent.
An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects.
The expansion of a T cell population by cell division. Follows T cell activation.
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein.
alpha-beta T lymphocyte receptor complex
alpha-beta T-lymphocyte receptor complex
The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
Any process that modulates the frequency, rate or extent of cell proliferation.
regulation of cell population proliferation
Any process that modulates the frequency, rate or extent of T cell proliferation.
regulation of T lymphocyte proliferation
regulation of T-lymphocyte proliferation
The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
Binding to a major histocompatibility complex molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
major histocompatibility complex binding
Note that this term does not include binding to the antigen peptide bound to the MHC protein, for this also annotate to 'peptide antigen binding ; GO:0042605' or one of its children.
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
The directed movement of a motile cell or organism in response to an external stimulus.
directed movement in response to stimulus
Interacting selectively and non-covalently with any chemokine receptor.
Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways.
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
Cytoplasmic organelles, spherical or oval in shape, that are bounded by a single membrane and contain oxidative enzymes, especially those utilizing hydrogen peroxide (H2O2).
Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
Any biological process involved in the maintenance of an internal steady state.
negative regulation of homeostatic process
positive regulation of homeostatic process
Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
defense response to bacterium, incompatible interaction
resistance response to pathogenic bacteria
resistance response to pathogenic bacterium
Interacting selectively and non-covalently with an identical protein or proteins.
Interacting selectively and non-covalently with an identical protein to form a homodimer.
The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Enables the transfer of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, from one side of a membrane to the other.
amide transmembrane transporter activity
A prolongation or process extending from a cell, e.g. a flagellum or axon.
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching.
The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin.
The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite.
extracellular structure organization and biogenesis
The nucleus of a germ cell, a reproductive cell in multicellular organisms.
Any process that activates or increases the activity of an enzyme.
positive regulation of metalloenzyme activity
positive regulation of catalytic activity
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
multicellular organismal macromolecule metabolic process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
The volume enclosed within the lysosomal membrane.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
intracellular non-membrane-enclosed organelle
intracellular non-membrane-bounded organelle
The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
A receptor complex found on immature T cells consisting of a T cell receptor beta chain and the pre-TCR-alpha chain, along with additional signaling components including CD3 family members and additional signaling proteins.
Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
The regulated release of cortisol, a steroid hormone that in humans is the major circulating hormone of the cortex, or outer layer, of the adrenal gland.
Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
regulation of MAP kinase kinase kinase cascade
regulation of mitogen activated protein kinase cascade
regulation of mitogen activated protein kinase kinase kinase cascade
regulation of mitogen-activated protein kinase cascade
regulation of mitogen-activated protein kinase kinase kinase cascade
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
positive regulation of MAP kinase cascade
positive regulation of MAP kinase kinase kinase cascade
positive regulation of mitogen activated protein kinase kinase kinase cascade
positive regulation of mitogen-activated protein kinase cascade
positive regulation of mitogen-activated protein kinase kinase kinase cascade
The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
response to polypeptide hormone stimulus
The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Any process that modulates the frequency, rate or extent of lipid kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a simple or complex lipid.
Any process that modulates the frequency, rate or extent of phosphatidylinositol 3-kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to an inositol lipid at the 3' position of the inositol ring.
regulation of phosphoinositide 3-kinase activity
regulation of phosphatidylinositol 3-kinase activity
Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
positive regulation of phosphoinositide 3-kinase activity
up regulation of phosphatidylinositol 3-kinase activity
up-regulation of phosphatidylinositol 3-kinase activity
upregulation of phosphatidylinositol 3-kinase activity
activation of phosphatidylinositol 3-kinase activity
stimulation of phosphatidylinositol 3-kinase activity
positive regulation of phosphatidylinositol 3-kinase activity
The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
cellular macromolecular complex organization
cellular macromolecular complex subunit organisation
cellular macromolecular complex subunit organization
macromolecular complex subunit organisation
macromolecular complex subunit organization
protein-containing complex subunit organization
The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system.
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
cellular component biogenesis at cellular level
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
positive regulation of molecular function
A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).
translation initiation (ternary) complex
The chemical reactions and pathways by which individual cells transform chemical substances.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
The chemical reactions and pathways involving lipids, as carried out by individual cells.
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, as carried out by individual cells.
main pathways of carbohydrate metabolic process
main pathways of carbohydrate metabolism
The chemical reactions and pathways involving polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages, as carried out by individual cells.
cellular polysaccharide metabolic process
The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
The directed movement of the hexose monosaccharide glucose into a cell as a result of an insulin stimulus.
cellular glucose import in response to insulin stimulus
glucose import in response to insulin stimulus
Any process evolved to enable an interaction with an organism of a different species.
interspecies interaction between organisms
interspecies interaction with other organisms
biological process involved in interspecies interaction between organisms
A biological process that directly contributes to the process of producing new individuals, involving another organism.
A multicellular organism process which involves another multicellular organism of the same or different species.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
microtubule-based flagellum organization
The chemical reactions and pathways resulting in the formation of glycerolipids, any lipid with a glycerol backbone.
A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand.
The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation.
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
Signaling at long or short range between cells that results in the commitment of a cell to a certain fate.
cell fate commitment, cell-cell signaling
cell fate commitment, cell-cell signalling
cell-cell signaling during in cell fate commitment
cell-cell signaling resulting in cell fate commitment
cell-cell signalling during cell fate commitment
cell-cell signalling resulting in cell fate commitment
cell-cell signalling involved in cell fate specification
cell-cell signaling involved in cell fate commitment
The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
The directed movement of a protein to a specific location.
The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus.
Note that IgM and IgD can be coexpressed by B cells via an alternate splicing mechanism, but true recombinational isotype switching to IgD has been demonstrated as well. Note that this term is best used to annotate gene products which are involved in the mechanism of DNA recombination used in isotype switching, like the B cell specific Swap70 factor in the mouse, rather than gene products which promote isotype switching such as cytokines or co-stimulatory molecules, which should instead be annotated to 'regulation of isotype switching ; GO:0045191'.
The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell.
external encapsulating structure organisation
external encapsulating structure organization and biogenesis
external encapsulating structure organization
A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.
The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
Any process that modulates the frequency, rate or extent of T cell differentiation.
regulation of T lymphocyte differentiation
regulation of T-lymphocyte differentiation
Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
Any process that modulates the frequency, rate or extent of lymphocyte differentiation.
regulation of lymphocyte differentiation
A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
Any process that modulates the frequency, rate or extent of angiogenesis.
Any process that activates or increases angiogenesis.
Any process that activates or increases the frequency, rate or extent of cell adhesion.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids.
up regulation of lipid metabolic process
up-regulation of lipid metabolic process
positive regulation of lipid metabolic process
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
positive regulation of cellular transcription, DNA-dependent
positive regulation of transcription, DNA-dependent
up regulation of transcription, DNA-dependent
up-regulation of transcription, DNA-dependent
upregulation of transcription, DNA-dependent
activation of transcription, DNA-dependent
stimulation of gene-specific transcription
stimulation of transcription, DNA-dependent
activation of gene-specific transcription
positive regulation of gene-specific transcription
up regulation of gene-specific transcription
up-regulation of gene-specific transcription
upregulation of gene-specific transcription
positive regulation of transcription, DNA-templated
Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
positive regulation of nucleobase-containing compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
positive regulation of phosphate metabolism
up regulation of phosphate metabolic process
up-regulation of phosphate metabolic process
upregulation of phosphate metabolic process
activation of phosphate metabolic process
stimulation of phosphate metabolic process
positive regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
activation of transcription from RNA polymerase II promoter
positive regulation of transcription from Pol II promoter
positive regulation of transcription from RNA polymerase II promoter
stimulation of transcription from RNA polymerase II promoter
up regulation of transcription from RNA polymerase II promoter
up-regulation of transcription from RNA polymerase II promoter
upregulation of transcription from RNA polymerase II promoter
stimulation of global transcription from RNA polymerase II promoter
activation of global transcription from RNA polymerase II promoter
positive regulation of gene-specific transcription from RNA polymerase II promoter
positive regulation of global transcription from Pol II promoter
positive regulation of transcription from RNA polymerase II promoter, global
up regulation of global transcription from RNA polymerase II promoter
up-regulation of global transcription from RNA polymerase II promoter
upregulation of global transcription from RNA polymerase II promoter
positive regulation of transcription by RNA polymerase II
The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
The chemical reactions and pathways involving xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids.
The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom.
The directed movement of the hexose monosaccharide glucose into a cell or organelle.
The chemical reactions and pathways resulting in the formation of ribose phosphate, any phosphorylated ribose sugar.
The chemical reactions and pathways resulting in the formation of membrane lipids, any lipid found in or associated with a biological membrane.
The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
glycerophospholipid biosynthetic process
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The chemical reactions and pathways involving glycerolipids, any lipid with a glycerol backbone. Diacylglycerol and phosphatidate are key lipid intermediates of glycerolipid biosynthesis.
The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.
The expansion of a lymphocyte population by cell division.
The controlled release of acid by a cell or a tissue.
The process of introducing one or more phosphate groups into a lipid, any member of a group of substances soluble in lipid solvents but only sparingly soluble in aqueous solvents.
The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis.
The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
phosphatidylinositol phosphate biosynthetic process
phosphatidylinositol phosphate phosphorylation
The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
The controlled release of a substance by a cell or a tissue.
The directed movement of substances within a cell.
Any process involved in the maintenance of an internal steady state of transition metal ions at the level of a cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
cellular transition metal ion homeostasis
The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
Enables the transfer of carboxylic acids from one side of a membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-).
carboxylic acid transmembrane transporter activity
The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
Catalysis of the reaction: cholesterol + NADP+ = cholesta-5,7-dien-3-beta-ol + NADPH + H+.
cholesterol:NADP+ delta7-oxidoreductase activity
The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein.
peptide antigen processing and presentation
antigen processing and presentation of peptide antigen
Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
In GO, a gene product with 'vascular endothelial growth factor-activated receptor activity ; GO:0005021' necessarily binds VEGF to transduce a signal. In contrast, the VEGFR refers to PR:000001971. To represent cross-talk between ligands and receptors, signaling pathways in GO are starting to be named after the receptor and/or the signal. GO:0048010 is for annotation of any pathway in which a ligand (VEGF or an alternative growth factor) binds and activates a VEGFR (PR:000001971). For annotation of signaling pathways where a VEGF binds to a cell surface receptor (VEGFR, PDGFR etc.), consider 'vascular endothelial growth factor signaling pathway ; GO:0038084'.
vascular endothelial growth factor receptor signaling pathway
A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
inositol phospholipid-mediated signaling
phosphatidylinositol-mediated signal transduction
phosphatidylinositol-mediated signalling
A series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids.
inositol lipid-mediated signal transduction
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line.
The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation.
vesicle targeting, to, from or within dictyosome
vesicle targeting, to, from or within Golgi
The creation of a single organelle from two or more organelles.
The creation of two or more organelles by division of one organelle.
The process in which the anatomical structures of the mesoderm are generated and organized.
The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place.
The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
positive regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
negative regulation of physiological process
negative regulation of biological process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
negative regulation of cellular physiological process
The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation.
haematopoietic or lymphoid organ development
haemopoietic or lymphoid organ development
hemopoietic or lymphoid organ development
hematopoietic or lymphoid organ development
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
positive regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
negative regulation of response to stimulus
The process in which the anatomical structures of the eye are generated and organized.
The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants.
embryonic anatomical structure morphogenesis
The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
reproductive process in a multicellular organism
multicellular organismal reproductive process
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
formation of an anatomical structure involved in morphogenesis
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
The process in which the anatomical structures of a tissue are generated and organized.
The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
branching morphogenesis of an epithelial tube
The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
Any process involved in the maintenance of an internal steady state at the level of the multicellular organism.
multicellular organismal-level homeostasis
Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
Any biological process involved in the maintenance of an internal steady state of a chemical.
The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure.
Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate.
sugar-phosphate phosphohydrolase activity
Catalysis of the reaction: H2O + sugar phosphorylated on the terminal carbon = a sugar + phosphate.
sugar-omega-phosphate phosphohydrolase activity
The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
Any process that modulates the frequency, rate or extent of lymphocyte proliferation.
The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances.
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
Any process that modulates the activity of an enzyme.
Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
Any process involved in the maintenance of an internal steady state of ions within an organism or cell.
negative regulation of crystal formation
The process in which a fluid solution, or part of it, changes into a solid or semisolid mass.
Interacting selectively and non-covalently with a cell adhesion molecule.
adhesive extracellular matrix constituent
Any process that modulates the frequency, rate or extent of T cell activation.
Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
Any process that activates or increases the frequency, rate or extent of activation.
Any process that activates or increases the frequency, rate or extent of T cell activation.
positive regulation of T lymphocyte activation
positive regulation of T-cell activation
positive regulation of T-lymphocyte activation
positive regulation of T cell activation
A organ system process carried out by any of the organs or tissues of neurological system.
Any process that modulates the levels of body fluids.
The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system.
A chemical homeostatic process involved in the maintenance of a steady state level of water within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell.
multicellular organismal water homeostasis
multicellular organismal-level water homeostasis
Any process in which nutrients are taken up from the contents of the intestine.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
The movement of a leukocyte within or between different tissues and organs of the body.
Any process pertaining to the functions of the nervous and muscular systems of an organism.
Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
sensory perception of mechanical stimulus
Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
positive regulation of developmental process
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
regulation of nitrogen compound metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
positive regulation of nitrogen metabolic process
positive regulation of nitrogen metabolism
up regulation of nitrogen metabolic process
up-regulation of nitrogen metabolic process
upregulation of nitrogen metabolic process
activation of nitrogen metabolic process
stimulation of nitrogen metabolic process
positive regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
The directed movement of vitamins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere.
Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs.
regulation of multicellular organismal process
Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs.
up regulation of multicellular organismal process
up-regulation of multicellular organismal process
upregulation of multicellular organismal process
activation of multicellular organismal process
stimulation of multicellular organismal process
positive regulation of multicellular organismal process
Any process that modulates the frequency, rate or extent of lymphocyte activation.
Any process that activates or increases the frequency, rate or extent of lymphocyte activation.
positive regulation of lymphocyte activation
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA.
positive regulation of RNA metabolic process
Any process that modulates the frequency, rate or extent of the movement of a cellular component.
regulation of cellular component movement
Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
positive regulation of cellular component motion
positive regulation of cellular component movement
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
positive regulation of transferase activity
Any process that modulates the internal pH of a cell, measured by the concentration of the hydrogen ion.
The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.
Any process in which an organelle is transported to, and/or maintained in, a specific location.
establishment and maintenance of organelle localization
A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane.
establishment and maintenance of cellular localization
establishment and maintenance of localization in cell or cell membrane
Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location.
establishment and maintenance of vesicle localization
Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
establishment of intracellular localization
establishment of localization within cell
The directed movement of a vesicle to a specific location.
The directed movement of an organelle to a specific location.
Any process in which a cell is transported to, and/or maintained in, a specific location.
establishment and maintenance of cell localization
establishment and maintenance of localization of cell
A biological process which involves another organism of the same or different species.
physiological interaction between organisms
physiological interaction with other organism
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+.
brain nitric-oxide synthase biosynthetic process
endothelial nitric-oxide synthase biosynthetic process
inducible nitric-oxide synthase biosynthetic process
nitric-oxide synthase (type 2) biosynthesis
nitric-oxide synthase (type 2) biosynthetic process
nitric-oxide synthase (type II) biosynthesis
nitric-oxide synthase (type II) biosynthetic process
nitric-oxide synthase 2 biosynthetic process
nitric-oxide synthase-1 biosynthetic process
nitric-oxide synthase-2 biosynthetic process
nitric-oxide synthase-3 biosynthetic process
nitric-oxide synthase biosynthetic process
Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell.
Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell.
Any process involved in the maintenance of an internal steady state of copper ions within an organism or cell.
Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell.
Any process involved in the maintenance of an internal steady state of transition metal ions within an organism or cell. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
Any process involved in the maintenance of an internal steady state of cations within an organism or cell.
Any process involved in the maintenance of an internal steady state of anions within an organism or cell.
Any biological process involved in the maintenance of an internal steady state of a chemical at the level of the cell.
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
ATP hydrolysis coupled transmembrane transport
Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes.
The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
nucleobase, nucleoside and nucleotide metabolism
nucleobase-containing small molecule metabolic process
The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body.
The regulation of body fluids process in which parasympathetic nerves stimulate the bladder wall muscle to contract and expel urine from the body.
A compound molecular function in which an effector function is controlled by one or more regulatory components.
The volume enclosed by a cytoplasmic vesicle.
cytoplasmic membrane-bounded vesicle lumen
cytoplasmic membrane-enclosed vesicle lumen
Signaling at short range between the head ectoderm and the optic vesicle that results in the head ectoderm forming a lens.
A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of macromolecule metabolic process
The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
microtubule-based flagellar cell motility
Movement of cilia mediated by motor proteins that contributes to the movement of a cell.
cilium movement involved in cell motility
The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation.
The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells.
The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange.
The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
The regulated release of a hormone into the circulatory system.
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
The membrane organization process that joins two lipid bilayers to form a single membrane.
The process in which the anatomical structures of a branched epithelium are generated and organized.
The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.
The process in which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.
The chemical reactions and pathways resulting in the formation of testosterone, an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4 C-5.
A process in which a protein is transported to, or maintained in, a location within a cilium.
A cytosolic protein complex that is capable of activating caspase-1.
An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells.
collagen-containing extracellular matrix
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
cellular protein-containing complex assembly
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell.
extracellular membrane-enclosed organelle
extracellular membrane-bounded organelle
An organelle lumen that is part of an intracellular organelle.
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
The covalent attachment and further modification of carbohydrate residues to a substrate molecule.
A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix.
The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body.
A renal system process in which water, ions, glucose and proteins are taken up from the collecting ducts, glomerulus and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures (e.g. protein absorption is observed in nephrocytes in Drosophila, see PMID:23264686).
A renal system process in which water is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures.
An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade may involve 4 different kinases, as it can also contain an additional tier: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell.
extracellular signal-regulated kinase 1/2 (ERK1/2) cascade
extracellular signal-regulated kinase 1/2 cascade
Note that this MAPKKK cascade is commonly referred to as the ERK pathway in the literature, but involves only ERK1 or ERK2 and should not be confused with cascades that involve other ERK kinases.
Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
regulation of ERK1 and ERK2 signaling pathway
regulation of ERK1 and ERK2 signalling pathway
Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
positive regulation of ERK1 and ERK2 signaling pathway
positive regulation of ERK1 and ERK2 signalling pathway
positive regulation of ERK1 and ERK2 cascade
A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis.
exocytic constitutive secretory pathway transport vesicle
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
The expansion of a leukocyte population by cell division.
Any process that modulates the frequency, rate or extent of leukocyte proliferation.
Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus.
The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
cellular response to bacteria associated molecule
cellular response to bacterial associated molecule
cellular response to bacterium associated molecule
cellular response to molecule of bacterial origin
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus.
cellular response to carbohydrate stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a monosaccharide stimulus.
cellular response to monosaccharide stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
cellular response to tumor necrosis factor
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
cellular response to polypeptide hormone stimulus
cellular response to peptide hormone stimulus
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
cellular response to organonitrogen compound
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
cellular response to lowered oxygen tension
Note that this term should not be confused with 'cellular response to anoxia ; GO:0071454'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism.
cellular response to endogenous stimulus
The movement of a mononuclear cell within or between different tissues and organs of the body.
Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location.
protein localisation in extracellular region
protein localization in extracellular region
protein localization to extracellular region
A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state.
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor superfamily cytokine production
The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
immunoglobulin heavy chain V-D-J recombination
The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
immunoglobulin light chain V-J recombination
A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.
RNA-protein complex subunit organization
protein-RNA complex subunit organization
ribonucleoprotein complex subunit organisation
ribonucleoprotein complex subunit organization
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
cellular component organization or biogenesis
The process in which urea, the water-soluble compound H2N-CO-NH2, is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures.
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain.
The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm.
extracellular vesicular exosome assembly
The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels.
The developmental process pertaining to the initial formation of an epithelial tube.
The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
A response to a stimulus that consists of a sequential series of modifications to a set of proteins where the product of one reaction acts catalytically in the following reaction. The magnitude of the response is typically amplified at each successive step in the cascade. Modifications typically include proteolysis or covalent modification, and may also include binding events.
Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell.
The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof.
purine-containing compound metabolic process
The chemical reactions and pathways resulting in the formation of a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof.
purine and derivative biosynthetic process
purine-containing compound biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Any process involved in the maintenance of an internal steady state of amino acid within an organism or cell.
Any process involved in the maintenance of an internal steady state of cysteine within an organism or cell.
Any process that modulates the size of an anatomical structure.
The joining of two lipid bilayers to form a single organelle membrane.
Any process that increases the frequency, rate or extent of lipid kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a simple or complex lipid.
positive regulation of lipid kinase activity
Any cellular metabolic process involving nucleic acids.
The chemical reactions and pathways resulting in the biosynthesis of deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose.
Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
All of the contents of a cilium, excluding the plasma membrane surrounding the cilium.
Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm".
The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'.
Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
induction of apoptosis by extracellular signals
This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.
A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
A renal system process in which fluid circulating through the body is filtered through a barrier system.
The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs.
An arrangement of closely apposed microtubules running parallel to each other.
Any of the two layers of lipid molecules that constitute a membrane.
The movement of a myeloid leukocyte within or between different tissues and organs of the body.
The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA).
Any vesicle that is part of the intracellular region.
The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.
anchoring of the basal body to the plasma membrane
Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella.
ciliary basal body-plasma membrane docking
The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.
vesicle targeting, trans-Golgi to periciliary membrane compartment
Any process involved in the controlled movement of a sperm cell.
The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism.
defence response incompatible interaction
defence response to pathogen, incompatible interaction
defense response, incompatible interaction
A cellular component consisting of one leaflet of a membrane bilayer and any proteins embedded or anchored in it or attached to its surface.
A membrane that is a (regional) part of the plasma membrane.
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
The attachment of one cell to another cell via adhesion molecules.
A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands).
A complex of collagen trimers such as a fibril or collagen network.
A supramolecular complex that consists of collagen triple helices associated to form a network.
Any collagen timer that is part of a basement membrane.
The process in which a cation is transported across a membrane.
ATP hydrolysis coupled cation transmembrane transport
The process in which an anion is transported across a membrane.
ATP hydrolysis coupled anion transmembrane transport
The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis.
The process in which an inorganic ion is transported across a membrane.
The process in which an inorganic anion is transported across a membrane.
A process in which an inorganic cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
transmembrane inorganic cation transport
inorganic cation transmembrane transport
Any subdivision of a chromosome along its length.
The attachment of one cell to another cell via adhesion molecules that are at least partially embedded in the plasma membrane.
cell-cell adhesion via plasma-membrane adhesion molecules
Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell.
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
The part of a synapse that is part of the presynaptic cell.
The part of a synapse that is part of the post-synaptic cell.
Any protein complex that is part of a membrane.
Any protein complex that is part of the plasma membrane.
Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system.
Any protein complex that is part of the plasma membrane and which functions as a signaling receptor.
plasma membrane signaling receptor complex
A membrane region with a lipid composition that is distinct from that of the membrane regions that surround it.
A cell projection supported by an assembly of actin filaments, and which lacks microtubules.
A cell part consisting of multiple, closely packed actin-based cell projections.
Cell-cell signaling from pre to post-synapse, across the synaptic cleft.
A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber.
A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space.
A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space.
A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits.
Cell-cell signaling to, from or within a synapse.
Cell-cell signaling in either direction across the synaptic cleft.
Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon.
plasma membrane bounded cell projection assembly
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon.
plasma membrane bounded cell projection organization
Contractions of the intestinal tract that include peristalsis (moving contents onward) and non-peristaltic movement (moving contents back and forth).
The chemical reactions and pathways involving an olefinic compound, any compound which contains a carbon-carbon double bond (aka C=C).
alkene substituted compound metabolic process
The chemical reactions and pathways resulting in the formation of an olefinic compound, any compound which contains a carbon-carbon double bond (aka C=C).
alkene substituted compound anabolic process
alkene substituted compound biosynthesis
alkene substituted compound biosynthetic process
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
The cellular processes that contribute to exocytosis.
The process in which a mitochondrial gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.
organelle localization by membrane tethering
Catalytic activity that acts to modify a protein.
The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content.
Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: anion(in) + solute(out) = anion(out) + solute(in).
The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis.
The directed movement of a lipid from a cell, into the extracellular region.
Receiving a signal and transmitting it in a cell to initiate an immune response.
Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host.
A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell.
multicellular organism level chemical homeostasis
multicellular organismal-level chemical homeostasis
The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways.
The chemical reactions and pathways involving carbohydrate derivative.
carbohydrate derivative metabolic process
The chemical reactions and pathways resulting in the formation of carbohydrate derivative.
carbohydrate derivative biosynthetic process
The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The chemical reactions and pathways resulting in the formation of a nucleoside phosphate.
nucleoside phosphate biosynthetic process
Any process that modulates the frequency, rate or extent of vasculature development.
regulation of vascular system development
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
organic cyclic compound biosynthetic process
Interacting selectively and non-covalently with heterocyclic compound.
The chemical reactions and pathways involving organonitrogen compound.
organonitrogen compound metabolic process
The chemical reactions and pathways resulting in the breakdown of organonitrogen compound.
organonitrogen compound catabolic process
The chemical reactions and pathways resulting in the formation of organonitrogen compound.
organonitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
The chemical reactions and pathways involving an alpha-amino acid.
The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid.
The chemical reactions and pathways involving organic hydroxy compound.
organic hydroxy compound metabolic process
The chemical reactions and pathways resulting in the formation of organic hydroxy compound.
organic hydroxy compound biosynthetic process
Enables the transfer of organic hydroxy compound from one side of a membrane to the other.
organic hydroxy compound transmembrane transporter activity
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus.
The chemical reactions and pathways involving quinone.
The chemical reactions and pathways resulting in the formation of quinone.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus.
cellular response to nitrogen molecular entity
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus.
cellular response to oxygen molecular entity
cellular response to oxygen-containing compound
Any process that modulates the frequency, rate or extent of leukocyte differentiation.
regulation of immune cell differentiation
The process in which chloride is transported across a membrane.
Any process that modulates the frequency, rate or extent of intracellular signal transduction.
regulation of intracellular signaling cascade
regulation of intracellular signaling chain
regulation of intracellular protein kinase cascade
regulation of intracellular signal transduction pathway
regulation of signal transmission via intracellular cascade
regulation of intracellular signaling pathway
regulation of signal transduction via intracellular signaling cascade
regulation of intracellular signal transduction
Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
positive regulation of intracellular signaling chain
up regulation of intracellular signal transduction
up regulation of intracellular signaling chain
up-regulation of intracellular signal transduction
up-regulation of intracellular signaling chain
upregulation of intracellular signal transduction
upregulation of intracellular signaling chain
activation of intracellular signal transduction
activation of intracellular signal transduction pathway
activation of intracellular signaling cascade
activation of intracellular signaling chain
activation of signal transmission via intracellular cascade
positive regulation of intracellular protein kinase cascade
positive regulation of intracellular signal transduction pathway
positive regulation of signal transmission via intracellular cascade
up regulation of intracellular signal transduction pathway
up regulation of signal transmission via intracellular cascade
up-regulation of intracellular signal transduction pathway
up-regulation of signal transmission via intracellular cascade
upregulation of intracellular signal transduction pathway
upregulation of signal transmission via intracellular cascade
activation of intracellular signaling pathway
activation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signaling cascade
positive regulation of intracellular signaling pathway
positive regulation of signal transduction via intracellular signaling cascade
up regulation of intracellular signaling cascade
up regulation of intracellular signaling pathway
up regulation of signal transduction via intracellular signaling cascade
up-regulation of intracellular signaling cascade
up-regulation of intracellular signaling pathway
up-regulation of signal transduction via intracellular signaling cascade
upregulation of intracellular signaling cascade
upregulation of intracellular signaling pathway
upregulation of signal transduction via intracellular signaling cascade
positive regulation of intracellular signal transduction
The directed movement of a proton across a membrane.
passive proton transport, down the electrochemical gradient
The chemical reactions and pathways involving secondary alcohol.
The chemical reactions and pathways resulting in the formation of secondary alcohol.
Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process.
up regulation of RNA biosynthetic process
up-regulation of RNA biosynthetic process
upregulation of RNA biosynthetic process
positive regulation of RNA biosynthetic process
Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion.
Exogenous expression of ASS1 or NOS3 in HUVECs enhances NO production and inhibits monocyte adhesion
regulation of leukocyte cell-cell adhesion
Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion.
positive regulation of leukocyte adhesion
positive regulation of leukocyte cell adhesion
up regulation of leukocyte cell adhesion
up regulation of leukocyte cell-cell adhesion
up-regulation of leukocyte cell adhesion
up-regulation of leukocyte cell-cell adhesion
upregulation of leukocyte cell-cell adhesion
activation of leukocyte cell-cell adhesion
positive regulation of leukocyte cell-cell adhesion
A process that is part of the mitotic cell cycle.
The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell.
Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
regulation of nucleic acid-templated transcription
Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription.
up regulation of nucleic acid-templated transcription
up-regulation of nucleic acid-templated transcription
upregulation of nucleic acid-templated transcription
activation of nucleic acid-templated transcription
positive regulation of nucleic acid-templated transcription
The chemical reactions and pathways involving liposaccharide.
Any vesicle that is part of the extracellular region.
Any process that modulates the frequency, rate or extent of hemopoiesis.
An example of this is Atg7 in mouse (UniProt symbol, Q9D906) in PMID:20080761, inferred from mutant phenotype.
The process in which an organic acid is transported across a membrane.
Any process that activates or increases the frequency, rate or extent of vasculature development.
up regulation of vasculature development
up-regulation of vasculature development
activation of vascular system development
positive regulation of vascular system development
up regulation of vascular system development
up-regulation of vascular system development
upregulation of vascular system development
positive regulation of vasculature development
The process in which glucose is transported across a membrane.
The process in which carboxylic acid is transported across a membrane.
The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone.
A macromolecular complex that contains both RNA and protein molecules.
Any process that modulates the frequency, rate or extent of multicellular organismal development.
regulation of multicellular organismal development
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
regulation of cellular macromolecule biosynthetic process
Any process that modulates the frequency, rate or extent of cell motility.
Any process that activates or increases the frequency, rate or extent of cell motility.
positive regulation of movement of a cell
Any epithelial cell proliferation that is involved in renal tubule morphogenesis.
epithelial cell proliferation involved in renal tubule morphogenesis
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
Root of all terms in the Human Phenotype Ontology.
Deviation from the norm of height with respect to that which is expected according to age and gender norms.
Multicystic dysplasia of the kidney is characterized by multiple cysts of varying size in the kidney and the absence of a normal pelvicaliceal system. The condition is associated with ureteral or ureteropelvic atresia, and the affected kidney is nonfunctional.
Multicystic kidney dysplasia is the result of abnormal fetal renal development in which the affected kidney is replaced by multiple cysts and has little or no residual function. The vast majority of multicystic kidneys are unilateral. Multicystic kidney can be diagnosed on prenatal ultrasound.
The pattern in which a particular genetic trait or disorder is passed from one generation to the next.
A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele.
A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygotes (two copies of the same mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele).
Repeated infections of the urinary tract.
The urinary tract comprises the kidneys, ureters, a bladder, and a urethra.
A type of bladder dysfunction caused by neurologic damage. Neurogenic bladder can be flaccid or spastic. Common manifestatios of neurogenic bladder are overflow incontinence, frequency, urgency, urge incontinence, and retention.
Lack of bladder control due to nervous system injury
Neurogenic bladder sphincter dysfunction (NBSD) can develop as a result of a lesion at any level in the nervous system, including the cerebral cortex, spinal cord, or peripheral nervous system. Neurologic conditions in children leading to neurogenic bladder dysfunction are predominantly congenital neural tube defects (including myelomeningocele, lipomeningocele, sacral agenesis, and occult lesions causing tethered cord). Acquired causes such as spinal cord tumors or trauma or sequelae of transverse myelitis are less frequent. Whereas from an etiologic standpoint neurogenic bladder dysfunction is a heterogeneous group, medical management will be similar irrespective of the underlying cause.
Functional abnormality of male internal genitalia
Absence of any measurable level of sperm in his semen.
An abnormality of male external genitalia.
Hermaphroditism refers to a discrepancy between the morphology of the gonads and that of the external genitalia. In male pseudohermaphroditism, the genotype is male (XY) and the external genitalia are imcompletely virilized, ambiguous, or complete female. If gonads are present, they are testes.
Hypogonadotropic hypogonadism is characterized by reduced function of the gonads (testes in males or ovaries in females) and results from the absence of the gonadal stimulating pituitary hormones: follicle stimulating hormone (FSH) and luteinizing hormone (LH).
Low gonadotropins (secondary hypogonadism)
An abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder.
The presence of a stenotic, i.e., constricted ureter.
Blockage of urine flow from the renal pelvis to the proximal ureter.
A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters.
The kidney is a paired organ whose primary function is the production of urine.
An abnormal functionality of the genital system.
Abnormality of reproductive system physiology
A duplication of the collecting system of the kidney, defined as a kidney with two (instead of, normally, one) pyelocaliceal systems. The pyelocaliceal system is comprised of the renal pelvis and calices. The duplicated renal collecting system can be associated with a single ureter or with double ureters. In the latter case, the two ureters empty separately into the bladder or fuse to form a single ureteral orifice.
Double urinary collecting systems on intravenous pyelography
A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism.
A connection of the right and left kidney by an isthmus of functioning renal parenchyma or fibrous tissue that crosses the midline.
A developmental defect in which a kidney is located in an abnormal anatomic position.
Oligomeganephronic renal hypoplasia differs from simple hypoplasia, in which the renal mass is reduced but the number of nephrons is normal.
Presence of cysts at the corticomedullary junction of the kidney in combination with tubulointerstitial fibrosis.
Nephronophthisis is here regarded as a phenotypic feature. The disease of the same name results in progressive symmetrical destruction of the kidneys involving both the tubules and glomeruli.
Morphologic abnormality of the renal tubules
The renal tubules are reabsorptive canals that are involved in the secreting, collecting, and conducting of the urine.
The presence of renal tubules with thick redundant basement membranes, or a reduction of greater than 50% in tubular diameter compared to surrounding non-atrophic tubules.
Atrophic tubules must be distinguished from acute tubular injury as both can show extensive tubular epithelial changes. In acute tubular injury, tubules are often dilated and tubular basement membranes are smooth and maintain normal thickness, in contrast to the contracted tubules with thickened and wrinkled tubular basement membranes of tubular atrophy. Further, in acute tubular injury, tubules are usually back-to-back or mildly separated by interstitial edema, while in tubular atrophy tubules can be separated by interstitial fibrosis. Uniform thickening of tubular basement membranes without shrinkage and otherwise healthy epithelial cells can be seen in diabetic nephropathy. Duplication, or lamellation, thickening, and disruption of tubular basement membranes with tubular dilatation can be seen in medullary cystic kidney disease/nephronophthisis.
Increased levels of protein in the urine.
Abnormality of renal glomerulus morphology
Morphologic abnormality of the renal glomerulus
Each human kidney contains approximately one million nephrons. The glomerulus is the most proximal component of the nephron. The glomerulus of the mammalian kidney is a highly developed vascular bed that acts as a filter, allowing a filtrate of small molecules, such as water, sugars, electrolytes and small proteins, to pass through a barrier that retains high molecular weight proteins and cells in the circulation.
Accumulation of scar tissue within the glomerulus.
Segmental accumulation of scar tissue in individual (but not all) glomeruli.
Focal and segmental glomerular sclerosis
Glomerular changes can be focal (only in some glomeruli) or diffuse (in all or almost all the glomeruli), and segmental (only a part of the glomerulus) or global (the entire glomerulus). FSGS is characterized by focal and segmental occurrence of lesions with mesangial sclerosis, obliteration of glomerular capillaries with hyalinosis and intracapillary foam cells, formation of adhesions between the glomerular tuft and Bowman's capsule, and podocyte hypertrophy. FSGS is not a disease entity, but rather a pattern of injury with quite diverse clinical behavior, morphology, and possibly also pathogenesis.
A height above that which is expected according to age and gender norms.
Nephrotic syndrome is a collection of findings resulting from glomerular dysfunction with an increase in glomerular capillary wall permeability associated with pronounced proteinuria. Nephrotic syndrome refers to the constellation of clinical findings that result from severe renal loss of protein, with Proteinuria and hypoalbuminemia, edema, and hyperlipidemia.
In adults, nephrotic syndrome is characterized by protein excretion of 3.5 g or more per day. In children, nephrotic syndrome is accompanied by protein excretion of more than 40 mg/m2/h and hypalbuminemia < 2.5 mg/dl.
An excessive volume of urination for an adult is more than 2.5 liters of urine per day.
Agenesis, that is, failure of the kidney to develop during embryogenesis and development.
Renal agenesis can occur as a unilateral or bilateral trait.
An abnormal increase in the size of the kidney.
The main causes of large kidney are hydronephrosis, polycystic disease, renal cell carcinoma, nephroblastoma/Wilms tumor (in children), and solitary cysts. If possible, a specific term should be used instead of this one. There are several ways of diagnosing enlarged kidney including intravenous urography.
The presence of multiple cysts at the border between the renal cortex and medulla.
The presence of developmental dysplasia of the kidney.
Increased number and size of the juxtaglomerular cells.
Renal juxtaglomerular cell hypertrophy/hyperplasia
A nonspecific term referring to disease or damage of the kidneys.
The presence of multiple cysts in both kidneys.
Polycystic kidney disease (PKD) is a leading cause of end-stage renal disease. Most commonly, PKD arises as an inherited trait. Tremendous enlargement of both kidneys is characteristic of the autosomal dominant form of PKD, with up to hundreds or thousands of renal cysts. This term does not refer to the disease entity but rather to the finding of numerous cysts in both kidneys.
Dysfunction of the proximal tubule, which is the portion of the duct system of the nephron of the kidney which leads from Bowman's capsule to the loop of Henle.
This is the root of the phenotypic abnormality subontology of the HPO.
The presence of any abnormality of the genitourinary system.
Nephrocalcinosis is the deposition of calcium salts in renal parenchyma.
Nephrocalcinosis can be intratubular or interstitial, and can be diagnosed by means of a radiologic exam (plain radiographs, ultrasonograms, or computed tomography scans) or via microscopic examination of the renal tissues. The term nephrocalcinosis most often applies to a generalized increase in renal calcium content.
A unilateral form of agenesis of the kidney.
The presence of inflammation affecting the kidney.
Abnormal function of the renal tubule. The basic functional unit of the kidney, the nephron, consists of a renal corpuscle attached to a renal tubule, with roughly 0.8 to 1.5 nephrons per adult kidney. The functions of the renal tubule include reabsorption of water, electrolytes, glucose, and amino acids and secretion of substances such as uric acid.
Abnormal function of filtrating structures in kidney
A developmental defect in which a kidney is located in an abnormal anatomic position within the pelvis.
Severe distention of the kidney with dilation of the renal pelvis and calices.
Hydronephrosis can be caused by reflux or by retrograde pressure on the kidney when the flow of urine is obstructed.
Reduced functioning of the gonads (ovaries or testes) with reduced production of sex hormones.
Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth.
The presence of a cleft in the oral cavity, the two main types of which are cleft lip and cleft palate. In cleft lip, there is the congenital failure of the maxillary and median nasal processes to fuse, forming a groove or fissure in the lip. In cleft palate, there is a congenital failure of the palate to fuse properly, forming a grooved depression or fissure in the roof of the mouth. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately.
Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation.
Too much cerebrospinal fluid in the brain
Hydrocephalus results from an imbalance between the rate of production of cerebrospinal fluid (CSF), mainly in the choroid plexus, and its reabsorption in the subarchnoid space over brain and spinal cord.
Any abnormality of the size of the skull.
Head circumference below 2 standard deviations below the mean for age and gender.
Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles [Hall et al. [2007]], others by standard deviations [Farkas, [1981]]. It is important to add an indication of how far below the normal standard the head circumference is if an accurate assessment of this can be made. Microcephaly is an absolute term. The term relative microcephaly can be used when the head size centile is less than the centile for height, for example, head size at the 3rd centile with height at the 75% for age and sex. On prenatal ultrasound, microcephaly is diagnosed if the head circumference or the biparietal diameter is more than three standard deviations below the mean.
A fold of skin starting above the medial aspect of the upper eyelid and arching downward to cover, pass in front of and lateral to the medial canthus.
In extreme cases, the skin fold can start as high as the eyebrow; this is called epicanthus superciliaris.
Abnormality of the region around the eyes
Anomaly of the orbital region of the face
Deformity of the orbital region of the face
Malformation of the orbital region of the face
An abnormality of the sensory perception of sound.
According to the World Health Organization, deafness refers to the complete loss of hearing ability in one or two ears. Hearing impairment refers to both complete and partial loss of the ability to hear.
A decreased magnitude of the sensory perception of sound.
Hearing loss can be categorized by which part of the auditory system is damaged, as conductive hearing loss, sensorineural hearing loss, and mixed hearing loss. Another axis of classification uses the degree of hearing impairment. The degree of hearing loss is computed by using a three frequency average taken at 500 Hz, 1,000 Hz and 2,000 Hz. The average of these three frequencies is called the Pure Tone Average (PTA). 0-20 dB is considered normal, 21-40 dB mild loss, 41-60 dB moderate loss, 61-70 dB moderately severe loss,71-90 dB severe loss, and greater than 90 dB profound loss. Note that the word deafness is occasionally used to describe partial hearing loss. The World Health Organization uses the word deafness to refer to complete loss of the ability to hear, and hearing impairment to refer to any degree of reduced hearing.
A type of hearing impairment in one or both ears related to an abnormal functionality of the cochlear nerve.
Hearing loss caused by damage or dysfunction of the auditory nerve (cranial nerve VIII, also known as the cochlear nerve).
Any abnormality of the eye, including location, spacing, and intraocular abnormalities.
A misalignment of the eyes so that the visual axes deviate from bifoveal fixation. The classification of strabismus may be based on a number of features including the relative position of the eyes, whether the deviation is latent or manifest, intermittent or constant, concomitant or otherwise and according to the age of onset and the relevance of any associated refractive error.
An abnormality in voluntary or involuntary eye movements or their control.
Abnormal motility of the globe of the eye
Abnormal movement of the globe of the eye
Glaucoma refers loss of retinal ganglion cells in a characteristic pattern of optic neuropathy usually associated with increased intraocular pressure.
The feature that differentiates glaucoma from other causes of visual morbidity is a characteristic pattern of damage to the optic nerve head. This is most easily recognised at the superior and inferior poles of the optic disc. The vertical cup:disc ratio (VCDR) has proved to be a simple, relatively robust index of glaucomatous loss of the neuroretinal rim. As with intraocular pressure, VCDR is a continuous variable within the population.
Abnormality of eyesight (visual perception).
Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery.
The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective).
An abnormality of the iris, which is the pigmented muscular tissue between the cornea and the lens, that is perforated by an opening called the pupil.
Abnormality of the iris characterized by, typically bilateral, complete or partial iris hypoplasia. The phenotype ranges from mild defects of anterior iris stroma only to almost complete absence of the iris.
Any deviation from the normal motor coordination of the eyes that allows for bilateral fixation on a single object.
An abnormality of the uvea, the vascular layer of the eyeball.
Inflammation of one or all portions of the uveal tract.
The uvea is the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid.
Retinal dystrophy is an abnormality of the retina associated with a hereditary process. Retinal dystrophies are defined by their predominantly monogenic inheritance and they are frequently associated with loss or dysfunction of photoreceptor cells as a primary or secondary event.
Breakdown of light-sensitive cells in back of eye
Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future.
Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degress in radius around central fixation.
Various scales have been developed to describe the extent of vision loss and define blindness. Total blindness is the complete lack of form and visual light perception and is clinically recorded as NLP (no light perception). Blindness is frequently used to describe severe visual impairment with residual vision. Those described as having only light perception have no more sight than the ability to tell light from dark and the general direction of a light source.
The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system.
An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities.
A loss of global cognitive ability of sufficient amount to interfere with normal social or occupational function. Dementia represents a loss of previously present cognitive abilities, generally in adults, and can affect memory, thinking, language, judgment, and behavior.
The presence of calculi (stones) in the kidneys.
Urinary stone disease is caused by supersaturation of the urine by stone forming substances including calcium, oxalate, and uric acid. Crystals or foreign bodies can act as a nidus for further stone formation. The resulting kidney stones (calculi) lead to symptoms if they become impacted in the ureter.
The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine).
The presence of uric acid-containing calculi (stones) in the kidneys.
A type of glomerulonephritis characterized by diffuse mesangial cell proliferation and the thickening of capillary walls due to subendothelial extension of the mesangium. The term membranoproliferative glomerulonephritis is often employed to denote a general pattern of glomerular injury seen in a variety of disease processes that share a common pathogenetic mechanism, rather than to describe a single disease entity
Membranoproliferative glomerulonephritis
The presence of immunoglobulin A deposits in the glomerulus.
Abnormal fat accumulation in the kidneys.
The presence of xanthine-containing calculi (stones) in the kidneys.
An anomaly of the adnexa, uterus, and vagina (in female) or seminal tract and prostate (in male).
The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions.
The presence of chronic increased pressure in the systemic arterial system.
Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both.
An abnormality of the parathyroid gland.
There are four parathyroid glands, which are small endocrine glands located in the neck behind the thyroid gland that produce parathyroid hormone.
A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia.
Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kindneys.
Excessive production of parathyroid hormone (PTH) by the parathyroid glands.
Elevated blood parathyroid hormone level
An abnormality of the renin-angiotensin system.
Abnormality of the renin-aldosterone axis
The renin-angiotensin system is a hormone system that regulates blood pressure and water (fluid) balance.
Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels.
An abnormality of the skull, the bony framework of the head which is comprised of eight cranial and fourteen facial bones.
An abnormality of the fossa cranii posterior (the posterior fossa), which is made up primarily of the occipital bone and which surrounds to the foramen magnum.
Abnormality of the posterior cranial fossa
The floor of the cranial cavity is divided into three distinct depressions called the anterior, middle, and posterior cranial fossa. The posterior cranial fossa, the most posterior and deep of the three cranial fossae, accommodates the brainstem and cerebellum. Abnormalities of the posterier cranial fossa can be demonstrated by cerebral magnetic resonance imaging or computer tomography.
Abnormal posterior cranial fossa morphology
Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean.
Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.
A darkening of the skin related to an increase in melanin production and deposition.
Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding.
An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body.
Edema may be related to one or more of the following factors: 1) increased capillary hydrostatic pressure, 2) decreased osmotic pressure of plasma, 3) decreased tissue tension and lymphatic drainage, 4) increased osmotic pressure of tissue fluids, and 5) increased capillary permeability.
An increased sensitivity of the skin to light. Photosensitivity may result in a rash upon exposure to the sun (which is known as photodermatosis). Photosensitivity can be diagnosed by phototests in which light is shone on small areas of skin.
An abnormality of the pigmentation of the skin.
Dermatological manifestations of systemic disorders
Any structural abnormality of the fundus of the eye.
A structural abnormality of the macula lutea, which is an oval-shaped highly pigmented yellow spot near the center of the retina.
The term macula derives from the presence of the xanthophyll pigments, lutein and zeaxanthin, in a region five to six millimetres in diameter at the posterior pole of the eye, appearing as a yellow spot (macula lutea), when viewed in red-free light.
Digits that appear disproportionately short compared to the hand/foot. The word brachydactyly is used here to describe a series distinct patterns of shortened digits (brachydactyly types A-E). This is the sense used here.
An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities.
Abnormality of prenatal development or birth
Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality.
Subnormal intellectual functioning which originates during the developmental period. Intellectual disability, previously referred to as mental retardation, has been defined as an IQ score below 70.
This term should be used for children at least five years old. For younger children, consider the term Global developmental delay (HP:0001263).
A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain.
A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold.
Cerebellar ataxia refers to ataxia due to dysfunction of the cerebellum. This causes a variety of elementary neurological deficits including asynergy (lack of coordination between muscles, limbs and joints), dysmetria (lack of ability to judge distances that can lead to under- or overshoot in grasping movements), and dysdiadochokinesia (inability to perform rapid movements requiring antagonizing muscle groups to be switched on and off repeatedly).
Ataxia can be differentiated into dyssynergy, asynergy, dysmetria (hypometria, hypermetria), dysdiadochokinesis, gait ataxia, truncal ataxia, limb ataxia, and dysarthria). Note: This term does not include sensory ataxia.
A motor disorder characterized by a velocity-dependent increase in tonic stretch reflexes with increased muscle tone, exaggerated (hyperexcitable) tendon reflexes.
Involuntary muscle stiffness, contraction, or spasm
Loss of previously present mental abilities, generally in adults.
A condition in which there is increased muscle tone so that arms or legs, for example, are stiff and difficult to move.
Spasticity is a term that is often used interchangeably with hypertonia. Spasticity, however, is a particular type of hypertonia in which the muscles' spasms are increased by movement. In this type, patients usually have exaggerated reflex responses.
A congenital brain malformation typically characterized by incomplete formation of the cerebellar vermis, dilation of the fourth ventricle, and enlargement of the posterior fossa. In layman's terms, Dandy Walker malformation is a cyst in the cerebellum (typically symmetrical) that is involved with the fourth ventricle. This may interfere with the ability to drain cerebrospinal fluid from the brain, resulting in hydrocephalus. Dandy Walker cysts are formed during early embryonic development, while the brain forms. The cyst in the cerebellum typically has several blood vessels running through it connecting to the brain, thereby prohibiting surgical removal.
Any structural abnormality of the cerebellum.
A malformed cerebellum may be abnormally small, dysplastic, or unusually large. The vermis and both hemispheres may be equally or disproportionately affected. Primary malformations of the pons, midbrain, and supratentorial structures are also seen in a substantial subset of patients. The wide range in morphological presentations results from the diversity of causes, including chromosomal abnormalities, specific genetic syndromes, and extrinsic factors.
Underdevelopment of the vermis of cerebellum.
It is important clinical to distinguish between muscle weakness, fatigue, and asthenia. Fatigue describes the inability to continue performing a task after multiple repetitions; in contrast, a patient with primary weakness is unable to perform the first repetition of the task. Asthenia is a sense of weariness or exhaustion in the absence of muscle weakness. Conditions that result in intrinsic muscle weakness can be divided into several main categories: infectious, neurologic, endocrine, inflammatory, rheumatologic, genetic, metabolic, electrolyte-induced, or drug-induced.
An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join.
Impairment of bile flow due to obstruction in bile ducts.
Slowed or blocked flow of bile from liver
A mode of inheritance that is observed for traits related to a gene encoded on the X chromosome.
Simultaneous enlargement of the liver and spleen.
A structural abnormality of the abdomen ('belly'), that is, the part of the body between the pelvis and the thorax.
A deficiency or slowing down of growth pre- and postnatally.
Poor or abnormally slow gains in weight or height in a child.
Accumulation of substantial excess body fat.
Excessive postnatal growth which may comprise increased weight, increased length, and/or increased head circumference.
An abnormality of the integument, which consists of the skin and the superficial fascia.
Abnormality of the fingernails and/or toenails.
Any abnormality of the cardiovascular system.
Abnormality of the cardiovascular system
The cardiovascular system consists of the heart, vasculature, and the lymphatic system.
The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction.
The presence of a stenosis (narrowing) of the aortic valve.
Aortic stenosis can lead to a pressure gradient between the left ventricle and the aorta and may result in left ventricular hypertrophy and decreased left ventricular compliance.
A complex congenital heart defect in which the aorta arises from the morphologic right ventricle and the pulmonary artery arises from the morphologic left ventricle.
A congenital malformation of the outflow tract of the heart. Conotruncal defects are thought to result from a disturbance of the outflow tract of the embryonic heart, and comprise truncus arteriosus, tetralogy of Fallot, interrupted aortic arch, transposition of the great arteries, and double outlet right ventricle.
The spleen is an abdominal organ that functions as a member of the hematopoietic system and of the immune system.
The abnormal accumulation of fluid in two or more fetal compartments, including ascites, pleural effusion, pericardial effusion, and skin edema.
The most common causes of hydrops fetalis are hematologic (inclusing isoimmunization because of Rhesus incompatibility and other causes), hereditary hemolytic disorders, fetal hemorrhage, disorders of red cell production), cardiovascular disorders, infections, certain intrathoracic malformations, and idiopathic forms.
An abnormality of the hematopoietic system.
Abnormality of blood and blood-forming tissues
Abnormality of the haematopoietic system
The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes.
An abnormal reduction in numbers of all blood cell types (red blood cells, white blood cells, and platelets).
Any structural abnormality of erythrocytes (red-blood cells).
An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects.
This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted.
A form of amyloidosis that affects the kidney. On hematoxylin and eosin stain, amyloid is identified as extracellular amorphous material that is lightly eosinophilic. These deposits often stain weakly for periodic acid Schiff (PAS), demonstrate a blue-to-gray hue on the trichrome stain and are typically negative on the Jones methenamine silver (JMS) stain. These tinctorial properties contrast with the histologic appearance of collagen, a major component of basement membranes, mesangial matrix and areas of sclerosis, which demonstrates strong positivity for PAS and JMS (See Figure 1 of PMID:25852856).
In the kidney, amyloid deposits may be found in any of the parenchymal compartments, including glomeruli, tubules, interstitium and/or vessels. Glomeruli are most commonly involved. In most instances, amyloid accumulation involves the mesangium before the capillary walls. In early cases, the process can be subtle and involves only a few mesangial regions and therefore can easily be missed by routine histologic evaluation. More extensive involvement results in marked expansion of the mesangium, which can take on a nodular appearance and mimic mesangial sclerotic processes such as diabetic glomerulosclerosis. However, the often negative staining with PAS and JMS is more typical of amyloid.
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies.
The presence of stenosis of the renal artery.
Abnormal acid accumulation or depletion of base.
When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis.
Metabolic acidosis (MA) is characterized by a fall in blood pH due to a reduction of serum bicarbonate concentration. This can occur as a result of either the accumulation of acids (high anion gap MA) or the loss of bicarbonate from the gastrointestinal tract or the kidney (hyperchloremic MA). By definition, MA is not due to a respirary cause.
The Henderson-Hasselbalch method defines metabolic acidosis by the presence of an acid-base imbalance associated with a plasma bicarbonate concentration below 20 mmol/L. The association of this imbalance with decreased pH is called acidemia, which is often described as severe when the pH is equal to or below 7.20. Arterial blood gas measurements can be performed in patients with a decreased plasma bicarbonate level so as to eliminate respiratory alkalosis, confirm the diagnosis of metabolic acidosis, and test for mixed acidosis.
Elevated body temperature due to failed thermoregulation.
Acidosis owing to malfunction of the kidney tubules with accumulation of metabolic acids and hyperchloremia, potentially leading to complications including hypokalemia, hypercalcinuria, nephrolithiasis and nephrocalcinosis.
Accumulation of acid in body due to kidney problem
Excessive thirst manifested by excessive fluid intake.
An abnormality of the mesangium, i.e., of the central part of the renal glomerulus between capillaries.
Abnormality glomerular mesangium morphology
Mesangial cells constitute the central stalk of the glomerulus and are in continuity with the extraglomerular mesangium and the juxtaglomerular apparatus. They have contractile properties generated by anchoring filaments to glomerular basement membrane opposite podocyte foot processes and at the paramesangial angles, thereby assisting in the maintenance of capillary organization and convolution. On the capillary lumen side, mesangial cells are in direct contact with endothelial cells without an intervening basement membrane.
Abnormal glomerular mesangium morphology
Diffuse sclerosis of the mesangium, as manifestated by diffuse mesangial matrix expansion.
Diffuse mesangial sclerosis glomerulopathy
This finding can be demonstrated by renal biopsy.
An abnormality that involves the tubules and interstitial tissue of the kidney.
A form of inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules.
An inability of the tubules in the kidney to reabsorb small molecules, causing increased urinary loss of electrolytes (sodium, potassium, bicarbonate), minerals, glucose, amino acids, and water.
Recurrent attacks of acute inflammatory arthritis of a joint or set of joints caused by elevated levels of uric acid in the blood which crystallize and are deposited in joints, tendons, and surrounding tissues.
A structural abnormality of the central nervous system.
Abnormality of the central nervous system
Morphological abnormality of the central nervous system
Morphological central nervous system abnormality
An abnormality of the viscera of the abdomen.
The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen.
Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.
Abnormally increased frequency of loose or watery bowel movements.
Nausea is a commonly encountered symptom that has been defined as an unpleasant painless subjective feeling that one will imminently vomit. Vomiting has been defined as the forceful expulsion of the contents of the stomach, duodenum, or jejunum through the oral cavity. While nausea and vomiting are often thought to exist on a temporal continuum, this is not always the case. There are situations when severe nausea may be present without emesis and less frequently, when emesis may be present without preceding nausea.
A condition in which the stomach contents leak backwards from the stomach into the esophagus through the lower esophageal sphincter.
An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen.
Abdominal pain can be crampy, achy, dull, intermittent or sharp. The terms stomach ache and stomach cramps are nonmedical terms often used to describe pain in the mid- or upper abdominal area, even though it is not the case that the (smooth) muscles of the stomach or the abdomen have cramps. Stomach pain is another layperson term commonly used to refer to abdominal pain.
A lack or loss of appetite for food (as a medical condition).
A type of renal tubular acidosis characterized by a failure of the proximal tubular cells to reabsorb bicarbonate, leading to urinary bicarbonate wasting and subsequent acidemia.
Any structural abnormality of the telencephalon, which is also known as the cerebrum.
An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles.
Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing.
An increase in size of the ventricular system of the brain.
An abnormally high level of uric acid in the blood.
An increased concentration of nitrogen compounds in the blood.
Abnormal levels of nitrogen-containing compounds, such as urea and creatinine.
An abnormal dilatation of the fourth cerebral ventricle.
Hemorrhage affecting the gastrointestinal tract.
An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine.
Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.
The cerebellar vermis is the unpaired, median portion of the cerebellum that connects the two hemispheres.
A functional anomaly of the upper motor neuron. The upper motor neurons are neurons of the primary motor cortex which project to the brainstem and spinal chord via the corticonuclear, corticobulbar and corticospinal (pyramidal) tracts. They are involved in control of voluntary movements. Dysfunction leads to weakness, impairment of fine motor movements, spasticity, hyperreflexia and abnormal pyramidal signs.
A functional deficit of the tract that conveys nervous impulses from the motor cortex of the brain to the spinal cord. The corticospinal tract mediates discrete voluntary skilled movements. Clinical features of corticospinal tract dysfunction may include spasticity and weakness, particularly affecting the lower limbs, as well as hyperreflexia, clonus at the ankles and knees, and extensor plantar responses (Babinski response).
A condition characterized by patchy atheromas or atherosclerotic plaques which develop in the walls of medium-sized and large arteries and can lead to arterial stenosis with reduced or blocked blood flow.
Strictly speaking, atherosclerosis is a specific type of arteriosclerosis ('hardening of the arteries'), although the terms are sometimes used interchangeably in clinical jargon.
Sclerosis (hardening) of the arteries with increased thickness of the wall of arteries as well as increased stiffness and a loss of elasticity.
Although arteriosclerosis and atherosclerosis are often used as if they were synonyms, they are not. Atherosclerosis is the most common type of arteriosclerosis, and is caused by plaque building up in the vessel, which in turn causes sclerosis, increased stiffness, and loss of elasticity of the affected arteries.
An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor).
The World Health Organization (WHO) classifies neoplasms into four main groups: (i) benign neoplasm, (ii) in situ neoplasm, (iii) malignant neoplasm, and (iv) neoplasm of uncertain or unknown behavior. A malignant neoplasm is also known as cancer.
The presence of a nephroblastoma, which is a neoplasm of the kidney that primarily affects children.
Nephroblastoma is characterized by an abnormal proliferation of the metanephric blastema cells, which are believed to be primitive embryologic cells of the kidney. Clinically, nephroblastoma usually presents as an abdominal mass, and in some cases with abdominal pain, hypertension, hematuria, and fever.
An abnormality of the base of the skull, which forms the floor of the cranial cavity and separates the brain from other facial structures. The skull base is made up of five bones: the ethmoid, sphenoid, occipital, paired frontal, and paired parietal bones, and is subdivided into 3 regions: the anterior, middle, and posterior cranial fossae. The petro-occipital fissure subdivides the middle cranial fossa into 1 central component and 2 lateral components.
The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages.
Cortisol is the main member of the glucocorticoid family in humans and together with aldosterone is one of the main secretions of the adrenal cortex.
Failure of the immune system to protect the body adequately from infection, due to the absence or insufficiency of some component process or substance.
This category describes not-primarily structural lesions.
Any abnormality of bones of the arms or legs.
An abnormally increased phosphate concentration in the blood.
Microscopic hematuria detected by dipstick or microscopic examination of the urine.
An abnormally decreased magnesium concentration in the blood.
An abnormality of the cerebrospinal fluid (CSF).
The cerebrospinal fluid (CSF) is secreted by the choroid plexus, and flows uninterrupted throughout the central nervous system (the central cerebrospinal canal of the spinal cord and through the four interconnected cerebral ventricles in the brain).
The occurrence of an immune reaction against the organism's own cells or tissues.
Absence or underdevelopment of tissue in the central nervous system.
Absent/underdeveloped central nervous system tissue
Aplasia/Hypoplasia involving the central nervous system
Abnormality originating in one or more muscles, i.e., of the set of muscles of body.
An abnormally increased calcium concentration in the blood.
Reduction in the concentration of albumin in the blood.
An increased concentration of glucose in the blood.
An increased concentration of glucose in the urine.
Glycosuria, the excretion of abnormal amounts of glucose in the urine, generally results in osmotic diuresis.
An abnormality of the composition of urine or the levels of its components.
Abnormality of the homeostasis (concentration) of a monoatomic ion.
The presence of an abnormal decrease or increase of one or more amino acids in the blood circulation.
Abnormal circulating amino acid concentration
An abnormally decreased calcium concentration in the urine.
Abnormally increased serum levels of alkaline phosphatase activity.
Elevated circulating alkaline phosphatase concentration
A disorder of muscle unrelated to impairment of innervation or neuromuscular junction.
The diagnosis of myopathy is often confirmed on the basis of myopathic changes in muscle biopsy.
An increased concentration of tyrosine in the blood.
Abnormal increased size of the viscera of the abdomen.
Visceromegaly is enlargement of the internal organs in the abdomen, including liver, spleen, stomach, kidneys, or pancreas.
Abnormally reduced serum levels of alkaline phosphatase.
Any anomaly in the composite material or the layered arrangement of the bony skeleton.
An decreased level of renin in the blood.
An increased concentration of an amino acid in the urine.
Increased levels of animo acids in urine
Reduced amount of myelin in the central nervous system resulting from defective myelinogenesis.
A reduction of the ratio of renal calcium clearance to creatinine clearance to below 0.01.
Reduced ration of kidney calcium clearance to creatinine clearance
Reduced ration of renal Ca clearance to creatinine clearance
Reduced ration of renal Ca2+ to creatinine clearance
Reduced ratio of renal calcium clearance to creatinine clearance
Any abnormality of the soft tissues, including both connective tissue (tendons, ligaments, fascia, fibrous tissues, and fat).
Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later.
Onset of signs or symptoms of disease between 28 days to one year of life.
Onset of signs or symptoms of disease within the first 12 months of life.
Onset of signs or symptoms of disease between the age of 5 and 15 years.
Signs and symptoms begin before 15 years of age
The presence of foam cells, a type of macrophage that localizes to fatty deposits on blood vessel walls, where they ingest low-density lipoproteins and become laden with lipids, giving them a foamy appearance.
Foam cells may contain polymorphic cytoplasmic inclusions consisting of lamellar osmiophilic membranes on electron microscopy.
The age group in which disease manifestations appear.
Adolescent is defined by WHO as a person between 10-19 years of age.
A degree of kidney failure severe enough to require dialysis or kidney transplantation for survival characterized by a severe reduction in glomerular filtration rate (less than 15 ml/min/1.73 m2) and other manifestations including increased serum creatinine.
Equivalent with the National Kidney Foundation's definition of stage 5 chronic kidney disease.
A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms).
An abnormal increase or decrease of weight or an abnormal distribution of mass in the body.
Any structural anomaly of the vitreous body.
The vitreous humor is the clear gel that fills the space between the lens and the retina.
An abnormality of the anterior segment of the eyeball (which comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens).
Abnormality of the anterior segment of the eye
Abnormality of the anterior segment of the eyeball
Abnormality of the anterior segment of the globe
The anterior segment comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens.
Abnormal anterior eye segment morphology
Abnormal morphology of the posterior segment of the globe
Abnormality of the posterior segment of the eye
Abnormality of the posterior segment of the eyeball
Abnormality of the posterior segment of the globe
The posterior segment comprises the anterior hyaloid membrane and all of the optical structures behind it: the vitreous humor, retina, choroid, and optic nerve.
Abnormal posterior eye segment morphology
Any deviation from the normal concentration of a aromatic amino acid in the blood circulation.
Abnormality of aromatic amino acid family metabolism
Abnormal circulating aromatic amino acid concentration
Abnormality of the vitamin B12 metabolism
This term applies to all changes in bone mineral density which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. Changes may affect all bones of the organism, just certain bones or only parts of bones and include decreased mineralisation as may be seen in osteoporosis or increased mineralisation and or ossification as in osteopetrosis, exostoses or any kind of atopic calicfications of different origin and distribution. The overall amount of mineralization of the bone-organ can be measured as the amount of matter per cubic centimeter of bones, usually measured by densitometry of the lumbar spine or hip. The measurements are usually reported as g/cm3 or as a Z-score (the number of standard deviations above or below the mean for the patient's age and sex). Note that measurement with this method does not reflect local changes in other bones, and as such might not be correct with regard the hole bone-organ.
Abnormality of bone mineralisation and ossification
Any deviation from the normal concentration of a carboxylic acid in the blood circulation.
Carboxylic acid refers to an organic compound that contains a carboxyl group (-COOH).
Abnormal circulating carboxylic acid concentration
An abnormality of the balance or maintenance of the balance of acids and bases in bodily fluids, resulting in an abnormal pH.
Any deviation from the normal concentration of calcium in the blood circulation.
Abnormal circulating calcium concentration
Any deviation from the normal concentration of a nitrogen compound in the blood circulation.
Ammonia (NH3), one of the most clinically important nitrogen compounds in human metabolism, is a substance containing nitrogen resulting from the catabolism of protein. It is converted to the less toxic substance urea prior to excretion in urine.
Abnormal circulating nitrogen compound concentration
An abnormality of alkaline phosphatase level.
Abnormality of alkaline phosphatase activity
Note that the alkaline phosphatase family has four isoenzymes in humans, each of which additionally can have different isoforms. The primary clinical importance of measuring alkaline phosphatase is to check the possibility of bone disease or liver disease.
Abnormality of alkaline phosphatase level
A pathological narrowing in the region above the aortic valve associated with restricted left ventricular outflow.
An abnormality of the normal developmental rotation of the kidney leading to an abnormal orientation of the kidney.
The final kidney position in the renal fossa results from the rotation of the kidney with an orientation of the renal pelvis to the medial and the renal calyces to the lateral. Malrotation of the kidney can lead to orientation of the renal pelvis anteriorly, posteriorly and laterally. In most cases, renal malrotation does not cause any symptoms, but, hydronephrosis or stone formation can be observed as complications of renal malformation.
Acute renal failure with resolution of manifestations.
An abnormality of the normal developmental rotation of the kidney leading to an abnormal axial orientation of the kidney.
An increase in amplitude of waves returned in ultrasonography of the kidney, which is generally displayed as increased brightness of the signal.
Increased echogenicity of the renal parenchyma
Normal renal parenchyma is similar (isoechoic) or slightly darker (hypoechoic) compared with liver and includes the cortex and medulla. The thickness of the renal cortex is measured from the outer border of the medullary pyramids (yellow line) or from the arcuate arteries to the renal capsule. The medullary pyramids (white arrow) contain fluid in parallel tubules, which is anechoic (black) and appear as regularly spaced dark pools at the inner margin of the parenchyma (arrow). Because fat is echogenic, the central renal sinus appears bright.
Prominent glomerular basement membrane (GBM), reflecting an increase in thickness (subjective estimate) of the basal lamina of the glomerulus of the kidney.
Thickening of the glomerular basement membrane
This finding is demonstrated on renal biopsy.
The presence of calcium-containing calculi (stones) in the kidneys.
The overwhelming majority of renal calculi contain calcium.
A defect in the ability to concentrate the urine.
An impairment in renal concentrating ability can be easily recognized by the maximum concentrating ability (Umax) as determined by the urine osmolality reached after a fixed period of dehydration. Inability to maximally concentrate the urine is related to one or both of two basic tubular defects: 1) a failure of maximal free-water generation by the diluting segment in the ascending limb of Henle's loop; and 2) a failure of the distal tubular epithelium to achieve maximum permeability to water during water deprivation.
Acute inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules.
A reduction in the ability of the kidneys to remove uric acid from the serum.
Uric acid fractional excretion decreased
Cysts of microscopic size confined to the cortex of the kidney.
A developmental anomaly in which the kidneys are fused and localized on the same side of the midline. This anomaly is thought to result from disruption of the normal embryologic migration of the kidneys.
Obliteration of the glomerular capillary lumen by increased collagenous matrix, with or without hyalinosis or foam cells. Sclerosis involves 100% of the glomerular tuft. Relative to other patent glomeruli in the sample, glomerular size is preserved, or increased/decreased by no more than 50%.
Glomerular changes can be focal (only in some glomeruli) or diffuse (in all or almost all the glomeruli), and segmental (only a part of the glomerulus) or global (the entire glomerulus).
An abnormality of the renal collecting system.
Abnormality of the renal collecting system
Abnormal renal collecting system morphology
Chronic inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules.
Electron dense deposits at the glomerular basement membrane,
Membranoproliferative glomerulonephritis type II
Subendothelial electron-dense deposits are a characteristc feature of dense-deposit disease.
Glomerular subendothelial electron-dense deposits
Bicarbonate-wasting renal tubular acidosis
An abnormality of magnesium ion homeostasis.
An atrial arrhythmia characterized by disorganized atrial activity without discrete P waves on the surface EKG, but instead by an undulating baseline or more sharply circumscribed atrial deflections of varying amplitude an frequency ranging from 350 to 600 per minute.
Abnormal increased size of the posterior cranial fossa.
An anomaly of the form or number of cells in the bone marrow.
Abnormality of bone marrow cell morphology
The presence of many cysts in the kidney.
A reduction in the count of nephrons per kidney.
A lack of differentiation between renal cortex and medulla on diagnostic imaging.
Absent renal corticomedullary differentiation
Loss of corticomedullary differentiation
Absence of renal corticomedullary differentiation
Reduced differentiation between renal cortex and medulla on diagnostic imaging.
Loss of definition of corticomedullary differentiation
Reduced renal corticomedullary differentiation
Increased percent tubular reabsorption of phosphorus
Increased renal tubular phosphate reabsorption
Decreased renal tubular phosphate excretion
A type of proximal renal tubulopathy characterized by resorption defects leading to glycosuria, aminoaciduria, tubular proteinuria, renal hypophosphatemia, and urate tubular hyporeabsorption without bicarbonate loss.
A thrombotic microangiopathy with presence of non-immune, intravascular hemolytic anemia, thrombocytopenia and acute kidney injury. A vicious cycle of complement activation, endothelial cell damage, platelet activation, and thrombosis is the hallmark of the disease.
A progressive detrimental connective tissue deposition (fibrosis) on the kidney parenchyma involving the tubules and interstitial tissue of the kidney. Tubulointerstitial injury in the kidney is complex, involving a number of independent and overlapping cellular and molecular pathways, with renal interstitial fibrosis and tubular atrophy (IF/TA) as the final common pathway. However, IF and TA are separable, as shown by the profound TA in renal artery stenosis, which characteristically has little or no fibrosis (or inflammation). For new annotations it is preferable to annotate to the specific HPO terms for Renal interstitial fibrosis and/or Renal tubular atrophy.
This finding is usually shown by renal biopsy. Fibrosis involves an excess accumulation of extracellular matrix and usually results in loss of function when normal tissue is replaced with scar tissue. Tubulointerstitial renal fibrosis, characterized as a progressive detrimental connective tissue deposition on the kidney parenchyma, appears to be a harmful process leading inevitably to renal function deterioration, independently of the primary renal disease which causes the original kidney injury. Epithelial to Mesenchymal Transition (EMT) of tubular epithelial cells which are transformed to mesenchymal fibroblasts migrating to adjacent interstitial parenchyma constitutes the principal mechanism of renal fibrosis along with local and circulating cells. (PMID:20011086)
Any impairment of reabsorption of chloride by the kidney.
Impaired renal tubular reabsorption of chloride
DIsruption and breaking up of the basement membrane of the tubules of the kidney.
Disintegration of the tubular basement membrane
Throughout the rest of the nephron, tubule epithelial cells are attached to the tubular basement membrane that overlies the subjacent interstitial connective tissue. The disruption of cell-basement membrane adhesion results in loss of cell orientation, abnormal cell function, and can lead to tissue destruction.
Tubular basement membrane disintegration
A type of carcinoma of the kidney with origin in the epithelium of the proximal convoluted renal tubule.
Cancer starting in small tubes in kidneys
Renal cell carcinoma (also known as hypernephroma) is the most common form of kidney cancer arising from the proximal renal tubule. The tissue of origin for renal cell carcinoma is the proximal renal tubular epithelium. Renal cell carcinoma can be classified as 1) clear cell carcinoma, 2) papillary carcinoma, 3) chromophobe renal carcinoma, and 4) collecting duct carcinoma.
An abnormality of corticomedullary differentiation (CMD) on diagnostic imaging such as magnetic resonance imaging, computer tomography, or sonography. CMD is a difference in the visualization of cortex and medulla.
On T1-weighted magnetic resonance imaging, the signal intensity of the normal renal cortex is typically higher than medulla, resulting in easily visualized corticomedullary differentiation (CMD). Loss of CMD can be seen in disorders such as glomerulonephritis, acute tubular necrosis, end-stage chronic renal failure, obstructive hydronephrosis, and acute allograft rejection. Progressive corticomedullary differentiation (CMD) can be visualized as an echogenic cortex and a hypoechoic medulla. This CMD should be visible during the midtrimester sonographic evaluation.
Abnormal renal corticomedullary differentiation
Obstruction of the flow of urine through the ureter.
An abnormality of the islet of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. These are the alpha cells, which produce glucagon, the beta cells, which produce insulin and amylin, the delta cells, which produce somatostatin, the PP cells, which produce pancreatic polypeptide, and the epsilon cells, which produce ghrelin.
Abnormality of the pancreatic islet cells
A type of papillary renal cell carcinoma in which the papillae are covered by large eosinophilic cells with pleomorphic nuclei, prominent nucleoli, and nuclear pseudostratification.
Papillary renal cell carcinoma type 2 is a common feature of hereditary leiomyomatosis and renal cell cancer; HLRCC (OMIM 150800).
The presence of an adenoma in the cortex of the kidney.
The presence of a carcinoma in the renal pelvis.
The presence of renal cell carcinoma in the renal papilla.
A subtype of renal cell carcinoma thought to originate from mature renal tubular cells in the proximal tubule of the nehpron.
A benign renal neoplasm composed of fat, vascular, and smooth muscle elements.
Angiomyolipoma is a benign renal neoplasm composed of fat, vascular, and smooth muscle elements.
Absence or underdevelopment of the vermis of cerebellum.
Aplasia/Hypoplasia of the cerebellar vermis
Abnormal aggressive, impulsive or violent behaviour
Abnormal aggressive, impulsive or violent behavior
Atrophy/Degeneration affecting the central nervous system
The presence of atrophy (wasting) of the cerebrum, also known as the telencephalon, the largest and most highly developed part of the human brain.
Atrophy/Degeneration affecting the cerebrum
A tumor (abnormal growth of tissue) of the genitourinary system.
Abnormal development (dysgenesis) of the anterior segment of the eye globe. These structures are mainly of mesenchymal origin.
Anterior segment developmental abnormality
In anterior segment mesenchymal ocular dysgenesis (ASMOD), multiple tissues are affected, including the iris, cornea, and lens as well as the Schlemm's canal and trabecular meshwork drainage structures located at the anterior segment angle where the iris and cornea meet. These abnormalities may result from a primary defect in the migration and/or differentiation of the mesenchymal cells that contribute to development of the cornea, iris, and drainage structures.
Macular dystrophy is a nonspecific term for premature retinal cell aging and cell death, generally confied to the macula in which no clear extrinsic cause is evident.
Ocular abnormality characterised by premature degeneration of the vitreous and the retina that may be associated with increased risk of retinal detachment.
Absence or underdevelopment of the iris.
Absence or underdevelopment of the uvea, the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid.
Absence or underdevelopment of the anterior segment of the eye.
Aplasia/Hypoplasia affecting the anterior segment of the eye
The presence of one or more bullae on the skin, defined as fluid-filled blisters more than 5 mm in diameter with thin walls.
A bulla is a large vesicle described as a rounded or irregularly shaped blister containing serous or seropurulent fluid, equal to or greater than 10mm.
The presence of microscopic crystalline calcium precipitates in the form of oxalate and/or phosphate in the renal parenchyma.
The qualifier microscopic is used to indicate that the nephrocalcinosis cannot be observed on visual or radiologic examination without further magnification (as can macroscopic nephrocalcinosis).
A type of renal tubular acidosis characterized by a failure of acid secretion by the alpha intercalated cells of the cortical collecting duct of the distal nephron. The urine cannot be acidified below a pH of 5.3, associated with acidemia and hypokalemia.
Presence of persistent islands of renal blastema in the postnatal kidney. Nephroblastomatosis represents a complex abnormality of nephrogenesis and has been defined as the persistence of metanephricblastema into infancy and childhood.
Uric acid urolithiasis independent of gout
A type of extracapillary glomerulonephritis characterized by the formation of crescent-like cellular proliferation.
The presence of many cysts in the medulla of the kidney.
This feature is the cardinal sign of medullary cystic disease, also known as medullary sponge disease.
A developmental defect characterized by absence or poor development of proximal renal tubules.
Renotubular dysgenesis is generally accompanied by early onset and persistent oligohydramnios that leads to the Potter sequence.
Impaired histidine renal tubular absorption
Incomplete maturation or aberrant formation of the male gametes.
The presence of calcium- and oxalate-containing calculi (stones) in the kidneys.
Nephrotic syndrome with onset within the first three months of life.
Absence or underdevelopment of the kidney.
Coagulative necrosis of tubular epithelial cells, defined as cells with increased cytoplasmic eosinophilia and nucleus that has a condensed chromatin pattern with fuzzy nuclear contour or has barely visible nuclear basophilic staining. The extent of cortical tubular necrosis is scoredsemiquantitatively as none, mild (less than 25% tubules with necrosis), moderate (25-50 percent), and severe (over 50%).
Renal tubular epithelial necrosis is a histomorphological definition that corresponds to the clinical term of acture tubular necrosis. Acute death of renal tubular cells that usually results from prolonged renal ischemia, nephrotoxins, or sepsis. The clinical course of acute tubular necrosis may be divided into initiation, maintenance, and recovery phases.
A disordered proliferation of mature tissues that are native to the kidneys.
A unilateral form of atrophy of the kidney.
A unilateral form of developmental dysplasia of the kidney.
The presence of a partially duplicated kidney.
Any structural abnormality of the renal artery.
An abnormality of the axial skeleton, which comprises the skull, the vertebral column, the ribs and the sternum.
The presence of a neoplasm of the kidney.
Nephrosclerosis refers to thickening or scarring ("sclerosis") resulting from damage to the renal arterioles, also referred to as arteriosclerosis of the kidney arteries.
Distichiasis can be defined as the abnormal growth of lashes from the orifices of the Meibomian glands on the posterior lamella of the tarsal plate, resulting in a double row of eyelashes.
Stridor is a high pitched sound resulting from turbulent air flow in the upper airway.
A congenital anomaly characterized by the presence of supernumerary fingers or toes.
More than five fingers or toes on hands or feet
Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Although the word paralysis is often used interchangeably to mean either complete or partial loss of muscle strength, it is preferable to use paralysis or plegia for complete or severe loss of muscle strength, and paresis for partial or slight loss. Paralysis due to lesions of the principle motor tracts is related to a lesion in the corticospinal, corticobulbar or brainstem descending (subcorticospinal) neurons.
Paralysis due to lesions of the principle motor tracts
Weakness due to upper motor neuron dysfunction
Severe or complete weakness of both lower extremities with sparing of the upper extremities.
Weakness of both lower extremities with sparing of the upper extremities. Paraplegia refers to a severe or complete loss of strength, whereas paraparesis refers to a relatively mild loss of strength.
A disordered proliferation of mature tissues that is native to the site of origin, e.g., exostoses, nevi and soft tissue hamartomas. Although most hamartomas are benign, some histologic subtypes, e.g., neuromuscular hamartoma, may proliferate aggressively such as mesenchymal cystic hamartoma, Sclerosing epithelial hamartoma, Sclerosing metanephric hamartoma.
A cystic lesion originating within the brain.
An abnormally increased level of alkaline phosphatase, tissue-nonspecific isozyme in the blood.
Elevated alkaline phosphatase, liver/bone/kidney
Tissue non-specific alkaline phosphatase (ALPP) is one of four distinct but related alkaline phosphatases. Entrez Gene ID 249, Uniprot P05186 (PPBT_HUMAN). The gene is also known as alkaline phosphatase, liver/bone/kidney (ALPL).
Elevated tissue non-specific alkaline phosphatase
An abnormally increased level of kidney isoforms of alkaline phosphatase, tissue-nonspecific isozyme in the blood.
Elevated alkaline phosphatase of renal origin
An abnormally reduced level of kidney isoforms of alkaline phosphatase in the blood.
Low alkaline phosphatase of renal origin
An abnormal accumulation of fluid beneath the skin of the legs.
The presence of a neoplasm of the urinary system.
An abnormal level of a circulating protein in the blood.
Abnormality of circulating protein level
Any deviation from the normal concentration of tyrosine in the blood circulation.
Abnormal circulating tyrosine concentration
An abnormality of divalent inorganic cation homeostasis.
Abnormality of divalent inorganic cation homeostasis
Abnormal blood inorganic cation concentration
An abnormality of a nucleobase metabolic process.
This term is used to refers to abnormality in chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
Abnormal circulating nucleobase concentration
An abnormality of the upper urinary tract.
The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters.
An abnormality of the lower urinary tract.
The lower urinary tract is a subdivision of urinary system which consists of the urinary bladder and the urethra.
Mild pyelectasis is defined as a hypoechoic spherical or elliptical space within the renal pelvis that measures at least 5mm and not more than 10 mm. The measurement is taken on a transverse section through the fetal renal pelvis using the maximum anterior-to-posterior measurement.
The renal pelvis is the part of the kidney that collects urine. Fetal pyelectasis is a prenatal ultrasound finding that is diagnosed with enlargement of the renal pelvis from 4 to 10 millimeters. In many cases, fetal pyelectasis resolves spontaneously. Note that dilatation of the renal pelvis to more than 10 mm is referred to as severe pyelectasis or hydronephrosis. Measurements less than 5mm are normal, should not be designated as pyelectasis, and should not be reported (PMID:16100637).
The presence of dilatation of the renal pelvis.
The fourth ventricle is the cerebral ventricle that extends from the cerebral aqueduct to the obex, and is located within the pons and the upper part of the medulla oblongata.
A bilateral form of agenesis of the kidney.
A functional abnormality of the immune system.
A mode of inheritance that is observed for traits related to a gene encoded on the sex chromosomes.
An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often referred to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones.
This term may be merged with Increased bone density in the future or made obsolete.
An abnormality of the systemic arterial tree, which consists of the aorta and other systemic arteries.
Abnormality of the systemic arterial tree
The speed at which disease manifestations appear and develop.
An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
An abnormality of the concentration of glucose in the blood.
Abnormality of blood glucose concentration
An abnormality of the concentration of glucose in the urine.
Abnormality of urine glucose concentration
An abnormality of the gastrointestinal tract.
Abnormality of the gastrointestinal tract
Abnormal functionality of the cardiovascular system.
Abnormality of cardiovascular system physiology
Abnormal cardiovascular system physiology
The presence of hemorrhage within the body.
An abnormality of the regulation of body fluids.
The presence of amyloid deposition in one or more tissues. Amyloidosis may be defined as the extracellular deposition of amyloid in one or more sites of the body.
The medical literautre on amyloidosis is confused with clinical and histochemical designations used when the amyloid disease processes were poorly understood. To be designated an amyloid fibril protein, the protein must occur in tissue deposits and exhibit affinity for Congo red and green birefringence when viewed by polarisation microscopy.
An abnormality of the cortex of the kidney.
An altered ability of the kidneys to void urine and/or specific substances.
A reduction in the overall amount of urine output.
Any morphological abnormality of the skin.
A significant descent of the kidney as the patient moves from the supine to the erect position.
Nephroptosis is diagnosed if the descent of the kidney is greater than 5 cm or two vertebral bodies on intravenous urogram. The kidney is capable of moving back to the normal position, which differentiates it from an ectopic kidney, which constantly remains in an abnormal position. Nephroptosis may be asymptomatic or may cause symptoms including pain and intermittent ureteric obstruction with hydronephrosis, and ischemia due to elongation, narrowing, or kinking of a renal artery.
Any abnormality of the morphology of the major calices or minor calices of the kidney.
An abnormality of the skin adnexa (skin appendages), which are specialized skin structures located within the dermis and focally within the subcutaneous fatty tissue, comprising three histologically distinct structures: (1) the pilosebaceous unit (hair follicle and sebaceous glands); (2) the eccrine sweat glands; and (3) the apocrine glands.
Abnormality of the urinary system physiology
An abnormality of calcium concentration in the urine.
Abnormality of urine calcium concentration
An abnormality of the hindbrain, also known as the rhombencephalon.
The hindbrain consists of two main structures: The pons and the cerebellum.
An abnormality of the metencephalon. The metencephalon is the part of the hindbrain that consists of the pons and the cerebellum.
A morphological abnormality of a digit, i.e., of a finger or toe.
An abnormality of the skin that is not localized to any one particular region.
An abnormality of the function of the inner ear.
The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium.
An abnormality of myelination of nerves in the central nervous system.
In the CNS, myelin is the product of oligodendrocytes (and not of Schwann cells, as in the PNS). This term refers to an abnormality of the process in which myelin sheaths are formed and maintained around neurons or the result of such an abnormality.
An finding upon obstetric ultrasound examination performed at around 16 to 20 weeks of gestation that is abnormal but not clearly identifiable as a fetal anatomic malformation or growth restriction. Such findings are known as soft markers since they are associated with increased risk for fetal aneuploidy or other disorders.
The screening ultrasound at 16 to 20 weeks should evaluate 8 markers, 5 of which (thickened nuchal fold, echogenic bowel, mild ventriculomegaly, echogenic focus in the heart, and choroid plexus cyst) are associated with an increased risk of fetal aneuploidy, and in some cases with nonchromosomal problems, while 3 (single umbilical artery, enlarged cisterna magna, and pyelectasis) are only associated with an increased risk of nonchromosomal abnormalities when seen in isolation (PMID:16100637).
An anomaly of the control or production of movement in the central nervous system.
Cognitive, psychiatric or memory anomaly.
Onset of disease at the age of between 1 and 5 years.
This term refers to ages up to but not including the fifth birthday (see Juvenile onset).
A deviance in the normal connections between two cardiac segements.
Abnormal connexion of the cardiac segments
Discordant connection of the cardiac segments
Abnormal connection of the cardiac segments
An abnormality of the circulatory connection between the ventricles and the pulmonary artery and aorta.
The cardiac malformations with abnormal ventriculo-arterial connections in situs solitus and atrio-ventricular concordance include the tetralogy of Fallot as well as different forms of double-outlet right ventricle and transposition of the great arteries.
Defect or defects of the morphogenesis of the aorta and pulmonary arteries.
Congenital malformation of the great arteries
A functional abnormality of the adrenal glands.
A functional abnormality of the parathyroid gland.
Abnormality of the parathyroid physiology
Neoplasm categorized according to type of histological abnormality.
Neoplasm categorized according to the anatomical site of origin of the neoplasm.
The presence of an embryonal neoplasm of the kidney that primarily affects children.
Presence of persistent islands of renal blastema in the postnatal kidney, anywhere within a renal lobe (a portion of a kidney consisting of a renal pyramid and the renal cortex above it).
Abnormally persistent foci of embryonal immature blastema located in the superficial cortical region (perilobar).
A type of papillary renal cell carcinoma that is characterized by small cuboidal cells covering thin papillae with a single line of uniform nuclei and small nucleoli.
A renal tumor originating from an oncocyte, which is an epithelial cell characterized by an excessive amount of mitochondria, resulting in an abundant acidophilic, granular cytoplasm.
Renal oncocytoma is seen in Birt-Hogg-Dube syndrome (OMIM 135150).
A functional abnormality of a skeletal muscle.
A structural abnormality of a skeletal muscle.
An abnormality of the form, structure, or size of the skeletal system.
An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles.
Abnormal appendicular skeleton morphology
Any anomaly in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
All bones are formed by the replacement by osteocytes of mesenchyme-derived connective tissue. Intramembranous ossification refers to the direct replacement of primitive mesenchyme with bone, and is responsible for bones such as the calvarium (e.g., frontals, parietals, interparietal) and the clavicula. In endochondral ossification, the mesenchyme differentiates into a cartilaginous intermediate, which serves as a template (anlange) that is subsequently removed and replaced by bone. Most bones are formed via endochondral ossification, including those at the base of the skull, the vertebral column, pectoral and pelvic regions and long bones of the extremities. A reduction in the amount of mineralized bone compared with that expected for a given developmental age. In clinicakl parlance, reduced ossification and delayed ossification are often used synonymously, but in principle a bone delayed ossification in a child can display normal ossification at a later developmental stage. The HPO will therefore treat poor, reduced, and decreased officiation as synonymous, and delayed ossification as a specific kind of reduced ossification.
One or more digit that appears disproportionately short compared to the hand/foot, whereby either the entire digit or a specific phalanx is shortened.
Note that the term brachydactyly is reserved for specific patterns of short digits, see HP:0001156.
An infection of the upper or lower respiratory tract.
Absence of any measurable level of sperm in his semen, resulting from post-testicular obstruction or retrograde ejaculation. This can be differentiated from obstructive azoospermia on the basis of testicular biopsy.
An anomaly of the function of the pancreas.
A function abnormality of the endocrine pancreas.
Abnormality of endocrine pancreas physiology
Deviation from normal concentration of albumin in the blood.
Abnormality of multiple cell lineages in the bone marrow
An abnormal functionality of the kidney.
An abnormally increased or reduced amount of fluid filtered out of plasma through glomerular capillary walls into Bowman's capsules per unit of time.
Glomerular filtration, the first step in urine formation, is the passive process of ultrafiltration of plasma from blood into Bowman's space as it traverses the glomerular capillaries. Because GFR varies by body size, it is indexed relative to an average body surface area (BSA) of 1.73 m2 and expressed as ml/min/per 1.73 m2. GFR cannot be measured directly; it can be assessed from clearance measurements or estimated from serum levels of endogenous filtration markers, such as creatinine or cystatin C. Clearance measurements require either multiple measurements of serum concentrations or timed urine collections and are not routinely performed. GFR is usually estimated from serum concentrations of a marker of filtration using GFR estimating equations.
An abnormal reduction in the volume of fluid filtered out of plasma through glomerular capillary walls into Bowman's capsules per unit of time.
Renal clearance is defined as the volume of plasma per minute needed to excrete the quantity of a solute appearing in the urine in a minute. Normal values for adults are 97 to 137 ml/min (male) and 88 to 128 ml/min (female). This term refers to a reduction below normal limits in the ability of the kidney to clear creatinine from the bloodstream.
An abnormal rise in the volume of water filtered out of plasma through glomerular capillary walls into Bowman's capsules per unit of time.
A structural or developmental anomaly of any of the tissues involved in the genital system.
An inflammation of the kidney involving the parenchyma of kidney, the renal pelvis and the kidney calices.
Pyelonephritis may be unilateral or bilateral and is often characterized by abdominal pain, fever, nausea, and vomiting.
An anomaly in the processes involved in the maintenance of an internal equilibrium.
A structural anomaly of the globe of the eye, or bulbus oculi.
Edema (swelling) of the bulbar conjunctiva.
Concentration or activity of an enzyme is above or below the limits of normal in the blood circulation.
Abnormal circulating enzyme concentration or activity
The deposition of calcium salts in the parenchyma of the renal medulla (innermost part of the kidney).
The deposition of calcium salts in the parenchyma of the renal cortex (the outer portion of the kidney between the renal capsule and the renal medulla).
A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain.
Partial or complete wasting (loss) of brain tissue that was once present.
Any anomaly in the process by which myelin sheaths are formed and maintained around neurons.
An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
A type of proximal renal tubulopathy characterized by resorption defects leading to glycosuria, aminoaciduria, tubular proteinuria, renal hypophosphatemia, and urate tubular hyporeabsorption with bicarbonate loss and resulting acidosis.
Increased numbers of mesangial cells per glomerulus, defined as more than 3 nuclei fully surrounded by matrix in one or more mesangial areas, not including perihilar region, on a standard 3-micron-thick tissue section, best evaluated on periodic acid-Schiff (PAS) stain.
The presence of complement 3 deposits in the glomerulus.
Decreased thickness of the glomerular basement membrane (GBM), measured from endothelial to visceral epithelial plasma membrane and mainly attributable to a decrease in thickness of the lamina densa, generally to an overall thickness more than 2 standard deviations less than that of the normal mean GBM thickness for health age- and sex matched individuals. May be focal or diffuse, although the term thin GBMs generally implies thinning of over 50% of GBMs.
A type of glomerulonephropathy characterized by thickening of the basement membrane and deposition of immune complexes in the subepithelial space.
The presence of minimal changes visible by light microscopy but flattened and fused podocyte foot processes on electron microscopy in a person with nephrotic range proteinuria.
The presence of calcium- and phosphate-containing calculi (stones) in the kidneys.
A bilateral form of developmental dysplasia of the kidney.
A two-sided form of atrophy of the kidney.
Hematuria that is visible upon inspection of the urine.
A form of nephrotic syndrome that does not respond to treatment with steroid medication, defined as persistent proteinuria despite 60mg/m2 or 2mg/kg for 8 weeks, after insuring no infection or non-adherence to medication.
Genetic studies and biopsy are necessary. Treatment depends on result. Genetic forms are treated symptomatically with ACE-inhibitor or angiotensin receptor blockers. Non-genetic forms are usually treated with calcineurin inhibitors. Prognosis is worse than in SSNS. 50 % progress into end-stage renal disease.
A form of nephrotic syndrome that does not respond to any immunosuppresive treatment.
An abnormality in the concentration of electrolytes in the urine.
Abnormal urinary electrolyte concentration
An anomalous finding in the examination of the urine for cells.
Functional anomaly of the kidney persisting for at least three months.
A type of chronic kidney disease with normal or increased glomerular filtration rate (GFR at least 90 mL/min/1.73 m2).
Proteinuria is commonly seen in stage 1 chronic kidney disease.
A type of chronic kidney disease with mildly reduced glomerular filtration rate (GFR 60-89 mL/min/1.73 m2).
A type of chronic kidney disease with moderately reduced glomerular filtration rate (GFR 30-59 mL/min/1.73 m2).
A type of chronic kidney disease with severely reduced glomerular filtration rate (GFR 15-29 mL/min/1.73 m2).
High urine calcium in the presence of hypocalcemia.
A functional anomaly of the nervous system.
Abnormality of nervous system physiology
A structural anomaly of the nervous system.
Abnormality of nervous system morphology
Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
A abnormal increase in the inflammatory response to injury or infection.
Abnormal structure of the gastrointestinal tract.
Morphological abnormality of the GI tract
Morphological anomaly of the digestive system
Morphological abnormality of the gastrointestinal tract
Abnormal functionality of the gastrointestinal tract.
Functional abnormality of the gastrointestinal tract
A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.
The European Respiratory Society Task Force recommended two possible definitions of cough: (1) A three-phase expulsive motor act characterized by an inspiratory effort (inspiratory phase) followed by a forced expiratory effort against a closed glottis (compressive phase) and then by opening of the glottis and rapid expiratory airflow (expulsive phase);and (2) A forced expiratory manoeuvre, usually against a closed glottis and associated with a characteristic sound. The term Cough or any of its more specific descendents can be modified by the terms Acute (HP:0011009), Subacute (HP:0011011), and Chronic (HP:0011010). There is agreement that an actue cough lasts less than 3 weeks, a subacute cough from 3 to 8 weeks, and a chronic cough longer than 8 weeks.
A deviation from normal of the neurological development of a child, which may include any or all of the aspects of the development of personal, social, gross or fine motor, and cognitive abilities.
This term should be used to describe abnormalities with onset in the developmental period.
A type of nephrogenic rest associated with multiple lesions in the periphery of the renal lobe.
Perilobar nephrogenic rests are associated with Beckwith-Wiedemann syndrome (BWS) and hemi-hyperplasia.
A type of nephrogenic rest usually representing single lesions within the renal lobe, renal sinus, or calyceal walls.
Intralobar nephrogenic rests are associated WAGR (Wilms tumor-aniridia-genital anomalies-retardation) syndrome and Denys-Drash syndrome (DDS).
Inflammation of the connective and adipose tissues surrounding the kidney.
An abnormal functionality of the male genital system.
Abnormal male reproductive system physiology
Any deviation of the concentration of one or more proteins in the urine.
Abnormal structure of the basement membrane of the renal tubulus.
Abnormal tubular basement membrane morphology
Increase in thickness of the basement membrane of the tubulus of the kidney.
Thickening of the tubular basement membrane
Increased visceral epithelial cell size, with or without cytoplasmic protein droplets.
Glomerular visceral epithelial cell hypertrophy
Hypertrophy of visceral epithelial cells
Podocytes, also called visceral glomerular epithelial cells, are terminally differentiated cells that line the outer surface of the glomerular basement membrane. Podocytes prevent protein leakage into the urinary space, and also provide important tensile strength to the glomerular capillaries, by opposing the hydrostatic pressure from within. In contrast to glomerular endothelial and mesangial cells, podocytes do not typically proliferate. Studies have shown that following podocyte loss, the inability of podocytes to proliferate contributes to the development of glomerulosclerosis. Consequently, in order to cover the denuded glomerular basement membrane, podocytes increase in size due to hypertrophy. Although this is initially compensatory, podocyte hypertrophy is likely maladaptive, and contributes to glomerulosclerosis.
Tubulointerstitial infiltration of bacteria identified on routine and/or special (Brown-Hopps) stains.
Renal tubulointerstitial bacterial organisms
Tubulointerstitial bacteria can be ascending or vascuolcentric/blood-born. This finding can be associated with neutrophil rich infiltrates.
Tubulointerstitial bacterial infiltration
Tubulointerstitial infiltration of yeast or hyphal-microrganisms identified on routine and/or special (PAS, silver) stains.
Renal tubulointerstitial fungal organisms
Tubulointerstitial fungi be ascending or vascuolcentric/blood-born. This finding can be associated with necrotizing tubulointerstitial lesions.
Widening of the wall of capillary blood vessels in the glomerulus. This feature may be produced by deposits and other changes affecting either subepithelial and subendothelial regions or the glomerular basement membrane itself.
Thickening of glomerular capillary wall
A structural anomaly of the capillary blood vessels in the renal glomerulus.
Abnormalities of the glomerular capillary wall
Abnormal glomerular capillary morphology
Abnormal vascular morphology
Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus.
Abnormality of the digestive system
A functional anomaly of the digestive system.
Abnormality of digestive system physiology
A structural anomaly of the digestive system.
Abnormality of digestive system morphology
Passage of many stools containing blood.
Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea.
A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual.
Note that we use the preferred term label constitutional symptom because this reflects common usage, but we do not restrict the term or its descendents to the narrow meaning of symptom, i.e., a complaint related by a patient to a physician. There is no generally accepted classification of what defines a constitutional symptom, but examples include weight loss, fatigue, general weakness, night sweats, shaking, chills, fever, and vomiting.
Short-lived and not permanent. This term applies to a phenotypic abnormality that is temporary and of short duration.
Reduced dimension of the solid part of the kidney (parenchyma, the renal cortex and medulla) as measured from the collecting system (renal calyces and pelvis) to the border of the kidney. This measurement can be performed by measuring the thickness of the parenchyma in computed tomography scans.
The thickness of the renal parenchyma decreases with age. The thickness of the renal parenchyma is correlated with renal function.
Decreased renal parenchymal thickness
An abnormal polygonal shape of the calices of the kidney (which normally have a rounded or cup-shaped appearance).
Polygonal renal calices
Increased number of calices of the kidney.
Polycalycosis
A structural anomaly of the pyramid of the adult kidney, cone-shaped structures with a broad base adjacent to the renal cortex and the narrow apex that is termed papilla.
Abnormality of medullary pyramid morphology
Abnormal medullary pyramid morphology
Undergrowth of the pyramid of the adult kidney, cone-shaped structures with a broad base adjacent to the renal cortex and the narrow apex that is termed papilla.
Renal medullary pyramid hypoplasia
Hypercellularity due to increased number of cells within glomerular capillary lumina, causing narrowing of the lumina.
The endocapillary compartment of the glomerulus includes the endothelial cells, mesangial cells, and any leukocytes in the capillary lumens or mesangium.
Glomerular endocapillary hypercellularity
Hypercellularity (increased number of cells) in the renal glomerulus but external to the glomerular capillaries, i.e., in the Bowman space or more than one layer of parietal or visceral epithelial cells.
Extracapillary glomerular hypercellularity
Glomerular extracapillary hypercellularity
Any anomaly of the structure of the spleen.
Patchy or diffuse ischemic destruction of all the elements of renal cortex resulting from significantly diminished renal arterial perfusion. Coagulative necrosis may be present, involving all tubular segments and glomeruli. Nuclei may be pale and pyknotic, or may no longer be apparent. Thrombi may be present in vessels at the edge of the infarct.
Renal cortical necrosis is a type of actue kidney injury that results from insufficient perfusion of the renal cortex. Cortical necrosis commonly manifests clinically as a rapid loss of glomerular filtration rate, often with oliguria, granular casts, and low-level proteinuria. The key diagnostic features of renal cortical necrosis are (i) pale tissue with typical appearance of coagulative necrosis, affecting both tubules and glomeruli; (ii) pyknotic nuclei; and (iii) simplified, flattened epithelium of proximal tubules.
Renal cortical necrosis
A functional abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder.
A type of nephrotic syndrome in which complete remission (albumin urine dipstick negative/trace or proteinuria <4mg/m2/d or urinary protein to creatinine ratio <200mg/g (<20 mg/mmol) for 3 consecutive days) is achieved within initial 4 weeks of corticosteroid therapy.
Steroid-sensitive nephrotic syndrome
A type of steroid-sensitive nephrotic syndrome in which relapses occur at a frequency of one relapse (albumin urine dipstick at least 3+ or proteinuria over 40 mg/m2/d or urinary protein to creatinine ratio at least 2000 mg/g for 3 consecutive days) within 6 months of initial response, or one to three relapses in any 12-month period.
No biopsy needed. Relapses are treated with steroids according to local protocols.
Steroid-sensitive nephrotic syndrome with infrequent relapses
A type of steroid-sensitive nephrotic syndrome in which relapses occur at a frequency of two or more relapses (albumin urine dipstick at least 3+ or proteinuria over 40 mg/m2/d or urinary protein to creatinine ratio at least 2000 mg/g for 3 consecutive days) within 6 months of initial response or four or more relapses in any 12-month period.
Biopsy is necessary to determine underlying histology. Treatment with levamisole or immunosuppression (e.g. calcineurin inhibitors, cyclophosphamide or mycophenolat mofetil) in order to reduce steroid toxicity.
Steroid-sensitive nephrotic syndrome with frequent relapses
A type of nephrotic syndrome in which two consecutive relapses (albumin urine dipstick at least 3+ or proteinuria greater than 40 mg/m2/d or urinary protein to creatinine ratio at least 2000 mg/g for 3 consecutive days) occur during corticosteroid therapy, or within 14 days of ceasing therapy.
Steroid-dependent nephrotic syndrome
Presence of abnormal additional layers of the basement membrane of the glomerulus.
Lamellated/basket-woven thickened glomerular basement membranes
Lamellation of the glomerular basement membrane
Glomerular basement membrane lamellation
Presence of struvite (magnesium ammonium phosphate) containing calculi (kidney stones).
Inability of the kidneys to produce either concentrated or dilute urine.
Isothenuria is seen in the final stages of renal failure. It reflects rapid flushing of fluid through the tubules in renal failure as the number of functioning nephrons decreases; the normal concentrating (particularly) and diluting mechanisms of the kidney do not have time to function. The consequence is that the specific gravity of the urine becomes approximately the same as that of the glomerular filtrate.
Abnormal consumption of fluids with excessive or insufficient consumption of fluid or any other abnormal pattern of fluid consumption.
Note that this HPO term refers to an abnormal habit of drinking fluids but does not directly refer to an psychological disorder.
Glomerulomegaly is a histologic finding that can be present in idiopathic pulmonary hypertension, congenital cyanotic heart disease, morbid obesity associated with sleep apnea syndrome, sickle cell disease, and polycythemic states.
A collection of clotted blood surrounding the kidney.
The causes of a spontaneous perirenal hematoma (SPH) include immunologic disorders, neoplasms (renal cell carcinomas and adenomas), and collagen vascular diseases, but the main cause of a secondary perirenal hematoma is traumatic injury.
A malignant tumor that arises from the transitional (urothelial) epithelial cells lining the urinary tract from the renal calyces to the ureteral orifice.
A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
Any structural anomaly of the heart and great vessels.
Abnormality of cardiovascular system morphology
Abnormal cardiovascular system morphology
A fluid-filled sac (cyst) located within the central nervous system.
Cysts of CNS are usually maldevelopmental in nature, but in some cases are acquired. The recognition of these cysts radiologically and confirmation by pathology is essential for prognostic purposes.
Renal fibrosis is the consequence of an excessive accumulation of extracellular matrix that occurs in virtually every type of chronic kidney disease.
Partial or complete dissolution of the mesangial matrix, identified by reduced staining on a periodic acid-Schiff (PAS) or silver stain.
Dissolution or attenuation of mesangial matrix and degeneration of mesangial cells. In essence, mesangiolysis is an injurious process which affects the glomerular mesangium without causing obvious damage to the capillary basement membranes. The matrix swells, loosens, and eventually dissolves; the mesangial cells may show only edema and vacuolization, or may undergo severe degeneration and necrosis.
A high-pitched whistling sound associated with labored breathing.
Wheezes and rhonchi are continuous musical lung sounds. The American Thoracic Society (ATS) Committee on pulmonary nomenclature defines wheezes as high-pitched continuous sounds with a dominant frequency of 400 Hz or more, and rhonchi as low-pitched continuous musical sounds with a dominant frequency of about 200 Hz or less
An anomalous (adventitious) sound produced by the breathing process.
Abnormal breath sounds characterized by discontinuous clicking or rattling.
Abnormal breath sounds characterized by low-pitched, snoring or rattle-like sounds.
An anomaly of the pulse pressure, which is defined as the systolic pressured minus the diastolic pressure.
Increased amplitude of the pulse pressure (systolic blood pressure minus diastolic blood pressure).
An abnormal accumulation of protein in the glomerulus.
A structural anomaly affecting a blood vessel involved in the circulation of the heart, i.e., the superior or inferior vena cava, the pulmonary arteries, the pulmonary veins, and the aorta.
Abnormal morphology of the great vessels
A chronic deviation from normal pressure in the systemic arterial system.
The kidney contributes towards acid-base homeostasis by excreting H+ ions and retaining bicarbonate. This process is known as acidification of the urine. The pH of urine ranges normally from 4.5 to 8. The inability to reduce the pH of the urine in a situation where it would be otherwise expected is known as an acidification defect.
An accumulation of fluid in one or more of the perinephric spaces, which consist of the subcapsular, perirenal, anterior and posterior pararenal spaces. This abnormality can be demonstrated by cross-sectional imaging, particularly computed tomography.
Any anomolous structure of the renal corpuscle, which is the initial component of the nephron that filters blood. The renal corpuscle consists of a knot of capillaries (glomerulus) that is surrounded by a double-walled capsule (Bowman capsule) that opens into a renal tubule.
A structural anomaly of the double-walled capsule (Bowman capsule) that opens into a renal tubule.
Abnormal renal glomerular capsule morphology
Any structural anomaly of the podocyte, which is a highly specialized cell of the Bowman capsule and which forms multiple interdigitating foot processes. Podocytes are interconnected by slit diaphragms and cover the exterior basement membrane surface of the glomerular capillary.
Abnormal visceral epithelial cell morphology
Podocytes (or visceral epithelial cells) are terminally differentiated cells lining the outer surface of the glomerular capillaries. As a major component of the ultrafiltration apparatus, podocytes have a complex cellular architecture consisting of cell body, major processes that extend outward from their cell body, forming interdigitated foot processes that enwrap the glomerular capillaries.
Abnormal glomerular visceral epithelial cell morphology
An anomaly of podocyte morphology characterized by the loss of the interdigitating foot process pattern (generally called foot process effacement; FPE). The term FPE designates the loss of the usual interdigitating pattern of foot processes of neighboring podocytes, leading to relatively broad expanses of podocyte processes covering the glomerular basement membrane (GBM). It is widely viewed as a pathological derangement that is associated with leakage of macromolecules such as albumin through the glomerular filtration barrier.
Two stages of podocyte foot process effacement (FPE) may clearly be distinguished. Within the first stage, foot processes undergo tremendous changes in shape, losing their regular interdigitating pattern and retracting into short irregularly shaped cell projections. Slit diaphragms are lost or displaced from their usual position at the base and replaced by occludens-type junctions between the deformed, broadened foot processes. These changes are necessarily associated with considerable movements of these processes in relation to the glomerular basemenet membrane (GBM). The second phase, the completed stage of FPE, includes retraction of the foot processes into the primary podocyte cell processes, leading to broad flattened disc-like projections that cover the GBM, finally merging with the cell bodies. At this point, the cell bodies have lost their usual position floating above the GBM within the filtrate in Bowman space. Instead they broadly adhere directly to the GBM. The subpodocyte space beneath the podocyte cell body has largely disappeared in this stage.
Any functional abnormality of a cardiac valve.
An atherosclerotic lesion located in the renal artery.
The majority of viral infections acquired by nonimmunosuppressed individuals are asymptomatic or result in mild clinical manifestations. These individuals are able to mount effective immune responses that either clear the virus from the body or, for viruses that establish latency, maintain the virus in a dormant state. For individuals who are immunocompromised, because of a genetic immunodeficiency or immunosuppressive drug therapy, viral infections may result in life-threatening disease. Such patients present with infections that are severe, persistent, recurrent, or refractory to therapy and are usually caused by viruses of low virulence prevalent in the community.
An unusually severe adenovirus infection.
Adenoviruses can cause an array of clinical diseases, including conjunctivitis, gastroenteritis, hepatitis, myocarditis, and pneumonia. Most of these occur in children younger than the age of 5 years and are generally self-limiting illnesses.
The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual.
Any structural anomaly of the mouth, which is also known as the oral cavity.
The renal arteries carry blood from the aorta to the kidney; normally one renal artery is present on each side of the body. Renal artery duplication refers to the presence of two rather than one renal artery on a given side of the body.
Double renal arteries with aortic origin is a benign condition representing the persistence of the embryonic vessels, the lateral branches of the mesonephros, within the renal ascent. The embryonic urogenital ridge from which the kidneys develop is supplied by several paired arteries: the rete arteriosum urogenitale. The later developing metanephric kidneys retain only a single pair of mesonephric arteries, however a variable number may persist.
An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.
A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections.
A type of infection that is regarded as a sign of a pathological susceptibility to infection because of unusual severity or intensity of the infection.
An abnormal level of an analyte measured in the blood.
Abnormal circulating metabolite concentration
An abnormality in the function of the chemical reactions related to processes including conversion of food to enter, synthesis of proteins, lipids, nucleic acids, and carbohydrates, or the elimination of waste products.
Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension.
Circumferential fibrosis in the interstitium surrounding Bowman's capsule
Periglomerular fibrosis is characterized by glomeruli with open capillaries, but lamellated, frequently wrinkled, Bowman capsular basement membrane and circumferential layers of interstitial-type collagen around, within, or between the usually thickened, frequently lamellated, Bowman capsule basement membrane.
Any structural anomaly of the interstitium of the kidney. The renal interstitium is defined as the intertubular, extraglomerular, extravascular space of the kidney. It is bounded on all sides by tubular and vascular basement membranes and is filled with cells, extracellular matrix, and interstitial fluid.
Accumulation of foam cells (FC) in the interstitium of the kidney. Renal FCs display phenotypic characteristics of macrophages and belong to the monocyte/macrophage lineage. Histologically, renal FCs are characterized by round cells with small nuclei and an abundant PAS-positive cytoplasm with lipid-containing vacuoles.
FCs are the outcome of cellular lipid accumulation due to lipid metabolic dysfunction. Normally, lipid is in a dynamic equilibrium outside and inside of the cell. When factors facilitate cell lipid intake or reduce its efflux, it subsequently resulted in cellular lipid accumulation and FC formation. Renal interstitial FCs are commonly encountered in Alport syndrome and are occasionally observed in various other kidney diseases, including idiopathic membranous nephropathy (IMN), IgA nephropathy (IgAN), focal and segmental glomerulosclerosis (FSGS), and membranoproliferative glomerulonephritis.
Accumulation of foam cells (FC) in glomeruli of the kidney. Renal FCs display phenotypic characteristics of macrophages and belong to the monocyte/macrophage lineage. Histologically, renal FCs are characterized by round cells with small nuclei and an abundant PAS-positive cytoplasm with lipid-containing vacuoles.
Increased numbers of neutrophils in the interstitial tissues of the kidney.
Renal interstitial neutrophil infiltration
Increased numbers of eosinophils in the interstitial tissues of the kidney.
Renal interstitial eosinophil infiltration
Increased numbers of plasma cells in the interstitial tissues of the kidney.
Renal interstitial plasma cell infiltration
The presence of birefringent calcium- and oxalate deposits in interstitial cells of the kidney.
Infiltration of the renal tubular epithelium by lymphocytes.
Infiltration of the renal tubular epithelium by neutrophils.
Deposition of hemosiderin (a golden-brown, granular pigment derived from ferritin) in interstitial cells of the kidney.
Hemosiderin is an iron-containing, golden-brown, granular pigment derived from ferritin, the initial iron-storage protein. As iron accumulates within the cell, aggregates of ferritin molecules form hemosiderin. Upon hemolysis of red blood cells, hemoglobin alpha-beta dimers are released that, if unbound to haptoglobin, are filtered by the glomerulus and appear in the urine as hemoglobinuria. The hemoglobin dimers are taken up by renal proximal tubular cells and degraded and the free chelatable iron is stored as hemosiderin in the lysosomes. Hemosiderin deposition in kidney tubular cells has been reported in different types of hemolytic anemia including autoimmune hemolytic anemia and paroxysmal nocturnal hemoglobinuria and sickle cell anemia and after cardiac valve replacement with residual valvular regurgitation or perivalvular leak.
Naked basement membranes without tubular epithelium.
Renal tubular basement membrane denudation
Tubular cross section with a space between the basolateral aspect of tubular epithelium and its basement membrane; classified as global when at least 2/3 circumference of the tubular cross section are involved and segmental when less than 2/3 are involved.
Renal tubular epithelial cell detachment
Tubular cross section with intracytoplasmic vacuoles in at least one tubular epithelial cell. This feature is classified as isometric when vacuoles are round and similar in size and coarse when vacuoles were not round in shape or varied in size.
Renal tubular epithelial cell cytoplasmic vacuolization
At least one free floating cell in the tubular lumen without attachment to adjacent cells or basement membrane in a tubular cross section without detachment. These cells must not aggregate into a tubular shape and completely fill the lumen, if so, it should be classified as a cast.
Tubular cross section with round/irregular cytoplasmic protrusion, shaped like the Greek capital letter Omega (or it may be more vertically elongated Omega), pinched off from apical membrane without apparent closure of the lumen, involving over 50 percent of the tubular cells in cross section. The feature can be further classified into proximal or distal tubule.
Blebbing of apical cytoplasm of renal tubular epithelial cells
Any structural anomaly of the renal tubular epithelial cells (RTEC), a layer of cells in the outer layer of the renal tubule. These cells play a role in the absorption of substances such as glucose and amino from the primary urine.
Abnormal renal tubular epithelial morphology
Tubular epithelium with round strongly PAS-positive cytoplasmic droplet material in at least one tubular epithelial cell.
Renal tubular epithelial cell hyaline droplets
Tubular epithelial cells with greater than 3 nuclei in a single epithelial cell, often overlapping with each other in a single plane of view.
Multinucleation of renal tubular epithelial cells
Tubular epithelium with nucleoli clearly visible at 100-fold magnification.
Prominent nucleoli of renal tubular epithelial cells
Tubular cross section with flattened tubular cell cytoplasm (height unequivocally less than width), with complete loss of brush border involving greater than 50 percent of the tubular cells in cross section, resulting in an apparent increase in the size of the lumen, without the presence of casts.
Renal tubular epithelial cell simplification
Tubular epithelial cells in any mitotic phase, identified by distinctively visible chromosome in either prophase, metaphase, anaphase or telophase configuration.
At least one tubular epithelial cell with average sized cytoplasmic area and a nuclear area 3 times greater than average sized nuclei.
High N/C ratio of renal tubular epithelial cells
High renal tubular epithelial cell N/C ratio
Presence of increased amount of lipofuscin, a yellow, granular cytoplasmic pigment in the renal tubules.
Tubular cross section lined entirely by tubular epithelium with convex apical cell membrane (i.e., cells are shaped like an upside down U, and lack a distinct smaller protrusion seen in blebbing as defined above) resulting in apparent complete closure of the lumen.
A type of renal tubular atrophy characterized by a thyroid-like appearance, with small round tubules with markedly flattened, simplified epithelium and uniform intratubular casts.
A type of renal tubular atrophy characterized by endocrine-like appearance of tubules, which are small and have narrow lumina, clear cells, and relatively thin basement membranes.
Endocrinization pattern of tubular atrophy
Renal tubulointerstitial infiltration of mycobacteria identified on acid-fast or Fite stains. Can be associated with granulomatous inflammation.
Renal tubulointerstitial mycobacterial organisms
Tubulointerstitial mycobacterial infiltration
Tubular epithelial cells containing cytoplasmic hemosiderin, brown-golden granular pigment.
Renal tubular epithelial cells process reabsorbed urinary hemoglobin to hemosiderin.
Renal tubular epithelial cell hemosiderin
Deposition of amyloid in the interstitial tissue of the kidney. Amyloid is is made up of 10 nm (on average) fibrils that are most commonly composed of monoclonal light chains (AL), transthyretin (TTR), amd LECT2, or occur in the setting of long standing systemic inflammation.
Amyloid deposits located in the glomeruli in a focal segmental, diffuse segmental or diffuse global fashion. This abnormality can be accompanied by mesangial involvement and in later stages also involvement of the peripheral capillaries.
Accumulation of an immunoglobulin in the interstitial tissue of the kidney. The immunoglobulin may be a monoclonal Ig or the corresponding heavy-chain (HC) or light-chain (LC) subunit. By convention this definition excludes Ig-derived amyloidosis (amyloidosis can be distinguished by its affinity for Congo red staining).
Renal interstitial immunoglobulin deposition
Monoclonal immunoglobulin deposition is characterized by nonorganized electron-dense granular deposits predominantly localized in basement membranes of the kidney (other organs may additionally be affected). By light microscopy, tubular lesions are characterized by the deposition of a refractile, eosinophilic, periodic acid-Schiff (PAS)-positive, ribbon-like material along the tubular basement membrane. immunofluorescence examination of the kidney. Immunofluoerescence may show evidence of monotypic light or heavy chain fixation along tubular basement membranes. Electron microscopy can show finely to coarsely granular electron-dense deposits along the outer (interstitial) aspect of the tubular basement membranes.
Renal interstitial immunoglobulin deposits
A focal collection of 20 or more red blood cells within the interstitium, that is irregular in shape (i.e., collections do not conform to the shape of tubules or capillary networks), without surrounding endothelium or tubular epithelium, and is in an area of intact core.
Cell death (necrosis) affecting one or more parts of the kidney.
A perinephric abscess is a collection of suppurative material in the perinephric space (i.e., the connective and adipose tissues surrounding the kidney).
Detecting its presence can be diagnostically challenging because, in its chronic form, it usually develops insidiously, and in some cases its appearance can even simulate a renal tumor. The presence of a perinephric collection of purulent material around the kidneys occurs more often insidiously as a secondary phenomenon to upper tract urosepsis, classically in association with an infective staghorn renal calculus.
An encapsulated collection of pus and necrotic material within the renal parenchyma. The destruction of renal parenchyma is associated with suppurative/neutrophil-rich inflammation and necrosis.
Most renal abscesses are caused by gram-negative bacteria and are commonly caused by ascending infection associated with urologic abnormality, obstruction or calculi.
At least one tubular cross section with all tubular epithelial nuclei having a chromatin pattern resembling normal mature lymphocytes.
Condensed chromatin of renal tubular epithelial cells
Hyperchromasia of renal tubular epithelial cells
Dilatation (expansion beyond the normal dimension) of the cavity (lumen) of tubules of the kidney. The tubular cross section displays an attenuated brush border (apical PAS positivity greater than 10 percent of the normal expected height, but unequivocally less than normal expected height), resulting in an apparent increase in the size of lumen.
By definition, ,tubular luminal dilatation excludes simplifcation, which is defined as a tubular cross-section with flattened tubular cell cytoplasm (height unequivocally less than width), with complete loss of brush borderinvolving over 50 percent of the tubular cells in cross-section, resulting in an apparent increase in the size of lumen, without presence of casts.
Urinary casts are formed in the distal convoluted tubule or the collecting duct by solidification of protein in the lumen of the kidney tubules. This term refers to casts located within the tubuli of the kidney. More precisely, casts are defined as a material that completely fills and expands the tubular lumen with simplification of surrounding tubular epithelium. Casts are classified as either nuclear debris/granular brown material, red blood cell, white blood cell, myeloma, or myoglobin cast.
Casts can be subsequently eliminated via the urine and may be seen by microscopy of the urine sediment, which should be coded separately using an appropriate term from the Cylindruria subhierarchy (HP:0012615). Intratubular casts may have various compositions with different morphologic and staining characteristics. Both hyaline and granular casts may be observed in a number of renal diseases. Commonly observed casts are hyaline (eosinophilic, homogeneous proteinaceous) casts associated with increased glomerular permeability such as with chronic progressive nephropathy and granular (necrotic cellular debris) casts.
A type of acelluar intratubular casts that have a surface composed of granules, which can vary in size. On H&E (red brown), PAS (amaranth purple), trichrome (red with ragged contours), Hall (olive-emerald green).
Casts that contain red blood cells and are located within the tubuli of the kidney.
Intratubular casts composed of vancomycin aggregates and uromodulin.
The casts appear as nonspecific proteinaceous casts within the tubular lumenss on light microscopy. Immunostaining can be used to confirm the presence of vancomycin.
Casts that contain white blood cells and are located within the tubuli of the kidney.
Intratubular crystals composed of 2,8-dihydroxyadenine are small needle-shaped brownish crystals that are highly birefringent under polarized light and black by Jones methenamine silver.
The presence of casts containing immunoglobulin light chains within the lumina of the renal tubules.
This feature can be ascertained by (i) Light microscopy: The biopsy shows chronic tubulointerstitial nephritis with fractured casts that first involve the distal tubules. The casts have a metachromatic appearance due to their mixed composition of light chain (Bence-Jones) and Tamm-Horsfall (uromodulin) proteins. Surrounding cellular reaction can extend to formation of syncytial giant cells, and in the early phase may be a polymorphonuclear granulocyte reaction. (ii) Immunofluorescence microscopy: Monoclonal staining of casts for either kappa or lambda light chains confirm the diagnosis, but clonal staining may be absent in some cases. Staining of formalin-fixed paraffin-embedded material after pronase digestion may unmask clonal staining in some of these cases. (iii) Electron microscopy: Glomeruli are unremarkable, and casts show granular electron-dense material. Crystalline substructure may be seen within these light chain casts. In rare cases, deposits of amyloid may form on the surface of the casts.
A type of acelluar intratubular casts that have a surface composed of granules, which can vary in size. The granules can be rather heterogeneous, ranging from fine (finely granular cast) up to coarse (coarsely granular cast), dark, clear, and pigmented. On H&E (red granular), PAS (purple), trichrome (red granular), Hall (yellow brown). Stain positively for Hemoglobin A.
Premature death of cells in the renal papilla (the apex of a renal pyramid which projects into the cavity of a calyx of the kidney and through which collecting ducts discharge urine). Histologically, one observes pale tissue with typical appearance of coagulative necrosis, affecting the renal papillae. Necrosis can be identified by pyknotic nuclei and simplified, flattened epithelium of proximal tubules. The tubular and glomerular basement membranes are still visible without viable nuclei.
A type of acellular urinary cast located within the distal tubules of the kidney and that is composed only of Tamm-Horsfall glycoprotein. Correspondingly, these casts have a low refractive index. Hyaline casts may display a spectrum of morphologies, which includes fluffy, compact, convoluted or wrinkled casts. Hyaline casts have a smooth texture and usually have parallel sides with clear margins and blunted ends.
Intratubular Tamm-Horsfall (uromodulin) casts
Casts located within the tubuli of the kidney and that contain myoglobin. Myoglobin casts are composed of round granules that may line up in chains or aggregate in clusters. Their color ranges from pink to red-brown with hematoxylin and eosin stain, light brown to black with Jones methenamine silver stain, pink to bright magenta with periodic acid-Schiff stain, and bright red with trichrome stain. Immunoperoxidase staining with antibody to myoglobin is stronglypositive in the casts.Electron microscopy shows globular casts with an electron-dense core and a somewhat less-intense periphery. Substructure is absent. This feature may be accompanied by acute tubular injury with variable flattening of tubular epithelial cells, loss of brush borders, and intratubular sloughed epithelial cells.
Infiltration of microorganisms into renal tubulointerstitial tissues as observed by appropriate staining procedures, e.g., bacteria on a bacterial stain (Brown and Hopps) or fungi on PAS or silver stain.
Tubulointerstitial microganismal infiltration
Infiltration of viruses into renal tubulointerstitial tissues as demonstrated on renal biopsy by viral inclusions which can be seen on routine stains or with immunohistochemistry.
Renal tubulointerstitial viral inclusions
Edema is characterized but the acute swelling of the stroma, with expansion of the interstitial space without the a concurrent increase in interstitial cells or extracellular matrix. Histologically this change is appreciated as interstitial areas of lower optical density.
Interstital aggregates of histiciocytes, occasionally multinucleated with associated lymphoplasmacytic and occasionally eosinophilic inflammation. Organization can range from poorly-to-well defined and multinucleated giant cells may be present.
An organized collection of histiocytes (specifically macrophages) localized in the interstitial tissue of the kidney. Through light microscopy, the activated histiocytes appear as epithelioid cells with round to oval nuclei, often with irregular contours and abundant granular eosinophilic cytoplasm with indistinct cell borders. They may also coalesce to form multinucleated giant cells. Granulomas may be associated with a peripheral cuff of lymphoplasmacytic and occasionally eosinophilic inflammation. Organization can range from poorly-to-well defined. Granulomas can present as necrotizing or non-necrotizing. Microscopically, necrotizing granulomas distinctly have central necrosis with a palisaded lymphohistiocytic reaction and a cuff of chronic inflammation.
Renal interstitial necrotizing granulomata
Granulomatous inflammation is a distinctive form of chronic inflammation produced in response to various infectious, autoimmune, toxic, allergic, and neoplastic conditions.
Renal interstitial necrotizing granulomas
Interstital aggregates of histiciocytes, occasionally multinucleated with associated lymphoplasmacytic and occasionally eosinophilic inflammation. Organization can range from poorly-to-well defined and multinucleated giant cells may be present with no necrosis.
Renal interstitial non-necrotizing granulomata
Renal interstitial non-necrotizing granulomas
Abnormal accumulation of a metabolite, protein, or protein-derived substance in the interstitial region of the kidney.
Presence of interstitial mononuclear leukocytes, i.e., white blood ceclls with a single round nucleus, including lymphocytes and monocytes but not including granulocytes (which have multilobed nuclei).
Renal interstitial mononuclear cell infiltration
Inflammation of interstitial tissues of the kidney consisting of foamy macrophages admixed with plasma cells, lymphocytes and neutrophils and occasional giant cells.
Renal interstitial xanthogranulomatous inflammation
Increased apoptosis (programmed cell death) of tubular epithelial cells. The cells arre rounded with increased eosinophilia and contain fragmented, densely basophilic nuclear debris.
The presence of cuboidal to columnar epithelium (height greater than width) lining the Bowman capsule, in an absence of adjacent segmental sclerosis, crescents, or collapsing variant of focal segmental glomerulosclerosis; scored as present or absent in at least one glomerulus.
Histopathological findings of inflammation of the renal interstitium potentially involving fibrotic as well as non-fibrotic areas, composed of lymphocytes, monocytes, plasma cells.
Histopathological findings of inflammation of the renal interstitium involving fibrotic as well as non-fibrotic renal cortex, composed of lymphocytes, monocytes, plasma cells.
Renal cortical interstitial inflammation
Histopathological findings of inflammation of the interstitium of the renal medulla, composed of lymphocytes, monocytes, plasma cells.
Renal medullary interstitial inflammation
The accumulation of collagen and related extracellular matrix (ECM) molecules in the interstitium of the kidney. The interstitium is expanded by the presence of collagen that stain blue on trichrome. Tubules are not back to back, but rather separated by fibrosis and can be atrophic.
Tubular atrophy (TA) is defined as loss of specialized transport and metabolic capacity and typically manifested by small tubules with cells with pale cytoplasm or dilated, thin tubules. TA is usually associated with IF, but probably has distinct mechanisms related to blood flow, glomerular filtration rate (GFR) or tubular continuity loss. However, IF and TA are separable, as shown by the profound TA in renal artery stenosis, which characteristically has little or no fibrosis (or inflammation).
The presence of interstitial aggregates of purple finely granular/laminated calcium- and phosphate deposits.
Renal interstitial calcium phosphate deposits
Abnormal structure or form of the lumen (opening) of kidney tubules.
Abnormal renal tubular luminal morphology
Viral cytopathic changes consist of smudgy basophilic intranuclear inclusions with enlarged nuclei of infected cells. Distal tubules are more commonly involved than proximal tubules. There is associated acute tubular injury, often with frank tubular necrosis and destruction, with acute interstitial nephritis, often with a pleomorphic infiltrate composed of lymphocytes, histiocytes, plasma cells, and variable numbers of neutrophils, with interstitial edema and hemorrhage. Tubular destruction may be associated with necrotizing interstitial granulomas. Severe granulomatous tubulointerstitial nephritis appears to be characteristic of adenoviral infection and is quite rare in other viral infections. Focal wedge-shaped necrosis may occur in renal parenchyma. Immunostaining for adenovirus shows strong nuclear and cytoplasmic staining in infected cells.
A type of renal tubular atrophy in which the tubules show thick tubular basement membranes lined by small cuboidal or flat cells. Generally accompanied by fibrosis.
Characteristic intranuclear glassy-appearing basophilic inclusions with surrounding halo (owl's eye-type inclusion) and marked increase in the size of the cell (cytomegaly), particularly in tubular epithelial cells and in endothelial cells. Often accompanied by cytopathic changes including patchy interstitial pleomorphic infiltrate with lymphocytes, plasma cells, and macrophages.
Renal tubular cytomegalovirus inclusions
Viral cytopathic changes consist of smudgy basophilic intranuclear inclusions with enlarged nuclei of infected cells. The inclusions stain positive for adenovirus (e.g., Figure 3 of PMID:29273157). Distal tubules are more commonly involved than proximal tubules. Occasionally glomerular visceral and parietal epithelial cells can be infected. There is associated acute tubular injury, often with frank tubular necrosis and destruction, with acute interstitial nephritis, often with a pleomorphic infiltrate composed of lymphocytes, histiocytes, plasma cells, and variable numbers of neutrophils, with interstitial edema and hemorrhage.
Renal tubular nuclear inclusions have a ground-glass appearance with irregular central clearing, or a coarse, vesicular appearance. Distal tubules are involved more often than proximal tubules. There may be only medullary involvement in early stages, and parietal epithelial cells may be involved in later stages of the infection. Infected epithelial cell nuclei stain with antibody to the large T antigen of the SV40 virus, which serves as a surrogate marker of human polyomavirus infection.
The inclusions are generally accompanied by a patchy pleomorphic interstitial infiltrate with lymphocytes, plasma cells, and occasional neutrophils with associated interstitial edema, tubulitis, and tubular injury. Infected tubular epithelial cells have enlarged nuclei with amorphous inclusions. Polyomavirus infection occurs in the transplanted allograft kidney and in the native kidney of immunosuppressed patients, and is usually related to BK virus (80%), JC virus (10%-20%), and less frequently simian virus 40 (SV40).
Renal tubular nuclear inclusions that stain positive for herpes simplex virus (HSV). HSV is typically associated with multinucleated giant cells with nuclear inclusions and may cause hemorrhagic interstitial nephritis.
Renal tubular herpes simplex virus inclusions
The presence of dysmorphic urinary erythrocytes. This feature can be observed by phase-contrastmicroscopy, differential interference microscopy, and bright-field microscopy. The acanthocyte or G1 cell, which is a doughnut-shaped cell with one or more blebs, is reported to constitute a special form of dysmorphic erythro-cyte (D cell) specific for glomerular hematuria.
Birefringent calcium- and oxalate-containing casts located within the tubuli of the kidney.
Purple and finely granular/laminated calcium- and phosphate-containing casts located within the tubuli of the kidney.
Dilated renal tubules (over twice the diameter of a normal proximal tubule) containing eosinophilic amorphous material. This feature is generally accompanied by scalloping of the cast profile. The epithelium lining the microcyst is generally flattened and does not reveal brush border.
A renal cyst characterized by epithelium lined space (squamous/columnar) with septations.
Accumulation of globotriaosylceramide (GL-3) in kidney tissues, which can be quantified as the number of globotriaosylceramide (GL-3) inclusions/kidney interstitial capillary (KIC).
Fabry disease is a rare, progressive lysosomal disorder caused by mutations in the GLA gene. GLA encodes the homodimeric glycoprotein, alpha-galactosidase A, which acts in lysosomes to degrade globotriaosylceramide (GL-3) and its deacylated form, globotriaosylsphingosine (lyso-Gb3). In Fabry disease, the activity of alpha-galactosidase A is deficient or absent, leading to progressive accumulation of glycolipids, primarily GL-3 and lyso-Gb3, in the plasma and numerous cell types throughout the body.
Renal interstitial globotriaosylceramide inclusions
An increased number of IgG4+ plasma cells in the interstitial space of the kidney.
IgG4-related tubulointerstitial nephritis is characterized by an increased number of IgG4+ plasma cells per high-power field on renal biopsy in addition to either elevated serum IgG4 or evidence of extra renal IgG4-related disease.
Renal interstitial IgG4+ plasma cell infiltration
An elevated level of a proteinogenic amino acid in the blood circulation. These are the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine.
Abnormal circulating proteinogenic amino acid concentration
An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body.
Abnormality of the musculoskeletal system
Anomalous echogenicity of the kidney on ultrasound examination.
For diagnostic ultrasonography, high-frequency sound waves are generated and received by the ultrasonography transducer, which is placed on the skin. Returning sound waves (echoes) are processed by a computer and displayed on a computer screen. A gray-scale image is produced when the ultrasonography machine operates in B-mode, or brightness mode, in which returning echoes are represented as bright dots; the brightness of the dots represents the strength of the reflected echoes. Echogenicity, therefore, refers to how bright or dark something appears in the gray-scale image; the brighter something appears, the more echogenic it is. With regard to the kidney, echogenicity generally refers to how bright or dark the kidney parenchyma appears in comparison to the liver.
Increased echogenecity of the medullary region of the kidney.
Increased echogenicity of the kidney parenchyma results from the increased presence of material that can reflect sound waves back, thus increasing its brightness on the ultrasonography image. Because fibrous tissue (e.g., glomerulosclerosis, interstitial fibrosis) increases echogenicity, CKD is typically associated with increased echogenicity. Inflammatory infiltrates may explain the increased echogenicity that occurs with acute interstitial nephritis and GN. Proteinaceous casts are thought to cause the increased echogenicity associated with acute tubular necrosis (ATN). Calcium deposits and stones are very echogenic; thus, medullary nephrocalcinosis is characterized by increased medullary echogenicity and a relatively normal-appearing cortex. Several renal diseases are associated with medullary nephrocalcinosis, including medullary sponge kidney, hyperparathyroidism, renal tubular acidosis, and vitamin D toxicity. Other kidney diseases that have been associated with a hyperechoic medulla include sickle cell disease and gout
Increased echogenecity of the kidney cortex.
Blockage (obliteration) of the capillary lumen by increased extracellular collagenous matrix, with or without hyalinosis or foam cells.
Obliterative abnormality of the renal glomerulus
Accumulation of amorphous, eosinophilic, glassy, periodic acid-Schiff (PAS)-positive, silver-negative material in the glomerulus. Distribution can include vascular pole, perihilar, tip or neither tip, perihilar or vascular.
Hyalin is a smooth, glassy-appearing, amorphous material resulting from the accumulation of serum proteins.
Accumulation of amorphous, eosinophilic, glassy, periodic acid-Schiff (PAS)-positive, silver-negative material in the glomerulus at the vascular pole/perihilum.
Accumulation of amorphous, eosinophilic, glassy, periodic acid-Schiff (PAS)-positive, silver-negative material in the glomerulus at the tip/tubular pole.
Glomerular hyalinosis at the tubular pole
Accumulation of amorphous, eosinophilic, glassy, periodic acid-Schiff (PAS)-positive, silver-negative material in the glomerulus at neither tip nor perihilar/vascular poles. Both the vascular and the tubular pole are present in the glomerular cross section.
Glomerular hyalinosis away from the vascular and tubular poles
Any structural abnormality of the parietal epithelial cells that line the inside of Bowman's capsule and form an inconspicuous sheet of flat epithelial cells in continuity with the proximal tubular epithelial cells at the urinary pole and with the podocytes at the vascular pole.
Abnormal glomerular parietal epithelial cell morphology
Increased number of parietal epithelial cells lining Bowman's capsule. Hyperplasia leads to the cells being present in 2 or more layers, often with crowding and multilayering.
Hyperplasia of the glomerular parietal epithelial cell
Glomerular parietal epithelial cell hyperplasia
An abnormality of the glomerular parietal epithelial cells characterized by (1) Increased parietal epithelial cell size, with or without cytoplasmic protein droplets; or (2) enlarged nuclei with prominent nucleoli. Both features can be present
Hypertrophy of the glomerular parietal epithelial cell
Glomerular parietal epithelial cell hypertrophy
An insudative accumulation of amorphous, eosinophilic, periodic acid-Schiff (PAS)-positive, silver-negative material protruding from Bowman's capsule into the urinary space. Although not always evident by light microscopy, this material is located between Bowman's capsule and the parietal epithelial cells, in some cases associated with newly formed matrix material.
Capsular hyaline drops within Bowman's capsule
An area of basement membrane continuity between the glomerular tuft and Bowman's capsule, without intervening crescent and not adjacent to an area of segmental sclerosis.
Abnormal number of its constituent cells of the mesangium of the glomerulus of the kidney.
Abnormal glomerular mesangial cellularity
Any structural anomaly of the glomerular matrix. Mesangial cells generate and embed in their own extracellular matrix. The mesangial matrix is different in composition from the glomerular basement membrane. Its constituents are type IV collagen (but only the alpha1 and alpha2 chains); type V collagen; laminin A, B1, and B2; and considerable amounts of fibronectin, heparan sulfate and chondroitin sulfate proteoglycans, entactin, and nidogen. Furthermore, small amounts of the proteoglycans decorin and biglycan are found in the mesangial matrix.
Abnormal glomerular mesangial matrix morphology
Mesangial immune deposit located adjacent to the paramesangial glomerular basement membrane.
Extracellular mesangial accumulation of moderately electron-dense, generally homogenous, amorphous-appearing extracellular material.
Detachment of visceral epithelial cells (podocytes) from underlying glomerular basement membrane with intervening new loose basement membrane material (pale on Hematoxylin and eosin, periodic acid-Shiff, trichrome, or silver stain) forming a so-called 'halo'.
Separation from GBM without intervening immune deposits. See Figure 5d of PMID:32866505.
Cytoplasmic projections into the urinary space from the luminal side of the podocyte.
Layer of hypertrophied visceral epithelial cells overlying a sclerosed segment of the tuft of the glomerulus.
Increase in diameter of a segment of the renal artery that can be defined as a focal, isolated dilatation of all three layers of the arterial wall over 1.5 times the diameter of the disease-free proximal adjacent arterial segment.
Lamellated intracytoplasmic lipid inclusions within podocytes.
Visceral epithelial cell hyperplasia with resulting cellular crowding of the the urinary space. In contrast with true crescents, these proliferations lack inflammatory cells and fibrin. The cells are typically plump (not spindle-shaped) and often vacuolated, and Bowman's capsule is usually intact.
Abnormal structural characteristics of the interior space of the capillary of the renal glomerulus.
Abnormal glomerular capillary lumen morphology
Wrinkling and folding of the capillaries without epithelial cell (podocyte) hyperplasia (formerly called ischemic type of collapse) involving o 80% of the glomerular tuft. The wrinkling is generally made by small regular folds of the glomerular basement membrane.
Collapse is generally accompanied by other descriptors such as hypertrophy and hyperplasia of overlying glomerular epithelial cells, halo, protein droplets in podocytes and glomerular parietal epithelial cells (PECs).
Wrinkling and folding of the glomerular basemement membrane (GBM) with partial or complete occlusion of the capillary lumen: wrinkling and folding of the GBM with partial or complete occlusion of the capillary lumen. The wrinkling is generally made by small and/or big irregular folds of the GBM.
Global distention of glomerular capillaries with intraluminal intact red blood cells.
Glomerular capillary dilatation due to loosening/detachment of the glomerular basement membrane (GBM) from its anchoring points, usually in the context of mesangiolysis or nodular glomerulosclerosis.
An abnormal structure of the glomerular endothelial cells, which are highly specialized cells with fenestrae and a charged luminal glycocalyx layer that contribute to the filtration barrier.
Abnormal glomerular endothelial cell morphology
Loss of round to oval discontinuities normally present in the glomerular capillary endothelial cell cytoplasm.
Loss of glomerular endothelial cell fenestration
Enlargement of glomerular endothelial cells by cytoplasmic swelling with resulting partial or complete occlusion of the lumen.
Inter-anastomosing tubular structures located within cisternae of endoplasmic reticulum, most often within endothelial cells and associated with exposure to interferon.
Glomerular endothelial tubuloreticular inclusion
Fibrin associated with glomerular basement membrane disruption and/or lysis of the mesangial matrix; this lesion does not require the presence of karyorrhexis.
Any abnormal sttructure of the glomerular basement membrane.
The (GBM) is an integral component of the glomerular filtration barrier; an important and highly complex capillary wall that is exposed to mechanical forces driven by capillary hydrostatic pressure. This barrier is permeable to water and small molecules, and selectively withholds cells and macromolecules such as albumin in the circulation.
Abnormal glomerular basement membrane morphology
Prominent glomerular basement membrane (GBM) reflecting a segmental and increase in thickness (subjective estimate) with no evidence of electron dense deposits by EM. Thickening is measured from endothelial to visceral epithelial plasma membrane and mainly attributable to an increase in thickness of the lamina densa, generally to an overall thickness more than 2 standard deviations greater than that of the normal mean GBM thickness for health age- and sex matched individuals.
Segmentally thickened glomerular basement membrane
Prominent glomerular basement membrane (GBM) reflecting an diffuse and relativly uniform increase in thickness (subjective estimate) with no evidence of electron dense deposits by EM. Thickening is measured from endothelial to visceral epithelial plasma membrane and mainly attributable to an increase in thickness of the lamina densa, generally to an overall thickness more than 2 standard deviations greater than that of the normal mean GBM thickness for health age- and sex matched individuals.
Diffusely thickened glomerular basement membrane
Prominent glomerular basement membrane (GBM) reflecting an increase in thickness (subjective estimate) with no evidence of electron dense deposits by electron microscopy.
Thickened glomerular basement membranes with no electron dense deposits
Thickened glomerular basement membranes with electron dense deposits
Lucent zones within the glomerular basement membranes. May reflect remote/resolved deposits.
This feature can be observed on silver staining or electron microscopy.
Delicate, silver positive projections that extend at right angles from the glomerular basement membrane (GBM) out into the urinary space, creating an irregular GBM profile.
Irregular folding of the glomerular basement membrane with an intact lamina densa.
Wrinkling and folding of the glomerular basement membrane (GBM) without glomerular epithelial cell hypertrophy and hyperplasia (formerly known an ischemic type of collapse). The urinary space is patent. The wrinkling is generally made by small regular infoldings of the GBM.
Expansion of the space between the glomerular endothelium and lamina densa by electron-lucent material.
Apoptotic, pyknotic, and fragmented nuclei within the glomerulus.
An aggregate of coagulated blood containing fibrin, with or without entrapped cellular elements, within a glomerular capillary lumen.
Intracapillary amorphous, eosinophilic material consisting of immune deposits.
Intracapillary silver-positive material that is finely vacuolated and laminated, and stains with oil red O on frozen sections.
Extracellular meangial accumulation of finely granular material corresponding to immunoglobulin and/or complement by immunofluorescence/immunohistochemistry; most typically electron-dense although this may decrease with resorption of the deposit.
Visceral epithelial cells with 2 nuclei. Can be observed on light or ultrastructral microscopy.
Visceral epithelial cells with more than two nuclei. Can be observed on light or ultrastructral microscopy.
Multinucleated visceral epithelial cells
Structural anomaly located in Bowman's space, which represents the beginning of the urinary space and is contiguous with the proximal convoluted tubule of the nephron.
Bowman's capsule is a part of the nephron that forms a cup-like sack surrounding the glomerulus. The capsule encloses a space called Bowman's space, which represents the beginning of the urinary space and is contiguous with the proximal convoluted tubule of the nephron. Bowman's capsule, Bowman's space, and the glomerular capillary network and its supporting architecture can collectively be thought of as composing the glomerulus.
Acellular collagenous matrix within Bowman's space, not associated with extracapillary hypercellularity or necrosis, associated with sclerosis or deflation of the tuft.
Increased number of visceral epithelial cells (2 or more layers), often with crowding and multilayering, but without continuity with the parietal epithelium.
Hyperplasia of visceral epithelial cells
Round to ovoid, Periodic acid-Schiff (PAS)-positive, fuchsinophilic cytoplasmic inclusions within visceral epithelial cells.
Glomerular crescent refers hyperplastic lesions involving 10% or more of the circumference of Bowman's capsule. Crescents can be composed of a variable mixture of epithelial/leukocyte hypercellularity, fibrous matrix, and fibrin.
The crescent is an unspecific histopathological lesion that can be triggered by a variety of different underlying disorders. Whenever, microvascular injury leads to rupture of the glomerular basement membrane (GBM), the leakage of plasma proteins drives parietal epithelial cell hyperplasia as the key cellular component of the crescent. Single nephron GFR decreases because of tuft collapse, rupture of the Bowman capsule, and influx of immune cells and fibroblasts are all secondary events that may or may not occur in individual glomeruli. Periglomerular immune cell infiltrates or fibrotic encasting of the activated parietal cells (fibrocellular crescents) are subsequent events that may affect the dynamics and prognosis of the disease.
A type of glomerular crescent characterized by extracapillary hypercellularity of greater than two cell layers and involving more than 10% of the capsular circumference, composed of greater than 75% cells with or without fibrin, and less than 25% fibrous matrix.
A type of glomerular crescent characterized by extracapillary hypercellularity of more than 2 cell layers and involving over 10% of the capsular circumference, composed of 25% to 75% cells with or without fibrin, and the remainder fibrous matrix.
A type of glomerular crescent characterized by extracapillary fibrosis composed of greater than 75% matrix and of less than 25% cells with or without fibrin, usually associated with disruption of Bowman's capsule and involving over 10% of the capsular circumference.
Loss of mesangial cells segmentally or globally.
Mesangial cell loss can be observed in the setting of mesangiolysis.
Globally sclerotic glomeruli are that are small and without hyalinosis and may appear with collapse of the tuft with collagenization of the urinary space. Bowman's capsule is completely or partially absent and there is no periglomerular fibrosis and glomerular size is decreased by more than 50% compared to all other glomeruli in the same biopsy. Obsolescent glomeruli may appear to be receding into the interstitium.
Double contouring of the original glomerular basement membrane (GBM)/additional layer(s) of overlying basement membrane matrix, with or without endocapillary hypercellularity and no evidence of interposed migrated cells (mesangial, endothelial, monocytes) between the layers of original GBM and de novo GBM.
Glomerular capillary wall duplication without cellular interposition
Double contouring of the original glomerular basement membrane (GBM)/additional layer(s) of overlying basement membrane matrix with interposed migrated cells (mesangial, endothelial, monocytes) between the layers of original GBM and de novo GBM.
Glomerular capillary wall duplication with cellular interposition
Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein).
Any deviation from the normal concentration of a metabolite in urine.
As water reabsorption in kidneys affect urinary solute concentrations, various methods are applied to normalize the measured concentration. Frequently, concentrations are reported as a ratio to urinary creatinine. The HPO terms in this subhierarchy therefore use the word 'level' to indicate that appropriate normalization has been performed before concluding that the amount of the indicated metabolite is abnormal.
Presence of ropey, eosinophilic material (brght red on Trichrome staining) consistent with extracapillary fibrin outside of capillary lumina.
Extracapillary fibrin can be associated with glomerular basement membrane (GBM) disruption. In this context, the word aextracapillary refers to abnormalities seen in Bowman's space outside of the GBM.
The presence of eosinophilic Periodic Acid Schiff (PAS)-positive cell free, protein-derived material occupying Bowman's space.
Folding of cytoplasmic processes of podocytes into the glomerular basement membrane (GBM) with thickening of the lamina densa and microspheres and/or microtubular structures within the GBM.
See Figure 3d of PMID:32393263 and Figures 1 and 2 of PMID:33276871 for examples.
A point of rupture in the glomerular basement membrane (GBM) where the discontinuous portions of GBM are still identifiable with a basement membrane stain such as Periodic acid Schiff (PAS) or silver.
Disruption of the glomerular basement membrane
Disruption of the glomerular basement membrane (GBM) may occur in settings of inflammation (ANCA/antiGBM antibodies) or could be seen due to structural weakness of the GBM (Collagen IV disorders). This feature can be associated with extracapillary fibrin. The definition of this term intends to exclude glomeruli at the edge of the core where rupture could be iatrogenic or mechanical.
Anomalous appearance or structure of the surface of the glomerular basement membrane.
Abnormal glomerular basement membrane texture
Punctate electron-dense material typically in a band-like distribution along the lamina rara interna and within tubular basement membranes within the subendothelial aspect of the glomerular basement membrane.
Glomerular basement membranes with powdery deposit
Glomerular basement membranes powdery deposit
Increased number of leukocytes internal to the glomerular basement membrane (GBM), but not limited to within glomerular capillaries.
Glomerular endocapillary hypercellularity consisting of leukocytes
The optimal demonstration of leukocytes may require immunohistochemistry.
Glomerular endocapillary leukocyte hypercellularity
Increased number of neutrophils internal to the glomerular basement membrane (GBM), but not limited to within glomerular capillaries.
Glomerular endocapillary neutrophil hypercellularity
Presence of lipid-filled cells, often a macrophage, with a vacuolated appearance in the glomerulus often occupying the endocapillary space.
Glomerular endocapillary foam-cell hypercellularity
A generalized global (over 80%) increase of mesangial matrix that is present throughout the mesangial stalk (with or without associated mesangial hypercellularity).
Reorganization of podocyte cytoskeletal proteins at the glomerular basement membrane (GBM) aspect of the cell, with associated cytoplasmic electron density at the GBM aspect of the podocyte.
Increased mesangial extracellular material with interspace width of over 2 mesangial cell nuclei, in one or more peripheral mesangial areas.
Amyloid spicules are projections of typically silver-positive material from the outer aspect of the glomerular capillary wall, perpendicular to the glomerular basement membrane (GBM), most often caused by amyloidosis with the latter confirmed by additional stains.
Glomerular basement membrane amyloid spicule
Segmental solidification of the glomerular tuft by increased extracellular matrix, causing glomerular capillary obliteration and can include hyalinosis, foam cells, hypertrophy of overlying glomerular epithelial cells, podocyte depletion, halo and adhesion of the tuft to the Bowman capsule.
Segmental solidification of the glomerular tuft by increased extracellular matrix, causing glomerular capillary obliteration is present at the vascular pole, involving less than 50% of the tuft. It can be accompanied by other descriptors such as hyalinosis, foam cells, hypertrophy of overlying glomerular epithelial cells, podocyte depletion, halo and adhesion of the tuft to the Bowman's capsule.
Segmental glomerulosclerosis, perihilar pattern
Segmental solidification of the glomerular tuft characterized by an adhesion at the tip of the glomerular tuft abutting the proximal tubular taek-off can be accompanied by increased extracellular matrix, causing glomerular capillary obliteration at the glomerular tip. Features including hyalinosis, foam cells, hypertrophy of overlying glomerular epithelial cells can also be observed.
Segmental glomerulosclerosis, tip variant
Tip variant segmental glomerulosclerosis
Segmental solidification of the glomerular tuft characterized by increased extracellular matrix, causing glomerular capillary obliteration at neirhter the tubular or vascular poles. Features including hyalinosis, foam cells, hypertrophy of overlying glomerular epithelial cells can also be observed.
Segmental glomerulosclerosis away from the vascular and tubular poles
Electron-dense deposits in the lamina densa with a ribbon or a sausage structure.
See Figure 1 of PMID:33329990 for an example.
Glomerular basement membrane electron dense deposits
Electron dense deposits in the glomerular basement membrane (GBM) subendothelial space associated with a prominent GBM reflecting an increase in thickness. This feature can be associated with GBM remodeling along the endothelial aspect.
The glomerular filtration barrier consists of two cells (podocytes and endothelial cells) and the glomerular basement membrane (GBM), a specialized extracellular matrix that lies between them.
Subendothelial glomerular basement membrane electron dense deposits
Prominent glomerular basement membrane (GBM) reflecting a diffuse and relativly uniform increase in thickness (subjective estimate) with exogenous material deposited between the outer (epithelial) aspect of the GBM and the visceral epithelial cell, with varying degrees of incorporation into the GBM.
Subepithelial glomerular basement membrane electron dense deposits
Extracellular mesangial accumulation of slender proteinaceous fibers.
Extracellular mesangial aggregates composed of randomly arranged, straight, non-branching fibrils that are thicker than amyloid fibrils (average diameter about 20 nm) and are often admixed with smudgy, electron-dense material.
Unbranched noncollagenous microfibrils within the mesangial matrix, composed of proteins not present within the glomerular basement membrane (GBM), most notably fibrillin-1, that attach to mesangial cells and GBM structural proteins.
Extracellular mesangial aggregates composed of non-branching fibrils, focally parralel over 30 nM in diameter. The term immunotactoid refers to highly organized immune depositions appearing as rod-like microtubular structures in ultrastructural examination.
Extracellular mesangial aggregates composed of fine, randomly oriented, non-branching fibrils 8-12 nm in diameter, often forming a cottony mass.
Lobular, round to oval mesangial lesions with an acellular hyaline/matrix core surrounded by compressed mesangial nuclei.
Nodular mesangiosclerosis is a pattern that can be observed together with mesangolysis but may also occur independently and so should be coded separately.
Large branching stones that fill part of all of the renal pelvis and renal calyces and they can be complete or partial depending on the level of occupancy of the collecting system.
Fibrillar deposits located between the outer (epithelial) aspect of the glomerular basement membrane (GBM) and the visceral epithelial cell, with varying degrees of incorporation into the GBM. This feature is associated with a prominent GBM reflecting an diffuse and relatively uniform increase in thickness (subjective estimate).
Fibrillar glomerular subepithelial deposits
A type of fibrillar glomerular subepithelial deposit characterized by extracellular aggregates composed of fine, randomly oriented, non-branching fibrils 8-12 nm in diameter, often forming a cottony mass. This feature is associated with a prominent glomerular basement membrane (GBM) reflecting an diffuse and relativly uniform increase in thickness (subjective estimate).
Glomerular amyloid subepithelial deposits
A type of fibrillar glomerular subepithelial deposit characterized by extracellular aggregates of randomly arranged, straight, non-branching fibrils that are thicker than amyloid fibrils (average diameter about 20 nm) and are often admixed with smudgy, electron-dense material. This feature is associated with a prominent glomerular basement membrane (GBM) reflecting an diffuse and relativly uniform increase in thickness (subjective estimate).
Fibrillary glomerular subepithelial deposits
A type of glomerular subepithelial deposit characterized by finely granular material deposited between the outer (epithelial) aspect of the glomerular basement membrane (GBM) and the visceral epithelial cell, with varying degrees of incorporation into the GBM and corresponding to immunoglobulin and/or complement by immunofluorescence/immunohistochemistry. This feature is associated with a prominent GBM reflecting an diffuse and relativly uniform increase in thickness (subjective estimate).
Glomerular subepithelial immune-complex deposits
A type of glomerular subepithelial deposit characterized by a moderately electron-dense, generally homogenous, amorphous-appearing extracellular material located between the outer (epithelial) aspect of the glomerular basement membrane (GBM) and the visceral epithelial cell, with varying degrees of incorporation into the GBM. This feature is associated with a prominent GBM reflecting an diffuse and relativly uniform increase in thickness (subjective estimate).
Glomerular hyaline subepithelial deposits
Deposits located between the outer (epithelial) aspect of the glomerular basement membrane (GBM) and the visceral epithelial cell, with varying degrees of incorporation into the GBM. This feature may be associated with a prominent GBM reflecting an diffuse and relativly uniform increase in thickness (subjective estimate).
Glomerulus showing markedly and irregularly thickened capillary walls with massive fuchsinophilic subendothelial deposits, resulting in narrowing of capillary lumina. This feature is said to resemble a wire loop.
Lupus nephritis is a type of glomerulonephritis that constitutes one of the most severe organ manifestations of systemic lupus erythematosus. Lupus nephritis is subclassified in six distinct classes, that represent different manifestations and severities of renal involvement and guide the therapeutic management.
A subclass of lupus nephritis with active or inactive diffuse, segmental or global endocapillary or extracapillary glomerulonephritis involving at least 50% of all glomeruli, typically with diffuse subendothelial immune deposits, with or without mesangial alterations.
A subclass of lupus nephritis with purely mesangial hypercellularity of any degree or mesangial matrix expansion by lightmicroscopy, with mesangial immune deposits. A few isolated subepithelial or subendothelial deposits may be visible by immunoflourescence or electron microscopy, but not by light microscopy.
A subclass of lupus nephritis with normal glomeruli by light microscopy, but mesangial immune deposits by immunofluorescence.
A lupus nephritis subclass with global or segmental subepithelial immune deposits or their morphological sequelae by light microscopy and by immunofluorescence or electron microscopy, with or without mesangial alterations. May occur in combination with class III or IV, in which case both classes are diagnosed. May show advanced sclerosis
A subclass of lupus nephritis with active or inactive focal, segmental or global endocapillary or extracapillary glomerulonephritis involving less than 50% of all glomeruli, typically with focal subendothelial immune deposits, with or without mesangial alterations
A subclass of lupus nephritis with at least 90% of glomeruli globally sclerosed without residual activity.
Decreased renal tubular reabsorption of magnesium.
96% of filtered magnesium is reabsorbed in the tubule. 10%-30% of the filtered magnesium is absorbed in the proximal tubule, the thick ascending limb absorbs 40%-70% of filtered magnesium.
Impaired renal tubular reabsorption of magnesium
Xanthogranulomatous pyelonephritis is a granulomatous inflammatory infiltrate composed of neutrophils, lymphocytes, plasma cells, xanthomatous histiocytes, and multinucleated giant cells.
Xanthogranulomatous pyelonephritis is an uncommon chronic destructive granulomatous process of renal parenchyma in association with long-term urinary tract obstruction and infection.
Decreased renal tubular reabsorption of uric acid.
Uric acid excretion rate is the product of the filtered load (which can be approximated as plasma ultrafilterable urate multiplied by tge glomerular filtration rate) and fractional excretion of urate (FEUA), which represents the percentage of filtered urate that is excreted in the final urine.
Impaired renal tubular reabsorption of uric acid
Anomalous structure of a blood vessel in the kidney.
An anomalous structure of an artery located in the kidney.
Abnormal kidney arterial blood vessel morphology
Anomalous structure of the arc-shaped arteries located at the border of the renal cortex and renal medulla.
Abnormal structure of a vein located inside the kidney parenchyma.
Any structural anomaly of the arcuate vein. The arcuate veins cross traverse along the corticomedullary junction (at the border of the kideny cortex and medulla).
Any structural anomaly of the interlobular veins of the kidney. An interlobular vein is surrounded by the renal cortex and located between renal lobules (consisting of the nephrons surrounding a single medullary ray and draining into a single collecting duct).
Any structural anomaly located in the the inside space of the interlobular veins of the kidney.
Abnormal morphology of the interlobular vein lumen
Abnormal interlobular vein lumen morphology
Needle-like or slit-like clefts within the interior space of interlobular veins. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cholesterol emboli within interlobular vein lumen
Mixture of fibrin, red blood cells, platelets partly or completely occluding vascular lumen of the interlobular veins of the kidney.
Intraluminal thrombi within interlobular veins
Thrombi containg fibrous tissue and capillary-like vascular channels located within the lumen of the interlobular veins of the kidney.
Organized thrombi within interlobular vein lumen
Anomalous structure of the capillaries that are derived from the efferent arteriole, forming a capillary network that surrounds the distal portions of the nephron tubule,
Abnormal peritubular capillary morphology
Anomalous structure of the peritubular capillaries located in the cortex of the kidney.
Abnormal cortical peritubular capillary morphology
Duplicated basement membranes of the peritubular capillaries located in the cortex of the kidney and arranged in multiple concentric layers.
Multilamellation of basement membranes within cortical peritubular capillaries
Multilamellation of cortical peritubular capillary basement membranes
Inflammation of the peritubular capillaries in the cortex of the kidney characterized by Inflammatory cells in over 10 percent of the interstitial capillaries in the cortex with at least some capillaries having three or more luminal cells.
Abnormal structural characteristics of the interior space of the peritubular capillary in the cortex of the kidney.
Abnormal cortical peritubular capillary lumen morphology
Anomalous structure of the peritubular capillaries located in the medulla of the kidney.
Abnormal medullary peritubular capillary morphology
Inflammation of the peritubular capillaries in the medulla of the kidney characterized by Inflammatory cells in over 10 percent of the interstitial capillaries in the cortex with at least some capillaries having three or more luminal cells.
Substantially increased numbers of red blood cells within capillaries surrounding tubules in the medulla of the kidney. This feature is assessed in histological images as the presence of numerous erythrocytes in a segment of the capillary such that the vessel appears to be congested (not open).
Medullary peritubular capillary erythrocyte congestion
Duplicated basement membranes of the peritubular capillaries located in the medulla of the kidney and arranged in multiple concentric layers.
Multilamellation of basement membranes within medullary peritubular capillaries
Multilamellation of medullary peritubular capillary basement membranes
Abnormal structural characteristics of the interior space of the peritubular capillary in the medulla of the kidney.
Abnormal medullary peritubular capillary lumen morphology
Needle-like or slit-like clefts within the interior space of peritubular capillaries located in the medulla of the kidney. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cholesterol emboli within the medullary peritubular capillary lumen
Medullary peritubular capillary lumen cholesterol emboli
Mixture of fibrin, red blood cells, platelets partly or completely occluding the vascular lumen of the peritubular capillaries located in the medulla of the kidney.
Intraluminal thrombi within medullary peritubular capillaries
Medullary peritubular capillary intraluminal thrombi
Thrombi containg fibrous tissue and capillary-like vascular channels located within the lumen of the peritubular capillaries of the medulla of the kidney.
Organised thrombi within the medullary peritubular capillary lumen
Organized thrombi within the medullary peritubular capillary lumen
Medullary peritubular capillary lumen organized thrombi
Needle-like or slit-like clefts within the interior space of peritubular capillaries located in the cortex of the kidney. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cortical peritubular capillary lumen cholesterol emboli
Mixture of fibrin, red blood cells, platelets partly or completely occluding the vascular lumen of the peritubular capillaries located in the cortex of the kidney.
Intraluminal thrombi within cortical peritubular capillaries
Cortical peritubular capillary intraluminal thrombi
Thrombi containg fibrous tissue and capillary-like vascular channels located within the lumen of the peritubular capillaries of the cortex of the kidney.
Cortical peritubular capillary lumen organized thrombi
Abnormal structural characteristics of the interior space (lumen) of the arcuate vein of the kidney.
Needle-like or slit-like clefts within the interior space of arcuate veins of the kidney. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cholesterol emboli within arcuate vein lumen
Mixture of fibrin, red blood cells, platelets partly or completely occluding the vascular lumen of the arcuate veins of the kidney.
Intraluminal thrombi within arcuate veins
Thrombi containg fibrous tissue and capillary-like vascular channels located within the lumen of the arcuate veins of the kidney.
Organised thrombi within arcuate vein lumen
Organized thrombi within arcuate vein lumen
Any structural anomaly located in the inner or middle layer of the arcuate veins of the kidney.
Abnormal arcuate vein intima/media morphology
Accumulation of edematous extracellular matrix in the inner layer (intima) of arcuate veins of the kidney. The material resembles mucus and appears pale blue on hematoxylin and eosin staining.
Intimal mucoid edema within arcuate veins
Intimal mucoid oedema within arcuate veins
Accumulation of myxoid material (mucus-like material) within the inner or middle layer of the arcuate vein of the kidney.
Myxomatous change within arcuate vein intima/media
Arcuate vein intimal/medial myxomatous degeneration
Amorphous extracellular substance in the inner or middle layer of the arcuate veins of the kidney. Amyloidosis stains Congo-red positive with typically an apple green birerfingence on polarization microscopy, and 8-12 nm fibrils on electron microscopy.
Amyloidosis within arcuate vein intima/media
Any structural anomaly of the radial arteries that branch off at right angles from the arcuate artery and carry blood toward the cortex of the kidney.
Abnormal cortical radial artery morphology
Abnormal structural characteristics of the interior space of the cortical radial arteries of the kidney.
Abnormal interlobular arterial lumen morphology
Abnormal cortical radial artery lumen morphology
Needle-like or slit-like clefts within the interior space of cortical radial arteries (interlobular arteries) of the kidney. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cortical radial artery lumen cholesterol emboli
Anomalous structure of the inner or middle layer of the arc-shaped arteries located at the border of the renal cortex and renal medulla.
Abnormalities of the arcuate arterial intima/media
Abnormal arcuate artery intima/media morphology
Amorphous extracellular substance in the glomerular, interstitial or vascular compartments of the interlobular arteries of the kidney. Congo-red positive with typically an apple green birerfingence on polarization microscopy, and 8-12 nm fibrils on electron microscopy
Amyloidosis within interlobular arterial intima/media
Interlobular arterial intima/media amyloidosis
Cortical radial artery intimal/medial amyloidosis
Any structural anomaly of the inner or middle layer of the cortical radial arteries (also known as interlobular arteries) of the kidney.
Abnormalities of the interlobular arterial intima/media
Abnormal cortical radial artery intima/media morphology
Any structural anomaly of the glomerular arterioles. The interlobar arteries of the kidney branch into arcuate arteries, cortical radiate arteries, and then into afferent arterioles. After passing through the renal corpuscle, the capillaries form the efferent arteriole. The afferent and efferent arterioles are difficult to distinguish histologically and are thus both included in this term and its descendents.
Renal blood flow originates at the hilum of the kidney through the renal artery. From the segmental artery to the interlobar artery, blood arrives parallel to the corticomedullary junction in the arcuate artery. This gives rise to the interlobular arteries that radiate toward the surface. Afferent arterioles branch off which ultimately leads into the glomerulus of Bowman's capsule. From here, efferent arterioles begin to form the venous system and subdivide into another set of capillaries known as the peritubular capillaries. Blood then leaves the kidney and enters the venous circulation. However, efferent arterioles that are located above the corticomedullary border travel downward into the medulla. They further divide into vasa recta which surround the Loop of Henle.
Abnormal structural characteristics of the interior space (lumen) of renal arterioles.
Abnormal renal arteriole lumen morphology
Needle-like or slit-like clefts within the interior space of arterioles of the kidney. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cholesterol emboli within the arteriolar lumen
Renal arteriolar lumen cholesterol emboli
Any structural anomaly located in the inner or middle layer of the arterioles of the kidney.
Abnormal renal arteriole intima/media morphology
Thrombi containg fibrous tissue and capillary-like vascular channels located within the lumen of the arterioles of the kidney.
Renal arteriolar lumen organized thrombi
Mixture of fibrin, red blood cells, platelets partly or completely occluding the vascular lumen of the arterioles of the kidney.
Any structural anomaly of the lining (endothelium) of the arterioles of the kidney.
Abnormal renal arteriole endothelium morphology
Abnormal structural characteristics of the interior space (lumen) of the arcuate artery of the kidney.
Abnormalities of the arcuate arterial lumen
Abnormal arcuate artery lumen morphology
Needle-like or slit-like clefts within the interior space of arcuate arteries of the kidney. Cholesterol emboli are visualized as clear spaces (cholesterol clefts) where the cholesterol crystals have been dissolved by routine processing. Acute lesions can be accompanied by inflammation and fibrin.
Cholesterol emboli within arcuate arterial lumen
Mixture of fibrin, red blood cells, platelets partly or completely occluding the vascular lumen of the arcuate arteries of the kidney.
Intraluminal thrombi within arcuate arterial lumen
Thrombi containg fibrous tissue and capillary-like vascular channels located within the lumen of the arcuate arteries of the kidney.
Organised thrombi within arcuate arterial lumen
Organized thrombi within arcuate arterial lumen
Amorphous extracellular substance in the inner or middle layer of renal arterioles. Amyloidosis stains Congo-red positive with typically an apple green birerfingence on polarization microscopy, and 8-12 nm fibrils on electron microscopy.
Amyloidosis within renal arteriolar intima/media
Renal arteriole intima/media amyloidosis
Any structural anomaly of the lining (endothelium) of the arcuate arteries of the kidney.
Abnormal arcuate artery endothelium morphology
Enlargement of endothelial cells of the arcuate arteries of the kidney because of cytoplasmic swelling.
Proliferation of endothelial cells (increased number of cells) of the lining (endothelium) of the arcuate arteries of the kidney.
Endoarterial hypercellularity within arcuate artery
Arcuate artery endoarterial hypercellularity
Accumulation of amorphous, eosinophilic, glassy, periodic acid-Schiff (PAS)-positive, silver-negative material (hyalinosis) in the inner or middle layer of the renal arterioles. This feature may be accompanied by hypertrophy of the media and intima fibrosis.
Thickening of the intima of the arcuate arteries of the kidney with fibrosis and/or duplication of the elastic lamina.
Arteriosclerosis within arcuate arterial intima/media
Arcuate artery intima/media arteriosclerosis
Inflammation of an arteriole of the kidney, which may involve only the intma or can be transmural.
Thickening of the intima of renal arterioles with fibrosis and/or duplication of the elastic lamina.
Renal arteriole intima/media arteriolosclerosis
Atrophy (wasting, decreased thickness) of of the middle layer of the arterioles of the kidney.
Increased thickness of middle layer of the arcuate veins of the kidney.
Atrophy (wasting, decreased thickness) of the middle layer of the arcuate veins of the kidney.
Increased thickness of the middle layer of the cortical radial arteries (also known as the interlobular arteries) of the kidney.
Medial hypertrophy within interlobular arteries
Cortical radial artery medial hypertrophy
Atrophy (wasting, decreased thickness) of the middle layer of the cortical radial arteries (also known as the interlobular arteries) of the kidney.
Medial atrophy within interlobular arteries
Inflammation of a the intima or the entire wall of cortical radial arteries (also known as the interlobular arteries) of the kidney.
Arteritis within interlobular arterial intima/media
Interlobular artery medial/intimal arteriitis
Cortical radial artery medial/intimal arteriitis
Amorphous extracellular substance in the inner or middle layer of the arcuate arteries of the kidney. Congo-red positive with typically an apple green birerfingence on polarization microscopy, and 8-12 nm fibrils on electron microscopy.
Amyloidosis within arcuate arterial intima/media
Accumulation of edematous extracellular matrix in intima resembling mucus. This feature appears pale blue on hematoxylin and eosin staining.
Thickening of the intima with fibrosis and/or duplication of the elastic lamina in arcuate veins.
Inflammation of the inner or middle layer of arcuate venules. This feature may involve only the intima or it can be transmural.
Venulitis within arcuate vein intima/media
Increased thickness of middle layer of the arterioles of the kidney.
Deposition of storage material other than amyloid (glycogen, glycosphingolipid in Fabry's disease, sphingomyelin in Nieman Pick disease, glucosylceramide in Gaucher's disease, gangliosides, mucopolysaccahrides, phytanic acid in Refsum disease) in the inner or middle layer of the arterioles of the kidney.
Accumulated storage material within arteriolar intima/media
Renal arteriole intima/media storage material accumulation
Abnormal and excessive number of cells (hypercellularity) in the lining (endothelium) of the arterioles of the kidney.
Endoarterial hypercellularity within arterioles
Renal arteriole endoarterial hypercellularity
A type of renal arteriole endoarterial hypercellularity due to increased number of white blood cells (leukocytes).
Renal arteriole leukocytic endoarterial hypercellularity
A type of renal arteriole leukocytic endoarterial hypercellularity due to the presence of lipid-filled cells, often a macrophage, with a vacuolated appearance in arteriolar lumen.
Endoarterial hypercellularity within arterioles consisting of foam cells
Renal arteriole foam cell endoarterial hypercellularity
A type of renal arteriole leukocytic endoarterial hypercellularity due to the presence of increased numbers of neutrophils within the arteriolar lumen.
Endoarterial hypercellularity within arterioles consisting of neutrophils
Renal arteriole neutrophil endoarterial hypercellularity
A type of renal arteriole leukocytic endoarterial hypercellularity due to the presence of increased number of lymphocytes in the arteriolar lumen.
Endoarterial hypercellularity within arterioles consisting of lymphocytes
Renal arteriole lymphocyte endoarterial hypercellularity
Myointimal hyperplasia arranged in multiple concentric layers in the inner or middle layer of the arterioles of the kidney.
Multilamellation (onion skinning) within renal arteriole intima/media
Renal arteriole intima/media multilamellation
Renal arteriole intimal/medial onion skinning
Renal arteriole intimal/medial multilamellation
Arcuate artery endoarterial hypercellularity due to increased numbers of white blood cells (leukocytes).
Endoarterial hypercellularity within arcuate artery consisting of leukocytes
Arcuate artery endoarterial leukocyte hypercellularity
A type of arcuate artery endoarterial leukocyte hypercellularity due to the presence of lipid-filled cells, often a macrophage, with a vacuolated appearance in arteriolar lumen.
Endoarterial hypercellularity within arcuate artery consisting of foam cells
Arcuate artery endoarterial foam cell hypercellularity
A type of arcuate artery endoarterial leukocyte hypercellularity due to the presence of increased numbers of neutrophils withinin the lumen of arcuate artery.
Endoarterial hypercellularity within arcuate artery consisting of neutrophils
Arcuate artery endoarterial neutrophil hypercellularity
A type of arcuate artery endoarterial leukocyte hypercellularity due to the presence of increased number of lymphocytes in the lumen of arcuate artery.
Endoarterial hypercellularity within arcuate artery consisting of lymphocytes
Arcuate artery endoarterial lymphocyte hypercellularity
Death of tissue in the inner or middle layer of the arcuate artery of the kidney.
A type of arcuate artery intima/media necrosis in which the necrotic tissue retains the outlines of the dead (necrotic) structures.
Coagulative necrosis within interlobular arterial intima/media
Arcuate artery intima/media coagulative necrosis
A type of arcuate artery intima/media necrosis in which the dead (necrotic) tissue breaks down such that cellular detail is no longer recognized.
Liquefactive necrosis of the arcuate artery intima/media
Arcuate artery intima/media liquefactive necrosis
Accumulation of material other than amyloid (glycogen, glycosphingolipid in Fabry's disease, sphingomyelin in Nieman Pick disease, glucosylceramide in Gaucher's disease, gangliosides, mucopolysaccahrides, phytanic acid in Refsum disease) in the inner or middle layer of the arcuate veins of the kidney.
Multilamellation (onion skinning) within arteriolar intima/media
Renal arteriole intima/media onion skinning
Arcuate vein intimal/medial storage material accumulation
Cell death (necrosis) in the inner or middle layer of the cortical radial arteries (also known as the interlobular arteries) of the kidney.
Necrosis within interlobular arterial intima/media
Cortical radial artery intima/media necrosis
A type of cortical radial artery intima/media necrosis in which the dead (necrotic) tissue breaks down such that cellular detail is no longer recognized.
Liquefactive necrosis within interlobular arterial intima/media
Cortical radial artery intima/media liquefactive necrosis
A type of cortical radial artery intima/media necrosis in which the dead (necrotic) tissue retains the outlines of the dead structures.
Cortical radial artery intima/media coagulative necrosis
Cell death (necrosis) in the inner or middle layer of the arterioles of the kidney.
A type of renal arteriole intima/media necrosis in which the dead (necrotic) tissue breaks down such that cellular detail is no longer recognized.
Liquefactive necrosis of the renal arteriolar intima/media
Renal arteriole intima/media liquefactive necrosis
A type of renal arteriole intima/media necrosis in which the dead (necrotic) tissue retains the outlines of the dead structures.
Renal arteriole intima/media coagulative necrosis
A type of renal intimal/medial arteriolitis characteriezed by circumscribed inflammatory lesions comprised primarily of macrophages present in inflamed arteries.
Granulomatous arteriolitis within arteriolar intima/media
Granulomatous arteriolitis of the arteriolar intima/media
Cell death (necrosis) of the inner or middle layer of the arcuate veins of the kidney.
Necrosis within arcuate vein intima/media
A type of arcuate vein medial/intimal necrosis in which the dead (necrotic) tissue retains the outlines of the dead structures.
Coagulative necrosis within arcuate vein intima/media
Arcuate vein medial/intimal coagulative necrosis
A type of arcuate vein medial/intimal necrosis in which the dead (necrotic) tissue breaks down such that cellular detail is no longer recognized.
Liquefactive necrosis within arcuate vein intima/media
Arcuate vein medial/intimal liquefactive necrosis
A type of arcuate intimal/medial venulitis characterized by circumscribed inflammatory lesions comprised primarily of macrophages present in inflamed veins.
Arcuate intimal/medial granulomatous venulitis
Deposition of crystals such as uric acid, oxalate, or cystine in the inner or middle layer of the arcuate veins of the kidney.
Arcuate vein intima/media crystal accumulation
Deposition of crystals such as uric acid, oxalate, or cystine in the inner or middle layer of the arterioles of the kidney.
Accumulated crystals within renal arteriolar intima/media
Renal arteriole intima/media crystal accumulation
Inflammation of the inner or middle layer of the arcuate arteries of the kidney.
Arteritis within arcuate arterial intima/media
A type of arcuate artery intima/media granulomatous arteriitis characterized by circumscribed inflammatory lesions comprised primarily of macrophages present in inflamed arteries.
Granulomatous arteritis within arcuate arterial intima/media
Arcuate artery intima/media granulomatous arteriitis
Mixture of fibrin, red blood cells, platelets partly or completely occluding vascular lumen within the interior space of cortical radial arteries (interlobular arteries) of the kidney.
Intraluminal thrombi within interlobular arterial lumen
Cortical radial artery intraluminal thrombi
Thrombi containing fibrous tissue and capillary-like vascular channels within the interior space of cortical radial arteries (interlobular arteries) of the kidney.
Organised thrombi within interlobular arterial lumen
Organized thrombi within interlobular arterial lumen
Cortical radial artery intraluminal organized thrombi
Abnormal structural characteristics of the lining (endothelium) of the cortical radial arteries (also known as interlobular arteries) of the kidney.
Abnormalities of the interlobular arterial endothelium
Abnormal cortical radial artery endothelium morphology
Enlargement of endothelial cells of the cortical radial arteries (also known as the interlobular arteries) of the kidney because of cytoplasmic swelling.
Endotheliosis within interlobular arteries
Proliferation of endothelial cells (increased number of cells) of the lining (endothelium) of the cortical radial arteries (also known as interlobular arteries) of the kidney.
Endoarterial hypercellularity within interlobular artery
A type of cortical radial artery endoarterial hypercellularity due to increased numbers of white blood cells (leukocytes).
Endoarterial hypercellularity within interlobular artery consisting of leukocytes
Cortical radial artery leukocyte hypercellularity
A type of cortical radial artery endoarterial leukocyte hypercellularity due to the presence of increased number of lymphocytes in the lumen of cortical radial arteries.
Endoarterial hypercellularity within interlobular artery consisting of lymphocytes
Cortical radial artery lymphocyte hypercellularity
A type of cortical radial artery endoarterial leukocyte hypercellularity due to the presence of increased numbers of neutrophils in the lumen of cortical radial arteries.
Endocapillary hypercellularity within interlobular arterial endothelium consisting of neutrophils
Cortical radial artery neutrophil hypercellularity
A type of cortical radial artery endoarterial leukocyte hypercellularity due to the presence of lipid-filled cells, often macrophages, with a vacuolated appearance in the lumen of cortical radial artery (also known as the interlobular artery) of the kidney.
Endocapillary hypercellularity within interlobular arterial endothelium consisting of foam cells
Cortical radial artery foam cell hypercellularity
Thickening of the intima of the cortical radial artery (also known as the interlobular artery) of the kidney characterized by fibrosis and/or duplication of the elastic lamina.
Arteriosclerosis within interlobular arterial intima/media
Cortical radial artery intima/media arteriosclerosis
Accumulation of edematous extracellular matrix in the intima of the cortical radial artery (also known as the interlobular artery) of the kidney. This material resembles mucus and stains pale blue on hematoxylin and eosin staining.
Intimal mucoid edema within interlobular arterial intima/media
Intimal mucoid oedema within interlobular arterial intima/media
Cortical radial artery intimal mucoid edema
Myointimal hyperplasia of the inner and middle layer of the cortical radial artery (also known as the interlobular artery) of the kidney, arranged in multiple concentric layers.
Cortical radial artery intima/media onion skinning
Multilamellation (onion skinning) within interlobular arterial intima/media
Cortical radial artery intima/media multilamellation
A type of cortical radial artery medial/intimal arteriitis that is characterized by circumscribed inflammatory lesions comprised primarily of macrophages present in inflamed arteries.
Cortical radial artery medial/intimal granulomatous arteriitis
Any structural anomaly of the inner or middle layer of the interlobular veins of the kidney.
Abnormal interlobular vein intima/media morphology
Thickening of the intima with fibrosis and/or duplication of the elastic lamina in interlobular veins of the kidney.
Venosclerosis within interlobular vein intima/media
Accumulation of edematous extracellular matrix in the intima of the interlobular vein of the kidney. This material resembles mucus and stains pale blue on hematoxylin and eosin staining.
Intimal mucoid edema within interlobular veins
Intimal mucoid oedema within interlobular veins
Amorphous extracellular substance in the glomerular, interstitial or vascular compartments of the interlobular veins of the kidney. Congo-red positive with typically an apple green birerfingence on polarization microscopy, and 8-12 nm fibrils on electron microscopy
Amyloidosis within interlobular vein intima/media
Interlobular vein intima/media amyloidosis
Inflammation of the interlobular veins of the kidney which may affect only the intima or may be transmural.
Venulitis within interlobular vein intima/media
Interlobular vein intima/media venulitis
A type of interlobular vein intima/media venulitis that is characterized by circumscribed inflammatory lesions comprised primarily of macrophages present in inflamed veins.
Granulomatous venulitis within interlobular vein intima/media
Interlobular vein intima/media granulomatous venulitis
Cell death (necrosis) in the inner or middle layer of the interlobular vein of the kidney.
Necrosis within interlobular vein intima/media
A type of interlobular vein intima/media necrosis in which the dead (necrotic) tissue breaks down such that cellular detail is no longer recognized.
Liquefactive necrosis within interlobular vein intima/media
Interlobular vein intima/media liquefactive necrosis
A type of interlobular vein intima/media necrosis in which the dead (necrotic) tissue retains the outlines of the dead structures.
Interlobular vein intima/media coagulative necrosis
Atrophy (wasting, decreased thickness) of the medial layer pf the interlobular veins of the kidney.
Medial atrophy within interlobular veins
Increased thickness of middle layer of the interlobular veins of the kidney.
Medial hypertrophy within interlobular veins
Myointimal hyperplasia of the inner and middle layer of the interlobular veins of the kidney, arranged in multiple concentric layers.
Interlobular vein intima/media onion skinning
Multilamellation (onion skinning) within interlobular vein intima/media
Interlobular vein intima/media multilamellation
Structural or functional abnormalities of the fetus. Note that this section comprises terms that describe abnormalities that are specific to the fetus or differ from the corresponding general terms. A term from anywhere in the Human Phenotype Ontology can be applied to a fetus if appropriate.
A type of cross fused renal ectopia characterized by fusion between the upper pole of the cross-fused ectopic kidney (located more inferiorly relative to the other kidney) and the lower pole of the other orthotopic kidney (located in a more superior position).
A type of cross fused renal ectopia where the normal side kidney is present superiorly and the direction of pelvic is medial, the kidney which crosses positioned inferiorly with direction of pelvic toward the lateral side. As kidneys fuse after complete rotation on the vertical axis, both renal pelves lie in correct orientation.
A type of cross fused renal ectopia where fusion occurs over a wide margin, both renal pelves anteriorly directed and placed more inferiorly.
A type of cross fused renal ectopia in which kidneys fuse along their medial borders.
A type of cross fused renal ectopia in which the crossed kidney lies inferiorly and transversely, fused with the lower pole of the normal kidney.
A type of cross fused renal ectopia in which the ectopic kidney lies superiorly and its lower pole fuses with the upper pole of the normal kidney. The renal pelvis of both kidneys lies anteriorly.
The presence of a thrombus (blood clot) in the major renal veins or its tributaries, generally leading to passive congestion that develops causes the affected kidney to swell and become engorged, leading to degeneration of nephrons and causing symptoms of flank pain, hematuria, and decreased urine output.
Diagnosis can be made by magnetic resonance angiography, Doppler ultrasonography, or computed tomography angiography.
An anomalous structural finding of the fetal genitourinary system. Terms in this subhierarchy are restricted to findings that can only be observed in the prenatal period. Other HPO terms can also be used to describe fetal phenotypes.
Abnormal fetal genitourinary system morphology
Increased loss of low-molecular weight proteins by the kidneys, measured in terms of the fractional excretion (FE). The FE of low-molecular-weight proteins such as beta2-microglobulin can be measured in terms of plasma and urine concentrations, since urinary low-molecular-weight protein concentrations can vary with water reabsorption.
Increased low molecular weight protein excretion
Urinary proteins are reabsorbed by the renal tubule cells, and increased low molecular weight protein fractional excretion can be a sign of tubular proteinuria.
Impaired renal tubular reabsorption of low molecular weight protein
Increased fractional excretion (FE) of glucose in the urine. The FE of glucose is the percentage of the glucose filtered by the kidney which is excreted in the urine. It is measured in terms of plasma and urine glucose, rather than by the interpretation of urinary glucose concentration alone, as urinary glucose concentrations can vary with water reabsorption.
Impaired renal tubular reabsorption of glucose
Increased fractional excretion (FE) of sodium in the urine. The FE of sodium is the percentage of the sodium filtered by the kidney which is excreted in the urine. It is measured in terms of plasma and urine sodium, rather than by the interpretation of urinary glucose concentration alone, as urinary glucose concentrations can vary with water reabsorption.
Impaired renal tubular reabsorption of sodium
Increased fractional excretion (FE) of glucose in the phosphate. The FE of glucose is the percentage of the phosphate filtered by the kidney which is excreted in the urine. It is measured in terms of plasma and urine phosphate, rather than by the interpretation of urinary phosphate concentration alone, as urinary glucose concentrations can vary with water reabsorption.
Impaired renal tubular reabsorption of phosphate
A highly aggressive, extremely rare neoplasm of the kidney that is usually seen in children. The term rhabdoid is used because the tumor cells resemble rhabdomyoblasts but lack myogenic markers, and pathologic diagnosis requires familiarity with these microscopic features plus awareness that adult onset is possible. It can be associated with abnormalities of chromosome 22. It is characterized by the presence of cells with a large eccentric nucleus, prominent nucleolus, and abundant cytoplasm.
Rhabdoid tumors are rare aggressive malignancies in infants and young children with a poor prognosis. The most common anatomic localizations are the central nervous system, the kidneys, and other soft tissues.
Concentration or activity of an enzyme is above or below the limits of normal.
Abnormal enzyme concentration or activity
The pathogenesis of cystic nephroma is controversial and there is no generally accepted classification.
A deviation from the normal concentration of renin in the blood, a central hormone in the control of blood pressure and various other physiological functions.
A deviation from the normal concentration of cobalamin (vitamin B12) in the blood. Vitamin B12 is one of the eight B vitamins.
An abnormally reduced head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. Microcephaly is defined as a head circumference (HC) that is great than two standard deviations below the mean of age- and gender-matched population based samples. Severe microcephaly is defined with an HC that is three standard deviations below the mean.
Although HC measures skull size, it typically also reflects overall brain volume and has been described as a widely used proxy of neural growth and brain size. Brain size outside of normal values is an important risk factor for cognitive and motor delay. Microcephaly at birth has been termed primary microcephaly and that acquired after birth is secondary microcephaly.
Tubular lumnal dilatation/prominence lined by simple layer of cuboidal-to-flat tublar epihelial cells.
An abnormality of movement with a neurological basis characterized by changes in coordination and speed of voluntary movements.
Movement disorders are characterized by the phenotypic abnormalities including abnormal involuntary movements, akathisia, akinesia, athetosis, ataxia, ballismus, bradykinesia, chorea, dyskinesia, dystonia, and myoclonus tics, tremor, spasms, and stereotypy.
A connective tissue neoplasm formed by proliferation of mesodermal cells. Bone and soft tissue sarcomas are the main types of sarcoma. Sarcoma is usually highly malignant.
A sarcoma (from the Greek sarx meaning flesh) is a general term describing a malignant neoplasm, or cancer, that arises from transformed connective tissue cells such as bone, cartilage and fat cells, which originate from embryonic mesoderm. This is in contrast to carcinomas, which are of epithelial origin (breast, colon, pancreas, and others). However, due to an evolving understanding of tissue origin, the term sarcoma is sometimes applied to tumors now known to arise from epithelial tissue. The term soft tissue sarcoma is used to describe tumors of soft tissue, which includes elements that are in connective tissue, but not derived from it (such as muscles and blood vessels).
A chronic autoimmune phenomenon characterized by fibrosis (or hardening) and vascular alterations of the skin.
A chronic autoimmune disease characterized by fibrosis (or hardening), vascular alterations, and autoantibodies. Sclerosis of the skin occurs in association with disorders as diverse as dermatomyositis, Werner's syndrome, porphyria, muscle glycogenesis, primary systemic amyloidosis, melorheostosis, and malignancy including the carcinoid syndrome. This term is intended to represent the phenotypic feature scleroderma rather than a particular disease.
Immunological states where the immune system produces harmful responses upon reexposure to sensitising antigens.
An anomaly in the metabolism of a vitamin.
Vitamins are organic substances that are essential in minute quantities and not produced within the body, instead being present in natural foodstuffs. Vitamins act as coenzymes or precursors of coenzymes in the regulation of metabolic processes.
Absence of urine, clinically classified as below 50ml/day.
Low output of urine, clinically classified as an output below 300-500ml/day.
The decreased output of urine may be a sign of dehydration, renal failure, hypovolemic shock, multiple organ dysfunction syndrome, or urinary obstruction/urinary retention.
An abnormality of phosphate homeostasis or concentration in the body.
Inflammation of the eye, parts of the eye or the periorbital region.
Abnormality in the process of thought including the ability to process information.
Narrowing or constriction of the inner surface (lumen) of an artery.
An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle.
An abnormal enlargement of the renal calices, the system of ducts of the kidney that collect urine.
The presence of many cysts in the glomerulus of the kidney related to dilatation of the Bowman's capsule.
Glomerular cysts, defined as Bowman space dilatation greater than 2 to 3 times normal size, are found in disorders of diverse etiology and with a spectrum of clinical manifestations. The term glomerulocystic kidney refers to a kidney with greater than 5% cystic glomeruli.
An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively.
The presence of hypertension related to stenosis of the renal artery.
Hypertension due to renal artery hyperplasia
Renal artery stenosis can lead to hypertension and chronic kidney disease (due to chronic renal ischemia). The hypertension is caused by activation of the renin-angiotensin-aldosterone system.
Inflammatory or noninflammatory diseases affecting the glomeruli of the nephron.
Cystic, urine-containing intrarenal cavities lined with transitional cell epithelium that communicate through a narrow channel with the collecting system.
Abnormally persistent clusters of embryonal cells, representing microscopic malformations (dysplasias) of the developing kidney.
Though NR are best known as precursors of Wilms tumor (WT), many alternative fates are observed, and most rests are destined for eventual atresia. Nephroblastomatosis refers to the presence of multifocal or diffuse nephrogenic rests.
Congenital mesoblastic nephroma is a type of kidney tumor that is usually found before birth by ultrasound or within the first 3 months of life. It contains fibroblastic cells (connective tissue cells), and may spread to the other kidney or to nearby tissue.
Congenital mesoblastic nephroma is more common in males.
Any structural abnormality of the medulla of the kidney.
The renal pyramids of the adult kidney resemble a cone with a broad base adjacent to the renal cortex and the narrow apex that is termed papilla. The adult renal medulla is made up of 10-18 pyramids. A pyramid consists of the medullary collecting ducts, loops of Henle, vasa recta (straight capillaries) and the interstitium. The main function of the medulla is to regulate concentration of the urine. The urine flows from the collecting ducts into the renal calyces and pelvis.
Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage.
Onset of disease manifestations before adulthood, defined here as before the age of 15 years, but excluding neonatal or congenital onset.
Decreased renal tubular reabsorption of bicarbonate.
Impaired renal tubular reabsorption of bicarbonate
A developmental anomaly of renal lymphatics that results from a failure of the lymphatics to make communication with the rest of the lymph trunks. The abnormal lymphatics thus dilate and form cystic spaces at the renal sinus and in the perinephric space.
Vasculitis (inflammation of blood vessels) in the kidney. Renal vasculitis can be observed with numerous disorders and presents clinically as rapidly progressive glomerulonephritis (RPGN) which is characterised by acute kidney injury (AKI), haematuria and proteinuria. Histological examination of the kidney reveals severe inflammation in the form of crescent formation, glomerular necrosis and vasculitis of small and medium sized vessels within the kidney.
Any structural anomaly of the proximal convoluted tubule, which is the first tubular component of the nephron and arises as a continuation of the Bowman space from the tubular pole of the renal corpuscle. The proximal convoluted tubule is located within the renal cortex.
Abnormal proximal convoluted tubule morphology
Heterogeneous, increased parenchymal echogenicity. This imaging appearance is caused by multiple tiny cysts smaller than or just approaching the size necessary for detection, which disrupt the echo pattern without being clearly distinguishable, and appear as white grains on renal ultrasound, mainly in a subcapsular location.
See Figure 2 of PMID:22034641 and Figure 11 of PMID:30599104.
Sonographic renal salt and pepper pattern
Accumulation of fibronectin in the glomerulus.
Fibronectin glomerulopathy (FNG) is characterized by extensive deposition of fibronectin in the glomeruli, especially in the mesangial and subendothelial regions.
Marked enlargement of nuclei observed predominantly in the proximal convoluted tubule cells.
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
Person: Alan Ruttenberg
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
a numeral that denotes an integer
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
density plot
Density plot of SSC-H and FSC-H.
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
a textual entity intended to identify a particular publication
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
table
| T F --+----- T | T F F | F F
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
hypothesis textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses an assertion that is intended to be tested.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Chris Stoeckart
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Bjoern Peters
Person:Melanie Courtot
assigning a centrally registered identifier
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
Entries in a Column of which the header is "Pubmed ID"
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
CRID
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
PERSON: Bill Baumgartner
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that needs to be perceived.
A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.
social act
the claim of a piece of land, the obligation to pay rent to the owner of a rental property
Socio-legal generically dependent continuants are generically dependent continuants that come into existence through declarations and are concretized as roles. They differ from information content entities in that they are not about something, but exist as quasi-abstract social entities. Socio-legal generically dependent continuants are not concretized as qualities inhering in independent continuants, but only as realizable entities borne by an organism or an aggregate of organisms.
socio-legal generically dependent continuant
my consenting verbally to buy a used TV set for $ 500, Jane Doe's signing of the divorce papers, John Robie's taking of Mrs. Steven's jewels
A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or revokes a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
Mathias Brochhausen
declaration
A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
document act input document
a judge's role of signing a court order, a hospital committee's to sanction conformance to a specific guideline for hospital employees.
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
declaration performer role
A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.
The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. For instance, whereas the NCIt definition restricted informed consent forms to clinical trials, the present definition does not.
Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte
informed consent document
NCIt C16468
See curator note for 'incomplete informed consent form'.
informed consent form
A social act that is a part of an informed consent process and has output of a signed informed consent form. The signing process leads to a legal obligation.
Alla Karnovsky, Frank Manion, Yongqun He, Jihad Obeid, Chris Stoeckert, and Mathias Brochhausen
This class is under group discussion as of 03/26/2019.
Signing here does not mean that we have to sign with a pen. It may happen in terms of signing a piece of a paper or an electronic form.
signing an informed consent form
A document act input document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and whose purpose is to assist in obtaining consent.
J. Neil Otte
Note: instances of 'incomplete informed consent form' include both blank informed consent forms that are waiting to be used in a process of informed consent, as well as those that have been left blank by a patient, whether on purpose or in error. Those that have been left blank on purpose have been used in a process of informed consent, where the patient must have reached a decision.
incomplete informed consent form
A document act input document that has, as part, an incomplete informed consent form, along with some additional parts, such as a signature, stamp, or initials, which serve as a record to an act of consent that had the incomplete informed consent form as a specified input.
complete informed consent form indicating consent
An information content entity that is a handwritten depiction of a name.
Jonathan Vajda, Cooper Stansbury, J. Neil Otte.
signature
A human patient who has the disease of acute kidney injury (AKI).
AKI patient
A human patient who has the disease of chronic kidney disease (CKD).
CKD patient
kidney disease biomarker
CKD biomarker
AKI biomarker
A biomarker as an indicator of a kidney cell lineage or cell type.
kidney cell lineage marker
kidney podocyte lineage marker
renal corpuscle cell lineage marker
kidney parietal epithelial cell lineage marker
kidney tubule cell lineage marker
kidney proximal tubule cell lineage marker
kidney looo of Henle, thin limb cell lineage marker
A podocyte marker that indicates the podocytopathy (podocyte injury). An example of such a marker is Ezrin (http://www.antibodybeyond.com/reviews/cell-markers/podocyte-marker.htm).
podocytopathy marker
A podocyte marker that indicates the DDS (Denys-Drash syndrome) in podocyte. An example of such a marker is VEGF (http://www.antibodybeyond.com/reviews/cell-markers/podocyte-marker.htm).
Denys-Drash syndrome podocyte marker
A podocyte marker that indicates the podocyte maturity. An example of such a marker is Vimentin (http://www.antibodybeyond.com/reviews/cell-markers/podocyte-marker.htm).
podocyte maturation marker
A biomarker that is an indicative of a specific biological state or identity associated with kidney
kidney biomarker
predictive CKD biomarker
diagnostic CKD biomarker
prognostic CKD biomarker
prognostic AKI biomarker
diagnostic AKI biomarker
predictive AKI biomarker
CKD protein biomarker
CKD RNA biomarker
CKD gene marker
urine hEGF
kidney podocyte cell lineage gene marker
A mental process that creates, modifies or has as participant some cognitive representation.
GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.'
Consciousness is an inseparable part of all mental processes. It is that part of the mental process that: a) confers a subjective perspective, a phenomenology, an experience of the mental process of which it is a part; and b) intends the object or event that the mental process is about, should such exist; i.e., it confers intentionality on the mental process.
Note that while there are different modes of consciousness corresponding to the different senses, the whole of conscious experience at any one time is largely experienced as a unity, that is, as a fused whole. Mental processes which are simultaneously ongoing are separable only in fiat, not in essence.
consciousness
A mental process is a bodily process that is of a type such that it can of itself be conscious. Examples include thinking, feeling pain, remembering and emotion as occurrent experiences.
A bodily process which brings into being, sustains or modifies a cognitive representation or a beahvior inducing state.
A dependent continuant which is about a portion of reality.
A representation which specifically depends on an anatomical structure in the cognitive system of an organism.
A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language.
bodily disposition
A mental disposition is a bodily disposition that is realized in a mental process.
mental disposition
Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something.
intentionality
A bodily quality is a quality that inheres in some extended organism.
bodily quality
A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning.
mental quality
An example of an intentional modality is the capacity to represent objects of intentionality as unfolding in time or being time contingent.
A structural capacity that shapes how an object of intentionality is represented for the subject.
intentional modality
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
inherited bleeding disorder, platelet-type
nephrolithiasis/osteoporosis, hypophosphatemic
Bifid nose is a rare congenital malformation of presumed autosomal dominant or recessive inheritance characterized by clefting of the nose ranging from a minimally noticeable groove in the columella to complete clefting of the underlying bones and cartilage (resulting in two half noses) with a usually adequate airway. Bifid nose may be seen in frontonasal dysplasia while other malformations such as hypertelorbitism and midline clefts of the lip may also be associated.
A hypercalcemia disease that occurs between 28 days to one year of life..
A disease involving the lower respiratory tract.
disease or disorder of lower respiratory tract
lower respiratory tract disease or disorder
Hantavirus hemorrhagic fever with renal syndrome, Seoul virus type
Hantavirus hemorrhagic fever with renal syndrome, Puumala virus type
Abnormally high level of phosphate in the blood.
Hantavirus hemorrhagic fever with renal syndrome, Dobrava-Belgrade virus type
Editor notes: most subtypes are isolated
A tuberculosis that occurs at body sites other than the lung.
An extrapulmonary tuberculosis that is located in gastrointestinal tract, located in peritoneum, located in omentum, located in mesentery, located in liver, located in spleen or located in pancreas.
A malignant neoplasm involving the respiratory system
malignant neoplasm of respiratory system
A infiltrating urothelial carcinoma that involves the renal pelvis.
infiltrating renal pelvis transitional cell carcinoma
A non-metastasizing neoplasm that arises from the male or female reproductive system. Representative examples include benign prostate phyllodes tumor, benign Sertoli cell tumor, uterine corpus leiomyoma, and benign ovarian serous tumor.
A benign abnormal growth of the cells that comprise the bladder.
Low serum levels of vitamin B12 (cobalamin) due to poor intestinal absorption, decreased dietary intake, or increased physiologic requirement.
inborn cobalamin metabolic process disorder
inborn error of cobalamin metabolic process
rare inborn error of cobalamin metabolic process
A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes.
A neurological syndrome characterised by clumsy and unco-ordinated movement of the limbs, trunk, and cranial muscles. It results from pathology in the cerebellum and its connections, or in the proprioceptive sensory pathways.
In ORDO this is called rare ataxia, we rename as ataxia since all forms are individually rare
Ochoa syndrome is characterized by the association of severe voiding dysfunction and a characteristic facial expression.
hydronephrosis with peculiar facial expression
inverted smile-neurogenic bladder syndrome
partial facial palsy with urinary abnormalities
inverted smile and occult neuropathic bladder
An impairment of the structure or function of the blood vessels which carry blood away from the heart.
A hardening of the kidney glomerulus caused by scarring of the blood vessels.
A final common manifestation of a wide variety of chronic kidney diseases characterized by glomerulosclerosis and tubulointerstitial fibrosis.
An anterior ischemic neuropathy that is the cause of vision loss that occurs in temporal arteritis (aka giant cell arteritis)
arteritic anterior ischemic optic neuropathy
A intellectual disability that is part of a larger syndrome.
syndrome associated with intellectual disability
Cerebellar ataxia that is transmitted from parent to child.
A hypersensitivity reaction type II disease that involves the central nervous system.
central nervous system autoimmune disease
central nervous system hypersensitivity reaction type II disease
autoimmune disease of central nervous system
A hypersensitivity reaction type II disease that involves the endocrine system.
endocrine system hypersensitivity reaction type II disease
Anemia, the cause of which is present at birth.
An autoimmune form of otorhinolaryngologic disease.
autoimmune disease of eyes, ear, nose and throat
Editor note: ENT typically excludes eye, but the DOID class includes this
autoimmune disease of ear, nose and throat
A hypersensitivity reaction type II disease that involves the musculoskeletal system.
musculoskeletal system autoimmune disease
musculoskeletal system hypersensitivity reaction type II disease
autoimmune disease of musculoskeletal system
A hypersensitivity reaction type II disease that involves the peripheral nervous system.
peripheral nervous system autoimmune disease
peripheral nervous system hypersensitivity reaction type II disease
autoimmune disease of peripheral nervous system
A cardiomyopathy that is due to abnormalities in heart muscle cells.
A hypersensitivity reaction type II disease that involves the genitourinary system.
autoimmune disease of genitourinary system
genitourinary system hypersensitivity reaction type II disease
A hypersensitivity reaction type II disease that involves the blood.
blood hypersensitivity reaction type II disease
A hypersensitivity reaction type II disease that involves the cardiovascular system.
cardiovascular system autoimmune disease
cardiovascular system hypersensitivity reaction type II disease
autoimmune disease of cardiovascular system
An immune system disease that has basis in dysregulation of the hypersensitivity reaction, an inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
familial juvenile hyperuricemic nephropathy
familial nephropathy associated with hyperuricemia
A disease of cellular proliferation that results in abnormal growths in the body, which do not invade or destroy the surrounding tissue but, given enough time, will transform into a cancer.
A non-metastasizing, functioning or non-functioning neoplasm that arises from an endocrine organ. Representative examples include thyroid gland follicular adenoma and parathyroid gland adenoma.
A benign neoplasm that involves the musculoskeletal system.
A malignant neoplasm involving the musculoskeletal system
malignant musculoskeletal system neoplasm
malignant neoplasm of musculoskeletal system
A non-neoplastic or neoplastic disorder that affects the thorax and/or the organs of the thoracic cavity. Representative examples include pleural infection, mediastinitis, thymoma, mediastinal lymphoma, and pleural mesothelioma.
disease or disorder of thoracic segment of trunk
thoracic segment of trunk disease or disorder
A benign neoplasm that involves the integumental system.
A non-metastasizing neoplasm that arises from the connective and soft tissue. Representative examples include lipoma, leiomyoma, fibroma, and osteoma.
benign connective and soft tissue neoplasm
benign neoplasm of the soft tissue and bone
benign tumor of the soft tissue and bone
connective and soft tissue neoplasm, benign
An inherited disorder that affects the metabolism of any acidic compound containing carbon in a covalent linkage.
inborn error of organic acid metabolic process
inborn organic acid metabolic process disorder
rare inborn error of organic acid metabolic process
A metabolic metabolic disorder characterized by excess urinary excretion of the purine base xanthine.
Editor note: this is used in DOID to encompass typically partial deletions
syndrome caused by partial chromosomal deletion
An autoimmune form of peripheral neuropathy.
Editor note: We do not draw a distinction between between neuropathy and peripheral neuropathy see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/20
The formation of a blood clot in the lumen of a vessel or heart chamber; causes include coagulation disorders and vascular endothelial injury.
A bone disease that results in formation or resorption abnormalities located in bone.
Any abnormality, anatomical or biochemical, evident at birth or during the neonatal period.
Inflammation of the mucous membranes lining the gastrointestinal tract.
gastrointestinal system mucosa inflammation
inflammation of gastrointestinal system mucosa
A Bartter disease that has material basis in simultaneous mutation in both the CLCNKA and CLCNKB genes.
neonatal Bartter syndrome type 4B with sensorineural deafness
Bartter syndrome, infantile, with sensorineural deafness
Bartter syndrome, type 4B, neonatal, with sensorineural deafness
An infectious disease involving a pathogenic inflammatory response in the intestinal mucosa.
A non-neoplastic or neoplastic disorder that affects the cornea. Representative examples include keratitis, bullous keratopathy, and squamous cell carcinoma.
A rare benign adipose tissue neoplasm of the kidney. It predominantly affects middle-aged females. It may originate from renal parenchymal fat or fat cells within the renal capsule. Clinical presentation includes hematuria and pain.
A atherosclerosis that involves the aorta.
An inherited blood disorder characterized by a decreased synthesis of one of the polypeptide chains that form hemoglobin. Anemia results from this abnormal hemoglobin formation.
Klippel Feil syndrome (KFS) is a congenital, musculoskeletal condition characterized by the fusion of at least two vertebrae of the neck. Common symptoms include a short neck, low hairline at the back of the head, and restricted mobility of the upper spine. This syndrome can cause chronic headaches as well as pain in both the neck and the back.Other features may involve various other body parts or systems. Sometimes, KFS occurs as a feature of another disorder or syndrome, such as Wildervanck syndrome or hemifacial microsomia. In these cases, people have the features of both KFS and the additional disorder. KFS may be caused by mutations in the GDF6 or GDF3 gene and inherited in an autosomal dominant manner; or, it may be caused by mutations in the MEOX1 gene and inherited in an autosomal recessive manner. Treatment is symptomatic and may include medications, surgery, and/or physical therapy.
Klippel-Feil deformity, deafness and facial asymmetry
autosomal dominant Klippel-Feil syndrome
congenital synostosis of cervical vertebrae
Usage notes: this class includes both isolated forms and forms that are features of other syndromes
A broad category of disorders characterized by an impairment to the intelligence an individual possesses. These impairments can result from trauma, birth, or disease and are not restricted to any particular age group.
A pre-eclampsia characterized by the presence of hypertension without evidence of end-organ damage, in a woman who was normotensive before 20 weeks' gestation.
A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.
Inflammation of the renal tubules and supporting tissues of the kidney.
Hypertension caused by the kidney's hormonal response to narrowing or occlusion of the renal arteries.
An acute or chronic condition that is characterized by the inability of the kidneys to adequately filter the blood.
Hypertension that presents without an identifiable cause.
A disorder characterized by an abnormal increase of cerebrospinal fluid in the ventricles of the brain.
hydrocephalus, nonsyndromic, autosomal recessive
A category of behaviors that can be loosely defined as the failure to resist an impulsive act or behavior that may be harmful to self or others.
A disease involving the lens of camera-type eye.
disease or disorder of lens of camera-type eye
lens of camera-type eye disease or disorder
Includes cataracts, lens subluxation and aphakia
Chronic form of rapidly progressive glomerulonephritis.
chronic glomerulonephritis with lesion of rapidly progressive glomerulonephritis
rapidly progressive glomerulonephritis, chronic
chronic rapidly progressive glomerulonephritis
An instance of thrombocytopenia that is acquired during the lifetime of the individual.
High blood pressure caused by an underlying medical condition.
Hypoparathyroidism is is an endocrine disorder in which the parathyroid glands in the neck do not produce enough parathyroid hormone (PTH). Common signs and symptoms includeabdominal pain, brittle nails, cataracts, dry hair and skin,muscle cramps,tetany, pain in the face, legs, and feet, seizures, tingling sensation,and weakened tooth enamel (in children). It may be caused byinjury to the parathyroid glands (e.g., during surgery). Other causes, include low blood magnesium levels, a side effect of radioactive iodine treatment for hyperthyroidism, metabolic alkalosis, DiGeorge syndrome, and type I polyglandular autoimmune syndrome. The goal of treatment is to restore the calcium and mineral balance in the body.
hypoparathyroidism, idiopathic (subtype)
A broad classification of inherited disorders presenting at birth that affect the cell-mediated aspect of the immune response. Circulating numbers of T lymphocytes are decreased or ineffective.
A disease involving the parathyroid gland.
disease or disorder of parathyroid gland
An inflammatory process that affects the choroid.
hypertensive renal disease, benign, without mention of renal failure
Any disease in which the causes of the disease is a perturbation of the kidney leading to its dysfunction.
A disease characterized by abnormal union between adjacent bones or parts of a single bone formed by osseous material, such as ossified connecting cartilage or fibrous tissue.
A primary or metastatic malignant neoplasm involving the female reproductive system. Representative examples include endometrial carcinoma, cervical carcinoma, ovarian carcinoma, uterine corpus leiomyosarcoma, adenosarcoma, malignant mixed mesodermal (mullerian) tumor, and gestational choriocarcinoma.
malignant female reproductive organ neoplasm
malignant female reproductive system neoplasm
malignant female reproductive system tumor
malignant neoplasm of female genital organ
malignant neoplasm of female reproductive organ
malignant neoplasm of female reproductive system
malignant neoplasm of the female reproductive system
malignant tumor of female reproductive system
malignant tumor of the female reproductive system
An endocrine disorder characterized by excessive production of aldosterone by the adrenal glands. Causes include adrenal gland adenoma and adrenal gland hyperplasia. The overproduction of aldosterone results in sodium and water retention and hypokalemia. Patients present with high blood pressure, muscle weakness, and headache.
Editor note: DOID class refers to adenoma-caused Conn syndrome
A decrease in the number of neutrophils found in the blood.
An abnormality in which a part of a structure in one or both eyes is missing.
Heart disease which occurs as a result of a primary pulmonary disease. Cor pulmonale most often manifests as right ventricular hypertrophy; it can also lead to right ventricular failure.
A carcinoma that arises from epithelial cells of the retroperitoneal space.
Acute inflammation of the intestine associated with infectious diarrhea of various etiologies, generally acquired by eating contaminated food containing toxins, biological derived from bacteria or other microorganisms. Dysentery is characterized initially by watery feces then by bloody mucoid stools. It is often associated with abdominal pain; fever; and dehydration.
The turning inward (inversion) of the edge of the eyelid, with the tarsal cartilage turned inward toward the eyeball. (Dorland, 27th ed)
hyperparathyroidism due to renal insufficiency
secondary hyperparathyroidism (of renal origin)
secondary hyperparathyroidism of renal origin
A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood.
postpartum coagulation defect with delivery
Acute kidney injury associated with microangiopathic hemolytic anemia and thrombocytopenia.
acute renal failure, thrombocytopenia, and microangiopathic hemolytic anemia associated with distorted erythrocytes ('burr cells')
Blockage of the normal flow of urine in the urethra.
A rare, lethal congenital malformation characterized by bilateral renal agenesis and the absence or decreased volume of amniotic fluid (oligohydramnios). The presence of oligohydramnios gives rise to congenital anomalies that include hypoplastic lungs, lower extremities abnormalities, and characteristic facial features (low-set ears, widely separated eyes, nose flattening, and receding chin). Newborn infants usually die of respiratory failure.
Editor note: check for subtypes, relationship to OMIM:263200
Abnormally high concentration of calcium in the peripheral blood.
Nephrocalcinosis is a disorder that occurs when too much calcium is deposited in the kidneys. It commonly occurs in premature infants. Individuals may not have symptoms or may have symptoms related to thecondition causing nephrocalcinosis. If kidney stones are present, symptoms may include blood in the urine, fever and chills, nausea and vomiting, and severe pain in the belly area, sides of the back (flank), groin, or testicles. Later symptoms may be associated with chronic kidney failure. It may be caused by use of certain medications or supplements, infection, or any condition that leads to high levels of calcium in the blood or urine including hyperparathyroidism, renal tubular acidosis, Alport syndrome, Bartter syndrome,and a variety of other conditions. Some of the underlying disorders that can cause nephrocalcinosis are genetic, with the inheritance pattern depending on the specific disorder. Treatment differs depending on the cause of nephrocalcinosis and often aims to prevent more calcium from being deposited in the kidneys.
A well-circumscribed benign smooth muscle neoplasm characterized by the presence of spindle cells with cigar-shaped nuclei, interlacing fascicles, and a whorled pattern.
leiomyomatous neoplasm (morphologic abnormality)
A decrease in the number of mature granulocytes (neutrophils, eosinophils, and basophils) in the peripheral blood.
Loss of intellectual abilities interfering with an individual's social and occupational functions. Causes include Alzheimer's disease, brain injuries, brain tumors, and vascular disorders.
Preeclampsia with a systolic blood pressure of 160 mmHg or higher, or a diastolic blood pressure of 110 mmHg or higher on two occasions at least 4 hours apart while on bedrest. It is associated with thrombocytopenia (platelets less than 100,000 per microliter), impaired liver function (twice normal elevation of hepatic transaminases; severe, persistent right upper quadrant or epigastric pain), progressive renal insufficiency (serum creatinine greater than 1.1 mg/dL or doubling of baseline in the absence of other renal disease), pulmonary edema, or new-onset cerebral or visual disturbances.
Inflammation of the glomeruli status post infection with nephritogenic streptococci, most often group A beta hemolytic streptococcus.
acute glomerulonephritis with lesion of proliferative glomerulonephritis
A histopathologic term for a pattern of diseases characterized by extensive crescent formation in the glomeruli; patients present clinically with rapid deterioration of renal function, and possible progression to end-stage renal failure within weeks or months.
Mild to moderate high blood pressure that is caused by an underlying medical condition.
Anemia characterized by the presence of unusually large erythroblasts in the bone marrow called megaloblasts. It is usually caused by vitamin B12 or folic acid deficiency. Other causes include toxins and drugs.
recessive hereditary megaloblastic anemia 1
An inborn condition characterized by deficiencies of red cell precursors that sometimes also includes leukopenia and thrombocytopenia.
In DO this is classified as idiopathic; however, ORDO classifies idiopathic as acquired which leads to an inconsistency
Hereditary disease characterized by seizures, mental retardation, developmental delay, and skin and ocular lesions. First signs usually occur during infancy or childhood but in rare cases may not occur until 2nd or 3rd decade.
Editor note: TODO check MONDO:0019341; consider placement under neoplastic syndrome
Hyperfunction of the parathyroid glands resulting in the overproduction of parathyroid hormone. It may be primary or secondary; primary hyperparathyroidism is caused by parathyroid adenoma, parathyroid hyperplasia, parathyroid carcinoma, and multiple endocrine neoplasia. It is associated with hypercalcemia and hypophosphatemia. Signs and symptoms include weakness, fatigue, nausea, vomiting, constipation, depression, bone pain, osteoporosis, cystic bone lesions, and kidney stones. Secondary hyperparathyroidism is caused by the chronic stimulation of the parathyroid glands in patients with chronic renal failure, rickets, and malabsorption syndromes.
Conditions with abnormally low levels of lipoproteins in the blood. This may involve any of the lipoprotein subclasses, including alpha-lipoproteins (high-density lipoproteins); beta-lipoproteins (low-density lipoproteins); and prebeta-lipoproteins (very-low-density lipoproteins).
A non-neoplastic or neoplastic disorder that affects the lacrimal apparatus.
disease or disorder of lacrimal apparatus
Acute post streptococcal glomerulonephritis is an immunologic response of the kidney to infection, characterized by the sudden appearance of edema, hematuria, proteinuria and hypertension. It is essentially a disease of childhood that accounts for approximately 90% of renal disorders in children. The disease occurs especially in children between the ages of 2 and 12 years and young adults, and more often in male than in female.
acute poststreptococcal glomerulonephritis
An acute inflammation of the glomeruli, in which all glomeruli are affected, resulting in acute renal failure.
A atherosclerosis that involves the renal artery.
A group of genetic disorders of the kidney tubules characterized by the accumulation of metabolically produced acids with elevated plasma chloride, hyperchloremic metabolic acidosis. Defective renal acidification of urine (proximal tubules) or low renal acid excretion (distal tubules) can lead to complications such as hypokalemia, hypercalcinuria with nephrolithiasis and nephrocalcinosis, and rickets.
A disease involving the endocrine pancreas.
disease or disorder of endocrine pancreas
A congenital disorder characterized by the presence of extremely hypoplastic gonads preventing the development of secondary sex characteristics.
A type of defective gonadal development in patients with a wide spectrum of chromosomal mosaic variants. Their karyotypes are of partial sex chromosome monosomy resulting from an absence or an abnormal second sex chromosome (X or Y). Karyotypes include 45,X/46,xx; 45,X/46,xx/47,xxx; 46,xxp-; 45,X/46,xy; 45,X/47,xyy; 46,xypi; etc. The spectrum of phenotypes may range from phenotypic female to phenotypic male including variations in gonads and internal and external genitalia, depending on the ratio in each gonad of 45,X primordial germ cells to those with normal 46,xx or 46,xy constitution.
Increased blood pressure in the arteries of the lungs; the etiology is unknown.
A cholesterol embolism that involves the kidney.
A rare autosomal recessive inherited disorder caused by mutations of the MUT, MMAA, MMAB, MMADHC, and MCEE genes. It is characterized by abnormalities in the metabolism of lipids and proteins. Signs and symptoms usually appear early in life and vary from mild to life threatening. They include vomiting, dehydration, hypotonia, developmental delays, hepatomegaly, lethargy, intellectual disabilities, and chronic kidney disease.
METHYLMALONICACIDURIA due to methylmalonic CoA mutase deficiency
METHYLMALONICACIDURIA, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin--Cbl A
METHYLMALONICACIDURIA, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin--Cbl B
methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency
methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblA type
methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblB type
A disease that involves the orbital region.
A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia.
A laboratory test result indicating that there is an abnormally small number of platelets in the circulating blood.
A disease involving the integumental system.
disease or disorder of integumental system
A disease involving the musculoskeletal system.
disease or disorder of musculoskeletal system
musculoskeletal system disease or disorder
A benign or malignant neoplasm arising from the epithelial cells of an endocrine organ. Representative examples include pituitary gland adenoma, pituitary gland carcinoma, thyroid gland carcinoma, carcinoid tumor, and neuroendocrine carcinoma.
A malignant neoplasm arising from the blood vessels.
blood vessel tumor (morphologic abnormality)
blood vessel tumors (morphologic abnormality)
A primary or metastatic malignant neoplasm involving the cardiovascular system.
malignant cardiovascular system neoplasm
malignant neoplasm of cardiovascular system
A malignant neoplasm involving the thyroid gland
Deposition of calcium in the tissues. It may be the result of a metabolic disorder or long-standing infection, or it may be associated with the presence of cancer.
A primary or metastatic malignant neoplasm affecting the bone or articular cartilage.
A non-neoplastic or neoplastic disorder affecting the optic nerve (second cranial nerve).
A congenital disorder characterized by abnormalities in the development of the sexual characteristics.
conditions affecting reproductive development
A disorder characterized by decreased function of the gonads. Clinical manifestations in both males and females include poor libido, infertility, and osteoporosis. Additional signs in males include erectile dysfunction, muscle atrophy, gynecomastia and increased abdominal fat. In females, additional signs include shrinking of the breasts and loss of, or failure to develop menstruation.
A malignant neoplasm involving the reproductive organ
malignant neoplasm of reproductive organ
malignant neoplasm of reproductive system
A malignant neoplasm involving the connective tissue
Disorders caused by abnormalities in platelet count or function.
A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition.
syndrome associated with disease or disorder
A non-neoplastic or neoplastic disorder that affects the cervix. Representative examples include cervicitis, endocervical polyp, and carcinoma.
Inflammation of the throat most often caused by viral and bacterial infections. Other causes include allergens, chemical substances, and trauma.
A non-neoplastic or neoplastic disorder that affects the testis or the ovary.
A disease involving the female reproductive system.
disease or disorder of female reproductive system
female reproductive system disease or disorder
An inflammatory disorder that affects the upper and lower gastrointestinal tract. Most commonly, this is attributed to viruses; however bacteria, parasites or adverse reactions can also be the culprit. Symptoms include acute diarrhea and vomiting.
infectious colitis, enteritis and gastroenteritis
An inherited metabolic disorder that involves plasma protein metabolism malfunction.
A vascular disorder characterized by thickening and hardening of the walls of the arteries.
arteriosclerotic cardiovascular disease, NOS
A reduction in the number of red blood cells, the amount of hemoglobin, and/or the volume of packed red blood cells. Clinically, anemia represents a reduction in the oxygen-transporting capacity of a designated volume of blood, resulting from an imbalance between blood loss (through hemorrhage or hemolysis) and blood production. Signs and symptoms of anemia may include pallor of the skin and mucous membranes, shortness of breath, palpitations of the heart, soft systolic murmurs, lethargy, and fatigability.
Anemia that is characterized by increased red blood cell volume.
A nonspecific term referring both to the pathologic finding of swelling of distal portions of axons in the brain and to disorders which feature this finding. Neuroaxonal dystrophy is seen in various genetic diseases, vitamin deficiencies, and aging. Infantile neuroaxonal dystrophy is an autosomal recessive disease characterized by arrested psychomotor development at 6 months to 2 years of age, ataxia, brain stem dysfunction, and quadriparesis. Juvenile and adult forms also occur. Pathologic findings include brain atrophy and widespread accumulation of axonal spheroids throughout the neuroaxis, peripheral nerves, and dental pulp. (From Davis & Robertson, Textbook of Neuropathology, 2nd ed, p927)
A benign, intermediate, or malignant neoplasm that arises from the dermis.
A condition characterized by an abnormally high level of thrombi. Causes include thrombotic thrombocytopenic purpura, disseminated intravascular coagulation, bone marrow disorders, and antiphospholipid antibody syndrome.
Retinal damage resulting from diminished blood flow/oxygenation due to abnormalities of the retinal vessels. Causes include hypertension, diabetes, thrombosis, embolism, and hemorrhage.
A metabolic disorder that affects the phosphate homeostasis.
An abnormality of the nervous system that is present at birth or detected in the neonatal period.
congenital abnormality of the nervous system
Neoplasms of the hematopoietic system, including hematopoietic cell neoplasms (e.g. leukemias, lymphomas) and non-hematopoietic cell neoplasms that can affect the hematopoietic system (e.g. lymph node and splenic sarcomas). --2003
hematopoietic and lymphoid system neoplasm
hematopoietic neoplasm (morphologic abnormality)
malignant hematopoietic neoplasm (morphologic abnormality)
Inflammation of the arteries that is characterized by the presence of granulomas.
Pathological processes involving the chondral tissue (cartilage).
An instance of nephrotic syndrome that is caused by an inherited modification of the individual's genome.
A non-neoplastic or neoplastic disorder that affects the pancreas. Representative examples of non-neoplastic disorders include pancreatitis and pancreatic insufficiency. Representative examples of neoplastic disorders include cystadenomas, carcinomas, lymphomas, and neuroendocrine neoplasms.
A benign epithelial neoplasm that projects above the surrounding epithelial surface and consists of villous or arborescent outgrowths of fibrovascular stroma.
papilloma (except papilloma of bladder M-81201) (morphologic abnormality)
papillomatosis NOS (morphologic abnormality)
A hemangiopericytoma arising from the kidney.
Primary or metastatic malignant neoplasm involving the kidney.
malignant neoplasm of kidney except pelvis
A benign encapsulated neoplasm of the kidney, characterized by the presence of cysts separated by septa. There are no solid areas present. The septa are lined by one layer of epithelial cells that have eosinophilic or clear cytoplasm. The cystic spaces contain serous or hemorrhagic fluid.
A rare, usually benign neoplasm that arises from the kidney. It usually affects females. It is characterized by the presence of a biphasic pattern with tubular and cystic structures in a spindle cell stroma. Patients usually present with flank pain and hematuria.
mixed epithelial and stromal tumour of kidney
mixed epithelial stromal tumor of the kidney
An adenoma arising from the renal cortex.
renal cell adenoma (morphologic abnormality)
A benign, solitary, and partially cystic neoplasm arising from the kidney. It occurs in children and adults. Presenting symptoms include hematuria and polycythemia. It is characterized by the presence of epithelial nodules embedded in a stroma containing spindle cells.
An inflammatory process affecting the skin. Signs include red rash, itching, and blister formation. Representative examples are contact dermatitis, atopic dermatitis, and seborrheic dermatitis.
A disease involving the auditory system.
An inherited metabolic disorder characterized either by defects in glycogen synthesis or defects in the breaking down of glycogen. It results either in the creation of abnormal forms of glycogen or accumulation of glycogen in the tissues.
inborn error of glycogen metabolic process
inborn glycogen metabolic process disorder
rare inborn error of glycogen metabolic process
Glycogenosis due to glucose-6-phosphatase (G6P) deficiency or glycogen storage disease, (GSD), type 1, is a group of inherited metabolic diseases, including types a and b, and characterized by poor tolerance to fasting, growth retardation and hepatomegaly resulting from accumulation of glycogen and fat in the liver.
glycogen storage disease due to G6P deficiency
glycogen storage disease due to glucose-6-phosphatase deficiency
Diseases that affect the structure or function of the cerebellum. Cardinal manifestations of cerebellar dysfunction include dysmetria, gait ataxia, and muscle hypotonia.
Inflammation of the glomeruli characterized by deposits at the intraglomerular mesangium, resulting in thickening of the glomerular basement membrane, activation of complement, and impaired kidney function secondary to damaged glomeruli.
membranoproliferative glomerulonephritis (disease)
A renal disorder characterized by damage in the glomeruli. It may be acute or chronic, focal or diffuse, and it may lead to renal failure. Causes include autoimmune disorders, infections, diabetes, and malignancies.
A congenital or acquired kidney disorder characterized by the presence of renal cysts.
A hereditary disorder characterized by excessive oxalate production, leading to hyperoxaluria.
Sudden and sustained deterioration of the kidney function characterized by decreased glomerular filtration rate, increased serum creatinine or oliguria.
A morphologic variant of adenocarcinoma. It is characterized by the presence of a papillary growth pattern. Representative examples include thyroid gland papillary carcinoma, invasive papillary breast carcinoma, and ovarian serous surface papillary adenocarcinoma.
infiltrating and papillary adenocarcinoma
papillary adenocarcinoma (morphologic abnormality)
papillary adenocarcinoma NOS (morphologic abnormality)
A non-metastasizing neoplasm that arises from the kidney. Representative examples include cystic nephroma, metanephric adenoma, oncocytoma, and urothelial papilloma of the renal pelvis.
A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma.
disease or disorder of hepatobiliary system
hepatobiliary system disease or disorder
An inherited metabolic disorder caused by an enzyme deficiency, resulting in an inability to oxidize fatty acids for energy production.
A benign or malignant tumor involving the skin. Representative examples of benign skin neoplasms include the benign melanocytic skin nevus, acanthoma, sebaceous adenoma, sweat gland adenoma, lipoma, hemangioma, fibroma, and benign fibrous histiocytoma. Representative examples of malignant skin neoplasms include basal cell carcinoma, squamous cell carcinoma, melanoma, and Kaposi sarcoma.
A neoplasm that is composed of squamous epithelial cells. Squamous cell carcinoma is a representative example.
An adenoma characterized by the presence of papillary epithelial patterns.
papillary adenoma NOS (morphologic abnormality)
An endophytic benign papillary epithelial neoplasm that results from the invagination and proliferation of epithelial cells in the underlying stroma. Representative examples are the inverted urothelial papilloma that arises from the urinary tract and inverted Schneiderian papilloma that arises from the nasal cavity or paranasal sinuses.
A metabolic disorder caused by mutations in proteins critical for lysosomal function, including lysosomal enzymes, lysosomal integral membrane proteins, and proteins involved in the post-translational modification and trafficking of lysosomal proteins.
A disease involving the central nervous system.
central nervous system disease or disorder
disease or disorder of central nervous system
A neoplasm with perivascular epithelioid cell differentiation often associated with tuberous sclerosis. It is characterized by a mixture of epithelioid cells, smooth muscle, vessels, and mature adipose tissue. The kidney is the most common site of involvement. Other sites of involvement include the liver, lung, lymph nodes, and retroperitoneum. The vast majority of cases follow a benign clinical course. However, cases of metastatic angiomyolipomas with sarcomatoid features have been described.
angiomyolipoma (morphologic abnormality)
A benign or malignant mesenchymal neoplasm arising from the perivascular cells of the connective and soft tissues. It is characterized by the presence of pericytes that grow in a circumferential pattern around vessels.
A small blood vessel hemorrhage into the skin and/or mucous membranes. Newer lesions appear reddish in color. Older lesions are usually a darker purple color and eventually become a brownish-yellow color.
A benign, intermediate, or malignant neoplasm that arises from the mesenchyma-derived cells of the soft tissue or bone. Representative examples include lipoma, leiomyoma, leiomyosarcoma and osteosarcoma.
An osteosarcoma arising from the soft tissue.
A non-neoplastic or neoplastic disorder that affects the uterine corpus or the cervix. Representative examples of non-neoplastic disorders include endometritis and cervicitis. Representative examples of neoplastic disorders include endometrial carcinoma, carcinosarcoma, and cervical carcinoma.
A non-neoplastic or neoplastic disorder that affects the uvea. Representative examples include uveitis, chorioretinitis, and uveal melanoma.
Primary or metastatic malignant neoplasm involving the uterine corpus and/or the cervix.
An aggressive malignant embryonal neoplasm usually occurring during childhood. It is characterized by the presence of large cells with abundant cytoplasm, large eccentric nucleus, and a prominent nucleolus and it is associated with abnormalities of chromosome 22. It can arise from the central nervous system, kidney, and the soft tissues. The prognosis is poor.
A rhabdoid tumor that arises from the kidney. It occurs in children and it is associated with abnormalities of chromosome 22. It is characterized by the presence of cells with a large eccentric nucleus, prominent nucleolus, and abundant cytoplasm. The prognosis is poor.
A kidney neoplasm that occurs during childhood.
Injury to any of the cranial nerves or their nuclei in the brain resulting in muscle weakness.
A term that refers to vascular neoplasms with a prominent hemangiopericytic growth pattern.
Editor note: TODO check relationship to spindle cell tumor
A malignant mesenchymal neoplasm arising from adipocytes.
malignant neoplasm of the adipose tissue
A malignant neoplasm involving the adrenal gland
A poorly differentiated transitional cell carcinoma characterized by the presence of malignant cells with spindle cell morphologic features.
transitional cell carcinoma, sarcomatoid
transitional cell spindle cell carcinoma
A metabolic disorder characterized by abnormal blood glucose levels.
A disease that involves the pilosebaceous unit.
disease or disorder of pilosebaceous unit
A malignant neoplasm arising from smooth muscle.
A rare malignant neoplasm with melanocytic differentiation characterized by the presence of polygonal or spindle shaped clear cells. This sarcoma usually affects the tendons and aponeuroses and is associated with a poor prognosis due to recurrences and metastases.
clear cell sarcoma (morphologic abnormality)
clear cell sarcoma/malignant melanoma of soft parts (excluding clear cell sarcoma of the kidney)
A malignant tumor composed of a mixture of carcinomatous and sarcomatous elements.
malignant mixed mesodermal (mullerian) tumor
mesodermal mixed tumor (morphologic abnormality)
mullerian mixed tumor (morphologic abnormality)
A primary or metastatic malignant neoplasm involving the cervix.
malignant neoplasm of the uterine cervix
A disorder characterized by the degeneration of the nervous system due to autoimmunity. Representative examples include multiple sclerosis, Guillain-Barre syndrome, and myasthenia gravis.
autoimmune disorders of the nervous system
nervous system hypersensitivity reaction type II disease
autoimmune disease of the nervous system
A renal cell carcinoma that occurs during childhood.
childhood renal cell carcinoma (disease)
pediatric renal cell carcinoma (disease)
renal cell carcinoma (disease) of childhood
An instance of renal cell carcinoma (disease) that is caused by an inherited modification of the individual's genome.
hereditary renal cell carcinoma (disease)
Overproduction of aldosterone by the adrenal glands, which may lead to hypokalemia and/or hypernatremia.
A rare type of renal cell carcinoma. It is a well-circumscribed multicystic mass without solid areas. The inner lining of the cystic structures is composed of clear cells.
multilocular clear cell renal cell adenocarcinoma
multilocular clear cell renal cell carcinoma
multilocular cystic clear cell renal cell neoplasm of low malignant potential
multilocular cystic renal cell adenocarcinoma
multilocular cystic renal cell carcinoma
multilocular cystic renal neoplasm of low malignant potential
A low grade carcinoma of the kidney characterized by the presence of tubules which are separated by mucinous stroma. Often the tubular structures have a spindle cell appearance. Patients are usually asymptomatic and occasionally they may present with hematuria or flank pain.
mucinous tubular and spindle cell carcinoma of the kidney
mucinous tubular and spindle cell renal carcinoma
renal mucinous tubular spindle cell carcinoma
mucinous tubular and spindle renal cell carcinoma
A high grade carcinoma of the kidney. It is not a distinct clinicopathological entity and includes a diverse group of renal cell carcinomas which have been transformed from a lower to a higher grade.
renal cell carcinoma with sarcomatoid features
A benign mesenchymal neoplasm arising from smooth, skeletal, or cardiac muscle tissue.
A benign papillary neoplasm composed of transitional cells and characterized by an endophytic growth pattern.
A solid, unencapsulated tumor of the kidney composed of spindle mesenchymal cells that resemble fibroblasts or muscle cells. The homogeneous mass typically extends into the renal parenchyma and replaces most of the kidney. In most cases, mesoblastic nephroma is benign and occurs in the fetus or newborn, and rarely in the older child or the adult.
mesoblastic nephroma (morphologic abnormality)
Inflammation of the glomeruli with infiltration by polymorphonuclear leukocytes.
A constellation of renal disorders characterized by an increase number of cells in the glomerulus; these disorders generally present with nephrotic syndrome, and generally progress to end stage renal failure over a matter of weeks to years, depending on the etiology. Examples include IgA nephropathy, membranoproliferative glomerulonephritis, and rapidly progressive glomerulonephritis.
Inflammation of a specific segment of glomeruli, which is associated with subacute bacterial endocarditis, and frequently produces microscopic hematuria without azotemia.
Inflammation of the glomeruli secondary to presence of autoantibodies directed at specific antigenic targets within the glomerular basement membrane, causing hematuria, proteinuria, and impaired renal function.
anti-glomerular basement Membrane antibody disease
anti-basement membrane glomerulonephritis
Inflammation of the glomeruli, in which all glomeruli are affected, resulting in renal failure.
A term that refers to glomerular damage resulting in hematuria, proteinuria, and azotemia. The histopathologic changes include rapidly progressive glomerulonephritis and membranoproliferative glomerulonephritis.
Mesangial proliferative glomerulonephritis (MPGN) is a condition that affects the kidneys. Many experts consider it a variant of minimal change disease, but some experts believe it is a separate condition. It may present with nephrotic syndrome, which is a group of symptoms that include protein in the urine (proteinuria), low blood protein levels, high cholesterol levels, high triglyceride levels, and swelling. It can also present with blood in the urine (hematuria). MPGN is characterized by an increased number of mesangial cells in the glomeruli in the kidneys and damage to the glomeruli. Glomeruli are the structures that help filter wastes and fluids. MPGN may occur in several renal diseases such as IgA nephropathy (commonly), IgM nephropathy, lupus nephritis, and C1q nephropathy.However, in some cases, the underlying cause of MPGN remains unclear. Treatment may depend on the cause (if known) and may include steroids, mycophenolate mofetil, and/or cyclophosphamide, and other therapies to treat specific symptoms. Most people with MPGN have a good prognosis, but some may develop chronic kidney disease, which can progress to end stage renal failure.
Mesangioproliferative glomerulonephritis
glomerulonephritis - mesangial proliferative
mesangial proliferative glomerulonephritis
Inflammation of the glomeruli characterized by the accumulation of antibody-antigen immune complexes, resulting in glomerular damage and impaired kidney function.
A disease involving the male reproductive system.
disease or disorder of male reproductive system
male reproductive system disease or disorder
A carcinoma that arises from glandular epithelial cells of the renal pelvis
A primary or metastatic malignant neoplasm affecting the tissues of the thorax.
malignant neoplasm of thoracic segment of trunk
malignant thoracic segment of trunk neoplasm
A benign smooth muscle neoplasm arising from the arrector pili muscle, tunica media of blood vessels, and dartos muscle of the genitalia. It is characterized by the presence of spindle cells with cigar-shaped nuclei, interlacing fascicles, and a whorled pattern.
A condition characterized by the presence of numerous small benign smooth muscle neoplasms located throughout the body.
leiomyomatosis, no ICD-O subtype (morphologic abnormality)
Wilms tumor of the kidney characterized by the absence of nuclear anaplasia.
Wilms tumor arising in the remaining kidney following treatment of the original Wilms tumor.
Wilms tumor of the kidney characterized by the presence of blastema, epithelial, and mesenchymal components (triphasic pattern) or a combination of two of them (biphasic pattern).
Wilms tumor of the kidney characterized by the predominance of the blastema component.
blastema predominant kidney adenosarcoma
blastema predominant kidney Wilms' tumor
Familial embryonal neoplasm derived from nephrogenic blastemal cells. Several lines of differentiation, including blastemal, stromal and epithelial, are usually expressed. Comprises approximately 1% of Wilms tumors. (AFIP fascicle version 2.0)
Wilms tumor of the kidney characterized by the predominance of the epithelial component. The epithelial cells may form papillary and tubular patterns and pseudorosettes.
epithelial predominant kidney Wilms tumor
epithelial predominant kidney adenosarcoma
epithelial predominant renal Wilm's tumor
epithelial predominant renal Wilms tumor
epithelial predominant renal Wilms' tumor
epithelial predominant renal adenosarcoma
Blockage of the normal flow of contents of the urinary tract.
Vasculitis affecting the blood vessels of the brain and/or spinal cord.
An aggressive malignant smooth muscle neoplasm, arising from the kidney. It is characterized by a proliferation of neoplastic spindle cells.
A disease involving the pituitary gland.
A cervical adenocarcinoma that arises from mesonephric remnants. It is usually characterized by the presence of tubular glands lined by cuboidal epithelial cells.
A movement disorder characterized by sustained or intermittent muscle contractions, resulting in abnormal movements and/or postures.
A neoplastic lesion of the urinary tract transitional cell epithelium characterized by papillary formations. -- 2003
papillary transitional cell neoplasm of the urinary tract
urinary tract papillary transitional cell neoplasm
urothelium papillary epithelial neoplasm
urinary tract papillary transitional cell benign neoplasm
A squamous cell carcinoma that involves the renal pelvis.
epidermoid carcinoma of the kidney pelvis
epidermoid carcinoma of the renal pelvis
kidney renal pelvis squamous cell cancer
squamous cell carcinoma of kidney pelvis
squamous cell carcinoma of the kidney pelvis
squamous cell carcinoma of the renal pelvis
A disease involving the oculomotor nerve.
A neoplastic or non-neoplastic disorder that affects one of the cranial nerves.
cranial neuron projection bundle disease
cranial neuron projection bundle disease or disorder
disease of cranial neuron projection bundle
disease or disorder of cranial neuron projection bundle
disorder of cranial neuron projection bundle
A rare malignant adipose tissue neoplasm of the fat cells surrounding the kidney, usually of the well-differentiated or myxoid type. It may be associated with tuberous sclerosis.
A disease involving the peripheral nervous system.
PNS (peripheral nervous system) diseases
disease or disorder of peripheral nervous system
disorder of the peripheral nervous system
peripheral nervous system disease or disorder
The presence of abnormal amounts of protein in the urine.
Urolithiasis in which the composition of the stones is predominantly urate.
A laboratory test result which indicates free hemoglobin in the urine.
May be obsoleted as it represents a finding
Anemia resulting from the premature destruction of the peripheral blood red cells. It may be congenital or it may be caused by infections, medications, or malignancies.
A congenital hemolytic anemia caused by defects of the erythrocyte membrane, enzyme deficiencies, or hemoglobinopathies.
A papillary transitional cell carcinoma that arises from the renal pelvis.
papillary carcinoma of the kidney pelvis
renal pelvis papillary urothelial carcinoma
A papillary tumor originating in the renal pelvis.
renal pelvis papillary urothelial neoplasm
A neoplasm (disease) that involves the renal pelvis.
A usually aggressive malignant neoplasm arising from the kidney. It is characterized by the presence of spindle-shaped fibroblasts and collagenous stroma formation in a herringbone growth pattern.
An osteosarcoma arising from the kidney.
A non-neoplastic or neoplastic disorder that affects the esophagus. Representative examples of non-neoplastic disorders include esophagitis and esophageal ulcer. Representative examples of neoplastic disorders include carcinomas, lymphomas, and melanomas.
non-invasive transitional cell neoplasm of the urinary tract
urinary tract non-invasive transitional cell neoplasm
Complete paralysis of the lower half of the body including both legs, often caused by damage to the spinal cord.
severe or complete loss of motor function in the lower extremities and lower portions of the trunk
A neoplasm of the renal pelvis in which the epithelial cells grow downward into the underlying supportive tissue.
A benign neoplasm of the renal pelvis that involves the transitional epithelium projecting above the surrounding epithelial surface and consisting of villous or arborescent outgrowths of fibrovascular stroma.
A disorder in which the immune system is unable to mount an adequate immune response.
A broad classification of disorders that affect the cell-mediated aspect of the immune response. Circulating numbers of T lymphocytes are decreased or ineffective.
A laboratory test result indicating a decreased number of white blood cells in the peripheral blood.
A familial carcinoma inherited in an autosomal dominant trait. It is characterized by the development of multiple, bilateral papillary renal cell carcinomas. The carcinomas range from microscopic lesions to clinically symptomatic tumors. It is associated with activating mutations of the MET oncogene.
hereditary papillary carcinoma of kidney
hereditary papillary carcinoma of the kidney
hereditary papillary renal cell carcinoma
A disease involving the articular cartilage of joint.
articular cartilage of joint disease or disorder
disease or disorder of articular cartilage of joint
disorder of articular cartilage of joint
articular cartilage disorder involving ankle and foot
articular cartilage disorder involving forearm
articular cartilage disorder involving hand
articular cartilage disorder involving multiple sites
articular cartilage disorder involving pelvic region and thigh
articular cartilage disorder involving shoulder region
articular cartilage disorder involving upper arm
articular cartilage disorder of ankle and/or foot
articular cartilage disorder of multiple sites
articular cartilage disorder of shoulder region
articular cartilage disorder of the pelvic region and thigh
articular cartilage disorder of upper arm
An inherited condition characterized by the development of kidney oncocytomas which are often bilateral and multifocal. This condition may be connected to Birt-Hogg-Dube syndrome.
A benign tumor of the kidney, characterized by the presence of large cells with abundant eosinophilic granular cytoplasm. The majority of these tumors are discovered incidentally, during work-up of other conditions.
A controversial term, used for renal papillary lesions which measure 1cm or less in diameter and contain small, regular nuclei.
A genetic deficiency of any of the component of the complement system (including the classical, alternative, and terminal pathway components), that can either be acquired or inherited.
immunodeficiency due to a complement cascade component deficiency
A disease that is caused by genetic modifications where those modifications are inherited from a parent's genome.
Usage note: this is intended only for diseases with an inherited genetic etiology. Somatic genetic mutations are excluded. Some ontologies use the term 'genetic disease' in the sense of inherited disorders only, we are here careful to distinguish.
A disease involving the connective tissue.
disease or disorder of connective tissue
An imbalanced nutritional status resulting from excessive intake of nutrients. Generally, overnutrition generates an energy imbalance between food consumption and energy expenditure leading to disorders such as obesity.
A benign neoplasm that can arise from any of the adrenal cortical layers. It can be associated with the overproduction of glucocorticoids (Cushing's syndrome), androgenic or estrogenic steroids (adrenogenital syndrome), or mineralocorticoids (Conn's syndrome). (Sternberg Diagnostic Surgical Pathology, 3rd ed.)
classic variant of chromophobe renal cell carcinoma
eosinophilic variant of chromophobe renal cell carcinoma
An infiltrating transitional cell carcinoma that arises from the renal pelvis and exhibits sarcomatoid features.
infiltrating renal pelvis urothelial carcinoma, sarcomatoid variant
kidney pelvis sarcomatoid transitional cell carcinoma
renal pelvis sarcomatoid transitional cell carcinoma
sarcomatoid transitional cell carcinoma of kidney pelvis
sarcomatoid transitional cell carcinoma of renal pelvis
sarcomatoid transitional cell carcinoma of the kidney pelvis
sarcomatoid transitional cell carcinoma of the renal pelvis
infiltrating renal pelvis and ureter transitional cell carcinoma
infiltrating renal pelvis and ureter urothelial carcinoma
infiltrating ureter transitional cell carcinoma
infiltrating renal pelvis/ureter urothelial carcinoma
Deficiency in the enamel tissue that results in the formation of grooves, pits, or dents on the surface of the affected teeth.
A rare benign condition, characterized by a papillary growth in the urinary tract with a central fibrovascular core. The latter is lined by normal urothelium.
Diseases caused by abnormal function of the mitochondria. They may be caused by mutations, acquired or inherited, in mitochondrial dna or in nuclear genes that code for mitochondrial components. They may also be the result of acquired mitochondria dysfunction due to adverse effects of drugs, infections, or other environmental causes.
inborn mitochondrial metabolism disorder
A group of heterogeneous lymphoid tumors generally expressing one or more B-cell antigens or representing malignant transformations of B-lymphocytes.
Anemia in which the red blood cell volume is normal.
Abnormal growth of the cells of the urethra (lower urinary tract) without malignant characteristics.
A non-metastasizing neoplasm that arises from the organs that comprise the urinary system. Representative examples include renal oncocytoma, bladder inverted papilloma, and urothelial papilloma.
A metaplastic lesion of the urothelium found in the urinary bladder. It is characterized by the presence of aggregates of cuboidal or hobnail cells and represents a reaction of the urothelium to injury caused by instrumentation, surgery or calculi.
nephrogenic adenoma of the urinary bladder
So-called nephrogenic adenoma is a distinct metaplastic lesion of the urothelium characterized by aggregates of cuboidal or hobnail cells. These cells line thin papillary fronds on the surface or form tubular structures within the lamina propria.
The loss of muscle tissue due to inactivity or disease.
A disease or disorder that involves the digestive system.
A cystic neoplasm which arises from the kidney and occurs in children. It includes the cystic partially differentiated nephroblastoma and cases in which nephroblastomatous elements are not present.
childhood multilocular cystic kidney neoplasm
childhood multilocular cystic kidney tumor
childhood multilocular cystic renal neoplasm
childhood multilocular cystic renal tumor
pediatric multilocular cystic kidney neoplasm
pediatric multilocular cystic kidney tumor
pediatric multilocular cystic renal neoplasm
pediatric multilocular cystic renal tumor
Long-standing and persistent renal disease with glomerular filtration rate (GFR) less than 15 ml/min.
Overactivity of the thyroid gland resulting in overproduction of thyroid hormone and increased metabolic rate. Causes include diffuse hyperplasia of the thyroid gland (Graves' disease), single nodule in the thyroid gland, and thyroiditis. The symptoms are related to the increased metabolic rate and include weight loss, fatigue, heat intolerance, excessive sweating, diarrhea, tachycardia, insomnia, muscle weakness, and tremor.
A congenital mesoblastic nephroma characterized by increased cellularity, sheet-like proliferation of fibroblastic cells, and increased mitotic activity. Necrotic changes are commonly present.
cellular congenital mesoblastic nephroma
A congenital mesoblastic nephroma characterized by the presence of interlacing fascicles of fibroblastic cells, low mitotic activity, and collagen formation.
A metaplastic lesion of the urothelium found in the urethra. It is characterized by the presence of aggregates of cuboidal or hobnail cells and represents a reaction of the urothelium to injury caused by instrumentation, surgery or calculi.
An angiomyolipoma occurring in childhood.
An angiomyolipoma arising from the kidney.
Hypertrophy and dilation of the right ventricle of the heart that is caused by pulmonary hypertension. This condition is often associated with pulmonary parenchymal or vascular diseases, such as chronic obstructive pulmonary disease and pulmonary embolism.
A malignant epithelial neoplasm which is confined to the epithelial layer without evidence of further tissue invasion.
Editor note: check pre-malignant vs malignant
An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus.
An inherited metabolic disorder that involves metabolic disturbances in the processing or distribution of dietary minerals.
Autosomal dominant form of polycystic kidney disease.
polycystic kidney disease, autosomal dominant
autosomal dominant polycystic kidney disease
An inherited disorder that affects the metabolism of the amino acids. Representative examples include alkaptonuria, homocystinuria, tyrosinemia, and phenylketonuria.
inborn cellular amino acid metabolic process disorder
inborn error of cellular amino acid metabolic process
rare inborn error of cellular amino acid metabolic process
An autosomal recessive inherited metabolic disorder caused by mutations in the CBS, MTHFR, MTR, and MTRR genes. It is characterized by abnormalities in the methionine metabolism and is associated with deficiency of cystathionine synthase. It results in the accumulation of homocysteine in the serum. It may affect the cardiovascular, musculoskeletal and the central nervous systems.
An autosomal recessive inherited metabolic disorder caused by mutations in the FAH, HPD, and TAT genes. It is characterized by deficiency of one of the enzymes that are involved in the metabolism of tyrosine. It results in elevated blood tyrosine levels and accumulation of tyrosine and its byproducts in the liver, kidney, nervous system and other organs.
A congenital abnormality consisting of one or more clefts (splits) in the upper lip, which may be accompanied by a cleft palate; it is the result of the failure of the embryonic parts of the lip to fuse.
A disorder characterized by excretion of large amounts of urine, accompanied by excessive thirst. Causes include deficiency of antidiuretic hormone or failure of the kidneys to respond to antidiuretic hormone. It may also be drug-related.
Global enlargement of the renal parenchyma in one or both kidneys.
A disease involving the upper respiratory tract.
disease or disorder of upper respiratory tract
upper respiratory tract disease or disorder
A neurodegenerative disease that involves the eye.
eyeball of camera-type eye neurodegenerative disease
neurodegenerative disease of eyeball of camera-type eye
A neoplasm of follicle centre B cells which has at least a partial follicular pattern. Follicular lymphomas comprise about 35% of adult non-Hodgkin lymphomas in the U.S. and 22% worldwide. Most patients have widespread disease at diagnosis. Morphologically, follicular lymphomas are classified as Grade 1, Grade 2, and Grade 3, depending on the percentage of the large lymphocytes present. The vast majority of cases (70-95%) express the BCL-2 rearrangement [t(14;18)]. Histological grade correlates with prognosis. Grades 1 and 2 follicular lymphomas are indolent and grade 3 is more aggressive (adapted from WHO, 2001).
Editor note: is a non-hodgkin in ONCOTREE
A clonal proliferation of immunoglobulin-secreting plasma cells. This category includes plasma cell myeloma, plasma cell leukemia, plasmacytoma, monoclonal immunoglobulin deposition disease, and monoclonal gammopathy of undetermined significance.
See https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/39
A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous). Representative examples of adenocarcinoma are ductal and lobular breast carcinoma, lung adenocarcinoma, renal cell carcinoma, hepatocellular carcinoma (hepatoma), colon adenocarcinoma, and prostate adenocarcinoma.
adenocarcinoma NOS (morphologic abnormality)
adenocarcinoma, no subtype (morphologic abnormality)
A neoplasm arising from the epithelium. It may be encapsulated or non-encapsulated but non-invasive. The neoplastic epithelial cells may or may not display cellular atypia or dysplasia. In the gastrointestinal tract, when dysplasia becomes severe it is sometimes called carcinoma in situ. Representative examples are pituitary gland adenoma, follicular adenoma of the thyroid gland, and adenomas (or adenomatous polyps) of the gastrointestinal tract.
acinar cell adenoma (morphologic abnormality)
In the same amount or manner; to the same degree; in the role, function, or capacity of.
A benign or malignant, primary or metastatic neoplasm of the bladder. - 2003
A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
A malignant tumor arising from epithelial cells. Carcinomas that arise from glandular epithelium are called adenocarcinomas, those that arise from squamous epithelium are called squamous cell carcinomas, and those that arise from transitional epithelium are called transitional cell carcinomas. Morphologically, the malignant epithelial cells may display abnormal mitotic figures, anaplasia, and necrosis. Carcinomas are graded by the degree of cellular differentiation as well, moderately, or poorly differentiated. Carcinomas invade the surrounding tissues and tend to metastasize to other anatomic sites. Lung carcinoma, skin carcinoma, breast carcinoma, colon carcinoma, and prostate carcinoma are the most frequently seen carcinomas.
A disease of the heart muscle or myocardium proper. Cardiomyopathies may be classified as either primary or secondary, on the basis of etiology, or on the pathophysiology of the lesion: hypertrophic, dilated, or restrictive.
A disease involving the cardiovascular system.
cardiovascular system disease or disorder
disease of subdivision of hemolymphoid system
disease or disorder of cardiovascular system
A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid.
Mesonephroma NOS (morphologic abnormality)
Mesonephroma, malignant (morphologic abnormality)
clear cell adenocarcinoma (morphologic abnormality)
clear cell adenocarcinoma NOS (morphologic abnormality)
water-clear cell adenocarcinoma (morphologic abnormality)
A malignant epithelial neoplasm of the kidney characterized by the presence of lipid-containing clear cells within a vascular network. The tumor may metastasize to unusual sites and late metastasis is common.
conventional (clear cell) renal cell adenocarcinoma
conventional (clear cell) renal cell carcinoma
renal cell carcinoma, clear cell adenocarcinoma
clear-cell metastatic renal cell carcinoma
A rare pediatric sarcoma affecting the kidney. It is characterized by the presence of epithelioid or spindle cells forming cords or nests, separated by fibrovascular septa. It is associated with internal tandem duplications in the BCOR gene. It metastasizes to lung, bone, brain and soft tissue.
childhood clear cell sarcoma of the kidney
Failure of the heart to pump a sufficient amount of blood to meet the needs of the body tissues, resulting in tissue congestion and edema. Signs and symptoms include shortness of breath, pitting edema, enlarged tender liver, engorged neck veins, and pulmonary rales.
A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization.
Progressive kidney disorder caused by vascular damage to the glomerular capillaries, in patients with diabetes mellitus. It is usually manifested with nephritic syndrome and glomerulosclerosis.
A variant of systemic scleroderma characterized by sclerosis of the skin, Raynaud phenomenon, and organ involvement, including pulmonary fibrosis, renal disease, and gastrointestinal tract involvement.
A non-neoplastic or neoplastic disorder that affects the small or large intestine.
Cardiomyopathy which is characterized by dilation and contractile dysfunction of the left and right ventricles. It may be idiopathic, or it may result from a myocardial infarction, myocardial infection, or alcohol abuse. It is a cause of congestive heart failure.
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
A disease involving the reproductive system.
disease or disorder of reproductive system
Increased pressure in the eyeball due to obstruction of the outflow of aqueous humor.
An abnormal increase in the number of cells in an organ or a tissue with consequent enlargement.
A condition in which the myocardium is hypertrophied without an obvious cause. The hypertrophy is generally asymmetric and may be associated with obstruction of the ventricular outflow tract.
A disorder resulting from an abnormality in the immune system.
Inability to conceive for at least one year after trying and having unprotected sex. Causes of female infertility include endometriosis, fallopian tubes obstruction, and polycystic ovary syndrome. Causes of male infertility include abnormal sperm production or function, blockage of the epididymis, blockage of the ejaculatory ducts, hypospadias, exposure to pesticides, and health related issues.
Editor note: dubious as to whether this is a disease as defined, check with clingen before obsoleting
An uncommon, aggressive malignant smooth muscle neoplasm, usually occurring in post-menopausal women. It is characterized by a proliferation of neoplastic spindle cells. Morphologic variants include epithelioid, granular cell, inflammatory and myxoid leimyosarcomas.
leiomyosarcoma (excluding uterine leiomyosarcoma)
A usually painless malignant tumor that arises from adipose tissue. Microscopically, it may contain a spectrum of neoplastic adipocytes ranging from lipoblasts to pleomorphic malignant adipocytes. Morphologic variants include: well differentiated, dedifferentiated, pleomorphic, and myxoid liposarcoma. The metastatic potential is higher in less differentiated tumors.
A malignant (clonal) proliferation of B- lymphocytes or T- lymphocytes which involves the lymph nodes, bone marrow and/or extranodal sites. This category includes Non-Hodgkin lymphomas and Hodgkin lymphomas.
This is potentially too broad as well as overlaps with leukemia and should be obsoleted.
A congenital disorder (due to inherited enzyme abnormality) or acquired (due to failure of a metabolically important organ) disorder resulting from an abnormal metabolic process.
A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
Preeclampsia is a hypertensive disorder of pregnancy that is characterized by new-onset hypertension with proteinuria presenting after 20 weeks of gestation, and depending on mild or severe forms may initially present with severe headache, visual disturbances, and hyperreflexia.
A disease that has its basis in the disruption of mental process.
A carcinoma that arises from glandular epithelial cells of the kidney
A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma.
disease or disorder of respiratory system
A usually aggressive malignant neoplasm of the soft tissue or bone. It arises from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels. Sarcomas occur in both children and adults. The prognosis depends largely on the degree of differentiation (grade) of the neoplasm. Representative subtypes are liposarcoma, leiomyosarcoma, osteosarcoma, and chondrosarcoma.
Any deviation from the normal structure or function of the skin or subcutaneous tissue that is manifested by a characteristic set of symptoms and signs.
An antiquated term that refers to benign or malignant mesenchymal neoplasms characterized by the presence of neoplastic spindle-shaped to round cells arranged around thin-walled branching vascular spaces.
hemangiopericytoma, malignant (morphologic abnormality)
A carcinoma arising from squamous epithelial cells. Morphologically, it is characterized by the proliferation of atypical, often pleomorphic squamous cells. Squamous cell carcinomas are graded by the degree of cellular differentiation as well, moderately, or poorly differentiated. Well differentiated carcinomas are usually associated with keratin production and the presence of intercellular bridges between adjacent cells. Representative examples are lung squamous cell carcinoma, skin squamous cell carcinoma, and cervical squamous cell carcinoma.
squamous cell carcinoma (morphologic abnormality)
squamous cell carcinoma NOS (morphologic abnormality)
A chronic disorder, possibly autoimmune, marked by excessive production of collagen which results in hardening and thickening of body tissues. The two types of systemic scleroderma, limited cutaneous and diffuse cutaneous are classified with focus on the extent of affected skin. A relationship exists between the extent of skin area affected and degree of internal organ/system involvement. Systemic scleroderma can manifest itself in pulmonary fibrosis, Raynaud's syndrome, digestive system telangiectasias, renal hypertension and/or pulmonary hypertension.
A benign, usually painless, well-circumscribed lipomatous tumor composed of adipose tissue.
lipomatous neoplasm (morphologic abnormality)
An infection caused by the human immunodeficiency virus.
Human immunodeficiency virus caused disease or disorder
Human immunodeficiency virus disease or disorder
Human immunodeficiency virus infectious disease
An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections.
Partial or complete opacity of the crystalline lens of one or both eyes that decreases visual acuity and eventually results in blindness. Some cataracts appear in infancy or in childhood, but most develop in older individuals. (Sternberg Diagnostic Surgical Pathology, 3rd ed.)
A carcinoma arising from either the exocervical squamous epithelium or the endocervical glandular epithelium. The major histologic types of cervical carcinoma are: squamous carcinoma, adenocarcinoma, adenosquamous carcinoma, adenoid cystic carcinoma and undifferentiated carcinoma.
Any condition related to a disturbance between proper intake and utilization of nourishment.
A chronic condition characterized by minimal or absent production of insulin by the pancreas.
A type of diabetes mellitus that is characterized by insulin resistance or desensitization and increased blood glucose levels. This is a chronic disease that can develop gradually over the life of a patient and can be linked to both environmental factors and heredity.
type 2 diabetes mellitus non-insulin dependent
diabetes mellitus, type 2, protection against
Increased pressure within the pulmonary circulation due to lung or heart disorder.
A disease involving the endocrine system.
A condition of diminution or cessation of secretion of one or more hormones from the anterior pituitary gland. This may result from surgical or radiation ablation, non-secretory pituitary neoplasms, metastatic tumors, infarction, pituitary apoplexy, infiltrative or granulomatous processes, and other conditions.
An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type.
cervical adenocarcinoma, not otherwise specified
liver and intrahepatic bile duct disorder
Inflammation of the brain and the spinal cord.
A neoplasm composed of a lymphocytic cell population which is usually malignant (clonal) by molecular genetic and/or immunophenotypic analysis. Lymphocytic neoplasms include Hodgkin and non-Hodgkin lymphomas, acute and chronic lymphocytic leukemias, and plasma cell neoplasms.
A malignant mesenchymal fibroblastic neoplasm affecting the soft tissue and bone.
fibrosarcoma (excluding infantile fibrosarcoma)
A neoplasm which is characterized by the absence of morphologic features associated with malignancy (severe cytologic atypia, tumor cell necrosis, and high mitotic rate). Benign neoplasms remain confined to the original site of growth and do not metastasize to other anatomic sites.
Editor note: see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/14
A disease involving the skeletal system.
A type of heart disorder referring to the inability of the ventricles to fill with blood because the myocardium (heart muscle) stiffens and looses its flexibility. Causes include replacement of the myocardium with scar tissue, abnormal cellular infiltration of the myocardium, or deposition of a substance (e.g., amyloid) in the myocardium.
A carcinoma arising from the epithelium of the renal parenchyma or the renal pelvis. The majority are renal cell carcinomas. Kidney carcinomas usually affect middle aged and elderly adults. Hematuria, abdominal pain, and a palpable mass are common symptoms.
An instance of cardiomyopathy that is caused by an inherited modification of the individual's genome.
Acquired, familial, and congenital disorders of skeletal muscle and smooth muscle.
Editor note: consider merging with child
A carcinoma that arises from epithelial cells of the collecting duct of renal tubule
carcinoma of collecting duct of renal tubule
carcinoma of collecting ducts of Bellini
carcinoma of the collecting ducts of Bellini
collecting duct of renal tubule carcinoma
A carcinoma that arises from the transitional epithelium of the renal pelvis. It is associated with tobacco use and usually presents with gross or microscopic hematuria. Urothelial carcinomas of the renal pelvis are usually of higher grade and higher stage compared to bladder urothelial carcinomas.
renal pelvis transitional cell carcinoma
transitional cell carcinoma of renal pelvis
transitional cell carcinoma of the renal pelvis
urothelial cell carcinoma of renal pelvis
urothelial cell carcinoma of the renal pelvis
A disorder affecting the peripheral nervous system. It manifests with pain, tingling, numbness, and muscle weakness. It may be the result of physical injury, toxic substances, viral diseases, diabetes, renal failure, cancer, and drugs.
Editor note: NCIT draws a distinction between neuropathy and peripheral neuropathy see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/20
A bacterial infectious process affecting any part of the urinary tract, most commonly the bladder and the urethra. Symptoms include urinary urgency and frequency, burning sensation during urination, lower abdominal discomfort, and cloudy urine.
Inability of the heart to pump blood at an adequate rate to meet tissue metabolic requirements. Clinical symptoms of heart failure include: unusual dyspnea on light exertion, recurrent dyspnea occurring in the supine position, fluid retention or rales, jugular venous distension, pulmonary edema on physical exam, or pulmonary edema on chest x-ray presumed to be cardiac dysfunction.
A disease involving the heart and/or pericardium.
An autoimmune disorder that manifests as different lupus-specific skin disorders; it can occur with systemic lupus erythematosus, or as a singular disease.
Any disorder affecting blood flow through the veins or arteries outside of the heart.
A condition of reduced bone mass, with decreased cortical thickness and a decrease in the number and size of the trabeculae of cancellous bone (but normal chemical composition), resulting in increased fracture incidence. Osteoporosis is classified as primary (Type 1, postmenopausal osteoporosis; Type 2, age-associated osteoporosis; and idiopathic, which can affect juveniles, premenopausal women, and middle-aged men) and secondary osteoporosis (which results from an identifiable cause of bone mass loss).
Impairment of the renal function secondary to chronic kidney damage persisting for three or more months.
A ciliopathy is a genetic disorder of the cellular cilia or the cilia anchoring structures, the basal bodies, or of ciliary function.
Build-up of fatty material and calcium deposition in the arterial wall resulting in partial or complete occlusion of the arterial lumen.
Note that NCIT distinguishes between atherosclerotic cardiovascular disease and atherosclerosis - we merge these here
A non-neoplastic or neoplastic disorder that affects the eye. Representative examples include conjunctivitis, glaucoma, cataract, conjunctival squamous cell carcinoma, uveal melanoma, and retinoblastoma.
disease or disorder of eyeball of camera-type eye
eyeball of camera-type eye disease or disorder
A group of inherited conditions characterized initially by hematuria and slowly progressing to renal insufficiency. The most common form is the Alport syndrome (hereditary nephritis with hearing loss) which is caused by mutations in genes for type IV collagen and defective glomerular basement membrane.
A disease of the muscle in which the muscle fibers do not function properly. This results in muscular weakness.
Editor note: TODO check this, relationship to myotonic disorder/syndrome, also check HP definition
Inflammation of a specific segment of glomeruli within the kidney.
A renal disorder characterized by sclerotic lesions in the glomeruli. Causes include drugs, viruses, and malignancies (lymphomas), or it may be idiopathic. It presents with asymptomatic proteinuria or nephritic syndrome and it may lead to renal failure.
FSGS - focal segmental glomerulosclerosis
A partial or complete loss of hearing in one or both ears. It is classified as conductive, sensory, or central.
The inability of the male to effect fertilization of an ovum after a specified period of unprotected intercourse. Male sterility is permanent infertility.
infertility disorder of male reproductive system
male reproductive system infertility disorder
A slowly progressive inflammation of the glomeruli characterized by immune complex deposits at the glomerular basement membrane, resulting in a thickened membrane, and nephrotic syndrome.
A collection of symptoms that include severe edema, proteinuria, and hypoalbuminemia; it is indicative of renal dysfunction.
A none disease characterized by death of bone tissue due to a lack of blood supply.
rare bone disease related to a common gene or pathway defect
A non-neoplastic or neoplastic disorder affecting the arteries, veins, or lymphatic vessels. Examples include vasculitis, thrombophlebitis, arteriosclerosis, lymphedema, hemangioma, and angiosarcoma.
Absent or premature cessation of ovarian function due to a pathologic process originating within the ovaries.
Neurological conditions resulting in abnormal voluntary or involuntary movement, which may impact the speed, fluency, quality and ease of movement.
Diabetic nephropathy is a progressive kidney disease caused by angiopathy of capillaries in the kidney glomeruli. In type 1 diabetes hyperglycaemia starts in the first decades of life and is usually the only recognized cause of nephropathy.
Diabetic nephropathy is a progressive kidney disease caused by angiopathy of capillaries in the kidney glomeruli. In type 2 diabetes hyperglycaemia starts after the forties, usually when the kidneys have already suffered the long‐term consequences of ageing and of other recognized promoters of chronic renal injury such as arterial hypertension, obesity, dyslipidaemia, and smoking.
A disease involving the bone development.
A congenital disorder of glycosylation involve disrupted synthesis of the lipid-linked oligosaccharide precursor.
congenital disorders of glycosylation, type I
congenital disorder of glycosylation type I
A congenital disorder of glycosylation that involves malfunctioning trimming/processing of the protein-bound oligosaccharide chain.
congenital disorders of glycosylation, type II
congenital disorder of glycosylation type II
A disease of mental health that occur during a child's developmental period between birth and age 18 resulting in retarding of the child's psychological or physical development.
Collection of urine in the renal pelvis that results in dilatation of the renal pelvis and calyces. It is caused by obstruction of urine flow, nephrolithiasis, or vesicoureteral reflux. Signs and symptoms include flank pain, nausea, vomiting, fever, and dysuria.
A term referring to disorders characterized by abnormalities in the development of bones and cartilage.
A carcinoma arising in the renal pelvis. The majority of renal pelvis carcinomas are transitional cell and less frequently squamous cell carcinomas.
Bone softening and weakening usually caused by deficiency or impaired metabolism of vitamin D. Deficiency of calcium, magnesium, or phosphorus may also cause rickets. It predominantly affects children who suffer from severe malnutrition. It manifests with bone pain, fractures, muscle weakness, and skeletal deformities.
vitamin D hydroxylation-deficient rickets
An acquired metabolic disease that is has its basis in the disruption of vitamin metabolic process.
inborn error of vitamin metabolic process
inborn vitamin metabolic process disorder
rare inborn error of vitamin metabolic process
A carcinoma arising from the renal parenchyma. There is a strong correlation between cigarette smoking and the development of renal cell carcinoma. The clinical presentation includes : hematuria, flank pain and a palpable lumbar mass. A high percentage of renal cell carcinomas are diagnosed when an ultrasound is performed for other purposes. Radical nephrectomy is the standard intervention procedure. Renal cell carcinoma is generally considered to be resistant to radiation treatment and chemotherapy.
A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact.
Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself.
A disorder that is caused by pathologic changes in the ocular vasculature.
disease or disorder of vasculature of eye
Inflammatory and degenerative diseases of connective tissue structures, such as arthritis.
This is an umbrella term encompassing conditions causing chronic, often intermittent pain affecting the joints and/or connective tissue
Glomerulonephritis in the context of systemic lupus erythematosus.
Defined in terms of GO calcium ion homeostatis. Also consistent with HPO. Note advice from GO as calcium ions are neither created or destroyed is not metabolic process in terms of go, but name retained for purposes of consistency with e.g. Snomed and Mesh, Consider relocating this as a sibling of metabolic disease.
A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function.
central nervous system degenerative disorder
central nervous system neurodegenerative disorder
degenerative disorder of central nervous system
Editor notes: DO treats this as two diseases
A disease affecting the brain or part of the brain.
Editor note: NCIT has different classes for brain disease and encephalopathy
Pathology involving the thoracic, thoracoabdominal, or abdominal aorta (including aneurysms). (ACC)
A usually malignant neoplasm composed of primitive (immature) tissues that resemble fetal tissues. Medulloblastoma, Ependymoblastoma, Pineoblastoma, and Wilms tumor are representative embryonal neoplasms. --2003
Blocking of a blood vessel by cholesterol-rich atheromatous deposits, generally occurring in the flow from a large artery to small arterial branches. It is also called arterial-arterial embolization or atheroembolism which may be spontaneous or iatrogenic. Patients with spontaneous atheroembolism often have painful, cyanotic digits of acute onset.
Softening and degeneration of the CARTILAGE. Pathological processes involving the chondral tissue (CARTILAGE).
Editor note: DO places this under articular cartilage disease
A disease involving the hematopoietic system.
disease of the blood and blood-forming organs
disease or disorder of hematopoietic system
hematopoietic system disease or disorder
hematological disorders and malignancies
An inflammatory process affecting a joint. Causes include infection, autoimmune processes, degenerative processes, and trauma. Signs and symptoms may include swelling around the affected joint and pain.
Editor note: osteoarthritis is primarily non-inflammatory which causes issues if we classify arthritis as inflammatory.
Cystic renal cell carcinoma includes any malignant neoplasm of renal tubular epithelium which presents as a fluid-filled mass. Approximately 15 per cent of cases of renal cell carcinoma will be cystic on radiologic and pathologic examination. The clinical features of cystic renal cell carcinoma are similar to those which are solid. The radiographic and pathologic findings of cystic renal cell carcinoma are often more confusing and less specific than the findings of renal cell carcinoma which are predominantly solid. There are four basic pathologic mechanisms resulting in cystic renal cell carcinoma: intrinsic multiloculated growth; intrinsic unilocular growth (cystadenocarcinoma); cystic necrosis; and origin from the epithelial lining of a preexisting simple cyst. There are three basic radiologic patterns of cystic renal cell carcinoma: unilocular cystic mass, multiloculated cystic mass, and discrete mural nodule in a cystic mass. Cystic renal cell carcinoma is often extremely difficult to differentiate from non-neoplastic, benign neoplastic, and other malignant neoplastic masses utilizing radiologic studies alone. This review presents the clinical, pathologic, and radiographic features of cystic renal cell carcinoma and discusses its radiologic differential diagnosis.
A benign papillary neoplasm composed of transitional cells which show preservation of the nuclear polarity.
transitional cell papilloma NOS (morphologic abnormality)
transitional cell papilloma, benign (morphologic abnormality)
An adenocarcinoma of the cervix or the vagina arising from mesonephric remnants.
A benign or malignant neoplasm that arises from and is composed of epithelial cells. This category include adenomas, papillomas, and carcinomas.
Any infection caused by a virus of the genus Hantavirus, which is transmitted by aerosolized rodent excreta or rodent bites, that can result in a variety of clinical manifestations from hemorrhagic fever with renal syndrome to a pulmonary syndrome.
A disorder caused by hantaviruses of the family Bunyaviridae. It is transmitted by rodents and is manifested with fever, hemorrhage, and renal failure. Other symptoms include headaches, abdominal and back pain, and blurred vision.
hantavirus hemorrhagic fever with renal syndrome
Renal disease in human immunodeficiency virus (HIV)-infected patients. It is characterized by nephrotic syndrome, azotemia, normal to large kidneys on ultrasound images, and focal segmental glomerulosclerosis on renal biopsy findings.
A disease involving the lymphatic part of lymphoid system.
disease of lymphatic part of lymphoid system
disease or disorder of lymphatic part of lymphoid system
disorder of lymphatic part of lymphoid system
lymphatic part of lymphoid system disease
lymphatic part of lymphoid system disease or disorder
Editor note: check alignment to anatomy, consider lymphoid system disease
Inflammation of the meninges and brain, generally secondary to an infectious cause. Pathogens may be bacterial, viral, fungal, or protozoan.
A malignant neoplasm composed of a carcinomatous epithelial component and a sarcomatous mesenchymal component. Representative examples include malignant mixed mesodermal (Mullerian) tumor of the female reproductive system and carcinosarcoma of the salivary gland and the lung.
mixed tumor, malignant (morphologic abnormality)
mixed tumor, malignant, NOS (morphologic abnormality)
Mixed connective tissue disease (MCTD) is a rare autoimmune disorder that is characterized by features commonly seen in three different connective tissue disorders: systemic lupus erythematosus, scleroderma, and polymyositis. Some affected people may also have symptoms of rheumatoid arthritis. Although MCTD can affect people of all ages, it appears to be most common in women under age 30. Signs and symptoms vary but may include Raynaud's phenomenon ; arthritis; heart, lung and skin abnormalities; kidney disease; muscle weakness, and dysfunction of the esophagus. The cause of MCTD is currently unknown. There is no cure but certain medications such as nonsteroidal anti-inflammatory drugs (NSAIDs), corticosteroids and immunosuppresivedrugsmay help manage the symptoms.
connective tissue disease overlap syndrome
A malignant neoplasm affecting the skeletal or smooth muscles. Malignant neoplasms arising from the skeletal muscles are called rhabdomyosarcomas. Malignant neoplasms arising from the smooth muscles are called leiomyosarcomas.
A primary or metastatic malignant neoplasm involving the nervous system.
malignant neoplasm of the nervous system
A lower than normal quantity of amniotic fluid in the amniotic sac as compared to normal values. Typically associated with an amniotic fluid index (AFI) of less than 5 cm or a single maximum vertical pocket (MVP) of less than 2 cm.
Consider obsoleting as represents a finding
Infection of the kidney due to mycobacteria.
A primary or metastatic malignant neoplasm involving the retroperitoneum. The vast majority of cases are carcinomas, lymphomas, or sarcomas.
malignant neoplasm of retroperitoneal space
malignant neoplasm of retroperitoneum and peritoneum
malignant retroperitoneal space neoplasm
malignant tumor of peritoneum and retroperitoneum
A general term for mycobacterium infections of any part of the urogenital system in either the male or the female.
Editor note: in ORDO this is classified 'rare disorder with obstructive azoospermia' but this is male specific, so we move to the male-specific subclass
An abnormally high acidity of the blood and other body tissues. Acidosis can be either respiratory or metabolic.
disease or disorder, autosomal recessive
recessive hereditary disorder (autosomal)
A disease involving the urinary bladder.
Hardening of the kidney due to infiltration by fibrous connective tissue (fibrosis), usually caused by renovascular diseases or chronic hypertension. Nephrosclerosis leads to renal ischemia.
A benign or malignant, primary or metastatic neoplasm affecting the male and female reproductive system.
An embryonal neoplasm characterized by the presence of epithelial, mesenchymal, and blastema components. The vast majority of cases arise from the kidney. A small number of cases with morphologic features resembling Wilms tumor of the kidney have been reported arising from the ovary and the cervix.
A benign mesenchymal neoplasm arising from smooth muscle tissue.
An adenoma of the adrenal cortex that produces cortisol. It may be associated with Cushing syndrome. Clinical presentation includes weight gain, round face, easy bruising, muscle weakness, emotional changes, hirsutism, and hypertension.
cortisol producing adrenal cortex adenoma
cortisol producing adrenal cortical adenoma
cortisol-producing adrenal cortex adenoma
A benign, intermediate, or malignant mesenchymal neoplasm characterized by the presence of neoplastic fibroblasts.
A type of renal carcinoma affecting mostly young African-Americans. It is located in the medulla of the kidney, and follows an aggressive clinical course. Most reported cases have shown metastatic disease at the time of diagnosis.
A primary or metastatic malignant tumor involving the urinary system. Common tumor types include carcinomas, lymphomas, and sarcomas.
A benign, well-circumscribed renal cortical neoplasm affecting females more often than males. Polycythemia has been reported in twelve-percent of patients.
metanephric adenoma (morphologic abnormality)
A non-invasive or invasive transitional cell carcinoma characterized by a papillary growth pattern. It may occur in the bladder or the renal pelvis.
papillary transitional cell carcinoma (morphologic abnormality)
A soft tissue neoplasm composed of perivascular epithelioid cells. Representative examples include angiomyolipoma, clear cell-sugar-tumor of the lung, and lymphangioleiomyomatosis.
neoplasm with perivascular epithelioid cell differentiation
tumor with perivascular epithelioid cell differentiation
MeSH defintion: A family of mesenchymal tumors composed of histologically and immunohistochemically distinctive perivascular epithelioid cells. These cells do not have a normal anatomic homolog. (From Fletcher CDM, et. al., World Health Organization Classification of Tumors: Pathology and Genetics of Tumors of Soft Tissue and Bone, 2002).
A group of kidney carcinomas characterized by the presence of different translocations involving the chromosome Xp11.2. These translocations result in the creation of gene fusions involving the TFE3 gene. Patients are usually children and young adults. Morphologically, the malignant epithelial cells form papillary patterns.
Xp11.2 translocation-related renal cell carcinoma
renal cell cancer associated with Xp11.2 translocations/TFE3 Gene fusions
renal cell carcinoma associated with Xp11.2 translocations/TFE3 gene fusions
translocation-associated renal cell carcinoma
A malignant epithelial neoplasm characterized by the presence of spindle cells and anaplastic morphologic features. Giant cells and a sarcomatous component may also be present.
spindle cell carcinoma (morphologic abnormality)
A benign, intermediate, or malignant neoplasm that arises from the soft tissue. The most common types are lipomatous (fatty), vascular, smooth muscle, fibrous, and fibrohistiocytic neoplasms.
Wilms tumor of the kidney characterized by the predominance of the mesenchymal component.
A malignant neoplasm arising from the transitional epithelium, usually affecting the urinary bladder, ureter, or renal pelvis. It may or may not have a papillary configuration. It is graded 1 to 3 or 4 according to the degree of cellular differentiation and architectural patterns. Grade 1 transitional cell carcinoma is histologically benign but it may recur. Transitional cell carcinomas may also affect the upper respiratory tract and the ovaries.
carcinoma of transitional epithelial cell
A renal cell carcinoma characterized by morphologic features that do not fit easily into one of the other well-defined categories of renal cell carcinoma. Examples of such features include mixtures of morphologic patterns, mucin production, and sarcomatoid morphology.
A usually aggressive malignant neoplasm arising from the uterine corpus and less often the cervix. It is characterized by the presence of two components: a malignant epithelial component and a sarcomatous component. In the uterine corpus the epithelial component is usually glandular whereas in the cervix is usually non-glandular. Carcinosarcoma of the cervix, although it is aggressive, it may have a better prognosis compared to the uterine corpus carcinosarcoma.
malignant mixed mesodermal (Mullerian) tumor of the uterus
malignant mixed mesodermal (Müllerian) tumor of the uterus
uterine malignant mixed mesodermal (Mullerian) tumor
uterine malignant mixed mesodermal (Müllerian) tumor
uterine carcinosarcoma/uterine malignant mixed mullerian tumor
A general term most often used to describe severe or complete loss of muscle strength due to motor system disease from the level of the cerebral cortex to the muscle fiber. This term may also occasionally refer to a loss of sensory function. (From Adams et al., Principles of Neurology, 6th ed, p45)
A benign and excessive tumor-like growth of mature cells and normal tissues which grow in a disorganized pattern.
An instance of metabolic disease that is acquired during the lifetime of the individual.
A malignant epithelial neoplasm characterized by a papillary growth pattern. A papillary carcinoma may be composed of glandular cells (papillary adenocarcinoma), squamous cells (papillary squamous cell carcinoma), or transitional cells (papillary transitional cell carcinoma). Bladder carcinoma is a representative example of papillary transitional cell carcinoma.
papillary carcinoma (morphologic abnormality)
papillary carcinoma NOS (morphologic abnormality)
Genetic defects in the selective or non-selective transport functions of the kidney tubules.
A malignant tumor that occurs in children. Representative examples include soft tissue and bone sarcomas (e.g. osteosarcoma) and embryonal neoplasms (e.g. hepatoblastoma and rhabdoid tumor).
Epidermolysis bullosa (EB) is a group of genetic skin diseases that cause the skin to blister very easily. Blisters form in response to minor injuries or friction, such as rubbing or scratching. There are four main types of epidermolysis bullosa: dystrophic epidermolysis bullosa Epidermolysis bullosa simplex Junctional epidermolysis bullosa Kindler Syndrome Identifying the exact type can be hard because there are many subtypes of EB. Within each type or subtype, a person may be mildly or severely affected. The disease can range from being a minor inconvenience to completely disabling, and fatal in some cases. Most types of EB are inherited. The inheritance pattern may be autosomal dominant or autosomal recessive. Management involves protecting the skin, reducing friction against the skin, and keeping the skin cool.
This class covers pigmentation disorders of the skin, as well as those affecting the eyes
A disease involving the sebaceous gland.
Skin diseases characterized by local or general distributions of blisters. They are classified according to the site and mode of blister formation. Lesions can appear spontaneously or be precipitated by infection, trauma, or sunlight. Etiologies include immunologic and genetic factors. (From Scientific American Medicine, 1990)
A chronic, pathological complication associated with diabetes mellitus, where nerve damages are incurred due to diabetic microvascular injury involving small blood vessels that supply these nerves, resulting in peripheral and/or autonomic nerve dysfunction.
Acute renal failure caused by the cell death of the renal tubules. Causes include nephrotoxins, cytotoxic drugs, and antibiotics.
acute renal failure with lesion of tubular necrosis
acute renal failure with tubular necrosis
A rare, usually large (greater than 5cm), malignant epithelial tumor arising from the adrenal cortical cells. Symptoms are usually related to the excessive production of hormones, and include Cushing's syndrome and virilism in women. Common sites of metastasis include liver, lung, bone, and retroperitoneal lymph nodes. Advanced radiologic procedures have enabled the detection of small tumors, resulting in the improvement of the 5-year survival.
adenocarcinoma, adrenocortical, malignant
adrenal cortical carcinoma (morphologic abnormality)
Excess production of adrenal cortex hormones.
Editor note: consider obsoleting as is phenotypic feature
Anterior ischemic optic neuropathy (AION) is an eye disease characterized by infarction of the optic disk leading to vision loss. It can be nonarteritic (nonarteritic anterior ischemic optic neuropathy or NAION) or arteritic, the latter being associated with giant cell arteritis (GCA; often termed temporal arteritis). Vision loss with both varieties is typically rapid (over minutes, hours, or days) and painless. Symptoms such as a general feeling of being unwell (malaise), muscle aches and pains, headaches over the temple, pain when combing hair, pain in the jaw after chewing, and tenderness over the temporal artery (one of the major arteries of the head) may be present with giant cell arteritis. At exam, visual acuity is reduced and the optic disc is swollen. In both subtypes, visual field examination is often reduced in the inferior and central visual fields. The visual loss is usually permanent, with some recovery possibly occurring within the first weeks or months. The arteritic variety is treated with corticosteroids. Treatment of the nonarteritic variety withaspirinor corticosteroids has not been helpful.
optic disc infarction leading to vision loss
Inflammation of the iris and anterior chamber of the eye.
A small vessel vasculitis affecting the skin and/or internal organs. It is characterized by the presence of neutrophils and fibrinoid necrosis in small arteries and venules. It may be idiopathic or the result of drug treatment, infections, food intake, collagen vascular disorders, inflammatory bowel disease, or cancer.
Joint ankylosis of the ankle and/or foot
Joint ankylosis of the pelvic region and thigh
ankylosis of joint of pelvic region and thigh
Death of cells in the kidney cortex, a common final result of various renal injuries including hypoxia; ischemia; and drug toxicity.
A complication of kidney diseases characterized by cell death involving kidney papilla in the kidney medulla. Damages to this area may hinder the kidney to concentrate urine resulting in polyuria. Sloughed off necrotic tissue may block kidney pelvis or ureter. Necrosis of multiple renal papillae can lead to kidney failure.
The least progressive form of systemic scleroderma with skin thickening restricted to the face, neck and areas distal to the elbows and/or knees, sparing the trunk. The crest syndrome is a form of limited scleroderma.
A glomerular disorder characterized by the electron microscopic finding of loss of podocyte foot processes. Light microscopic examination does not show glomerular changes. Patients present with proteinuria and nephrotic syndrome.
nephrotic syndrome with lesion of minimal change glomerulonephritis
nephrotic syndrome with lesion of minimal change nephrotic syndrome
idiopathic minimal change nephrotic syndrome
Severe hypertension that is characterized by rapid onset of extremely high blood pressure.
Inflammation of the choroid as well as the retina and vitreous body. Some form of visual disturbance is usually present. The most important characteristics of posterior uveitis are vitreous opacities, choroiditis, and chorioretinitis.
Editor note: choroid=PU. in MESH PUitis is defined to be choroid+retina+VB, and isa panuveitis. TODO check ORDO, GARD
An inflammatory process affecting the kidney. The cause is most often bacterial, but may also be fungal in nature. Signs and symptoms may include fever, chills, flank pain, painful and frequent urination, cloudy or bloody urine, and confusion.
A group of inherited kidney disorders characterized by the abnormally elevated levels of amino acids in urine. Genetic mutations of transport proteins result in the defective reabsorption of free amino acids at the proximal renal tubules. Renal aminoaciduria are classified by the specific amino acid or acids involved.
Narrowing or occlusion of the renal artery or arteries. It is due usually to atherosclerosis; fibromuscular dysplasia; thrombosis; embolism, or external pressure. The reduced renal perfusion can lead to renovascular hypertension (hypertension, renovascular).
Abnormalities of bone mineral metabolism associated with chronic kidney disease.
High blood pressure secondary to renal artery stenosis.
Overproduction of parathyroid hormone in response to influence external to the parathyroid glands.
A benign or malignant myomatous neoplasm arising from smooth muscle.
A disease involving the calcareous tooth.
Group of diseases mediated by the deposition of large soluble complexes of antigen and antibody with resultant damage to tissue. Besides serum sickness and the arthus reaction, evidence supports a pathogenic role for immune complexes in many other immune system diseases including glomerulonephritis, systemic lupus erythematosus (lupus erythematosus, systemic) and polyarteritis nodosa.
hypersensitivity reaction type III disease
A clinical syndrome associated with the retention of renal waste products or uremic toxins in the blood. It is usually the result of renal insufficiency. Most uremic toxins are end products of protein or nitrogen catabolism, such as urea or creatinine. Severe uremia can lead to multiple organ dysfunctions with a constellation of symptoms.
Chronic, destructive infection of the kidney characterized by lipid-laden macrophages in the setting of obstruction secondary to infected renal stones, most commonly caused by Proteus or Escherichia coli.
Branchiootorenal (BOR) syndrome is characterized by branchial arch anomalies (branchial clefts, fistulae, cysts), hearing impairment (malformations of the auricle with pre-auricular pits, conductive or sensorineural hearing impairment), and renal malformations (urinary tree malformation, renal hypoplasia or agenesis, renal dysplasia, renal cysts).
(from orpha.net)nSummarynnBranchiootorenal (BOR) syndrome is characterized by branchial arch anomalies (branchial clefts, fistulae, cysts), hearing impairment (malformations of the auricle with pre-auricular pits, conductive or sensorineural hearing impairment), and renal malformations (urinary tree malformation, renal hypoplasia or agenesis, renal dysplasia, renal cysts). Prevalence is 1/40,000. Renal involvement can lead to chronic renal insufficiency. The expression of the disease varies widely from one family to another and among individuals of the same family. Some families do not present with renal abnormalities or a urinary tree malformation. BOR syndrome is transmitted in an autosomal dominant manner. The causative gene, EYA1, is located on the long arm of chromosome 8. Point mutations and deletions in EYA1 have been identified in approximately 40% of affected individuals. Mutations have also been identified in the SIX1 and SIX5 genes, the products of which interact with EYA1 to form transcription factor complexes. Prenatal testing can be proposed to families in which the disease-causing mutation has been identified, but genetic counseling is difficult because of the clinical heterogeneity between individuals. Management of affected patients includes excision of branchial fistulae or cysts, hearing aids and education programs appropriate for the hearing impaired, and follow-up by a nephrologist. Dialysis or renal transplantation may be required.
Prune belly syndrome is a rare congenital disorder, belonging to the group of fetal lower urinary tract obstructions (LUTO), involving variable dilation of the lower urinary tract in association with partial or complete absence of the lateral and inferior abdominal wall musculature and in males bilateral non-palpable undescended testes.
syndrome of agenesis of abdominal muscles
abdominal muscles, absence of, with urinary tract Abnormality and cryptorchidism
A condition that is characterized by degeneration of the distal phalanges.
Acroosteolysis dominant type (AOD) is a rare genetic osteolysis syndrome characterized by acroosteolysis of distal phalanges and generalized osteoporosis, associated with additional ossification anomalies, craniofacial dysmorphism, dental anomalies and a wide range of other characteristics.
acroosteolysis with osteoporosis and changes in skull and mandible
serpentine fibula-polycystic kidney syndrome
serpentine fibula-polycystic kidneys syndrome
Acrorenal syndrome comprises a wide spectrum of congenital malformative disorders characterized by the co-occurrence of distal limb anomalies (usually bilateral cleft feet and/or hands) and renal defects (e.g. unilateral or bilateral agenesis), that can be associated with a variety of other anomalies such as those of genitourinary tract (genital anomalies, ureteral hypoplasias, vesicoureteral reflux), abdominal well defects, intestinal atresias, and lung malformations. Familial cases have been reported in which an autosomal recessive inheritance was suspected.
Pseudohypoparathyroidism type 1A (PHP1a) is a type of pseudohypoparathyroidism (PHP) characterized by renal resistance to parathyroid hormone (PTH), resulting in hypocalcemia, hyperphosphatemia, and elevated PTH; resistance to other hormones including thydroid stimulating hormone (TSH), gonadotropins and growth-hormone-releasing hormone (GHRH); and a constellation of clinical features known as Albright hereditary osteodystrophy (AHO).
Albright hereditary osteodystrophy with multiple hormone resistance
Albright hereditary osteodystrophy-PHP syndrome Ia
Familial hyperaldosteronism type I (FH-I) is a rare heritable, glucocorticoid remediable form of primary aldosteronism (PA) characterized by early-onset hypertension, hyperaldosteronism, variable hypokalemia, low plasma renin activity (PRA), and abnormal production of 18-oxocortisol and 18-hydroxycortisol.
ACTH-dependent hyperaldosteronism syndrome
aldosteronism, sensitive to dexamethasone
glucocorticoid-suppressible hyperaldosteronism
Autosomal dominant Alport syndrome isa genetic condition characterized by kidney disease, hearing loss, and eye abnormalities. Most affected individuals experience progressive loss of kidney function, usually resulting in end-stage kidney disease. People with Alport syndrome frequently develop sensorineural hearing loss in late childhood or early adolescence. The eye abnormalities seen in this condition seldom lead to vision loss. Alport syndrome can have different patterns of inheritance.Alport syndrome has autosomal dominant inheritance in about 5 percent of cases. People with this form of Alport syndrome have one mutation in either the COL4A3 or COL4A4 gene in each cell.
renal failure and sensorineural hearing loss
hereditary amyloidosis with primary renal involement
Townes-Brocks syndrome (TBS) is a rare genetic disorder characterized by the triad of imperforate anus, dysplastic ears often associated with sensorineural and/or conductive hearing impairment, and thumb malformations. These features are often associated with other signs mainly affecting the kidneys and heart.
imperforate anus with hand, foot and ear anomalies
sensorineural deafness with imperforate anus and hypoplastic thumbs
Townes-Brocks-branchiootorenal-like syndrome
anus, imperforate, with hand, foot and ear anomalies
anus, imperforate, with hand, foot, and Ear anomalies
deafness, sensorineural, with imperforate anus and hypoplastic thumbs
deafness, sensorineural, with imperforate anus and thumb anomalies
A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis).
hypersensitivity reaction type II disease
Bechet disease (BD) is a chronic, relapsing, multisystemic vasculitis characterized by mucocutaneous lesions, as well as articular, vascular, ocular and central nervous system manifestations.
Brachydactyly - arterial hypertension is a rare genetic brachydactyly syndrome characterized by the association of brachydactyly type E with hypertension (due to vascular or neurovascular anomalies) as well as the additional features of short stature and low birth weight (compared to non-affected family members), stocky build and a round face. The onset of hypertension is often in childhood and, if untreated, most patients will have had a stroke by the age of 50.
brachydactyly type E, with short stature and hypertension
brachydactyly type E with short stature and hypertension
brachydactyly, type E, with short stature and hypertension
brachydactyly-arterial hypertension syndrome
Cat eye syndrome (CES) is a rare chromosomal disorder with a highly variable clinical presentation. Most patients have multiple malformations affecting the eyes (iris coloboma), ears (preauricular pits and/or tags), anal region (anal atresia), heart and kidneys. Intellectual disability is usually mild or borderline normal.
Alagille (AGS) syndrome is variably characterized by chronic cholestasis due to paucity of intrahepatic bile ducts, peripheral pulmonary artery stenosis, vertebrae segmentation anomalies, characteristic facies, posterior embryotoxon/anterior segment abnormalities, pigmentary retinopathy, and dysplastic kidneys.
Hepatofacioneurocardiovertebral syndrome
Renal coloboma syndrome (RCS) is a genetic condition characterized by optic nerve dysplasia and renal hypodysplasia.
CAKUT with or without ocular abnormalities
coloboInOwlma of optic nerve with renal disease
congenital anomalies of the kidney and urinary tract with or without ocular abnormalities
optic coloboInOwlma, vesicoureteral reflux and renal anomalies
papillo-renal syndrome, optic nerve coloboInOwlma with renal disease
renal-coloboInOwlma syndrome with macular abnormalities
optic coloboInOwlma, vesicoureteral reflux, and renal anomalies
optic nerve coloboInOwlma with renal disease
Mixed cryoglobulinemia (MC) is a rare multisystem disease characterized by the presence of circulating cryoprecipitable immune complexes in the serum, manifested clinically by a classical triad of purpura, weakness and arthralgia.
A chronic tubulointerstitial nephropathy that affects people in certain rural areas along the Danube river in the Balkans. It leads to end-stage renal disease.
Congenital unilateral hypoplasia of depressor anguli oris is a congenital anomaly, characterized by the unilateral hypoplasia/agenesis of the depressor anguli oris muscle, resulting in an asymmetric crying facies in neonatal period/ infancy (drooping of one corner of the mouth during crying) while eye closure, nasolabial fold and forehead wrinkling are symmetric. While it can be isolated, this anomaly is also seen in 22q11.2 deletion syndrome and can be accompanied by other major congenital anomalies of the cardiovascular system, as well as less frequently the musculoskeletal, cervicofacial, respiratory, genitourinary, and, rarely, endocrine systems. When isolated, the condition is cosmetically insignificant as the infant gets older (as the muscle does not contribute significantly to facial expression in childhood/ adulthood).
depressor anguli oris muscle, hypoplasia of
Editor note: TODO check relationship to 22q11.2 deletion syndrome
congenital unilateral hypoplasia of depressor anguli oris
Hereditary central diabetes insipidus is a rare genetic subtype of central diabetes insipidus (CDI) characterized by polyuria and polydipsia due to a deficiency in vasopressin (AVP) synthesis.
hereditary neurogenic diabetes insipidus
vasopressin defective diabetes insipidus
diabetes insipidus, nephrogenic, autosomal
Dyschondrosteosis - nephritis is characterized by the association of short stature due to mesomelic shortening of the limbs and Madelung deformity, with hereditary nephritis.
mesomelic shortening and hereditary nephritis
An EEC syndrome characterized by autosomal dominant inheritance that has material basis in variation in the chromosome region 7q11.2-q21.3.
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome type 1
ectrodactyly, ectodermal dysplasia, and cleft LIP/palate syndrome 1
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 1
Beckwith-Wiedemann syndrome (BWS) is a genetic disorder characterized by overgrowth, tumor predisposition and congenital malformations.
exomphalos-macroglossia-gigantism syndrome
Beckwith-Wiedemann syndrome chromosome region
exomphalos macroglossia gigantism syndrome
Fanconi syndrome is a condition in which the kidneys do not absorb certain substances into the body. These substances, such as cysteine, fructose, galactose, or glycogen, are lost in the urine. Fanconi syndrome is thought to be caused by genetic and environmental factors, and it may be diagnosed at any age. Symptoms of Fanconi syndrome include increased urine production (which may cause dehydration), weakness, and abnormalities of the bones.
familial Mediterranean fever, autosomal dominant
Birt-Hogg-Dube (BHD) syndrome is characterized by skin lesions, kidney tumors, and pulmonary cysts that may be associated with pneumothorax. It is a rare clinicopathologic condition named after the three Canadian physicians who reported the syndrome in 1977.
fibrofolliculomas with trichodiscomas and acrochordons
Fish eye disease (FED) is a form of genetic LCAT (lecithin-cholesterol acyltransferase) deficiency characterized clinically by corneal opacifications, and biochemically by significantly reduced HDL cholesterol and partial LCAT enzyme deficiency.
alpha-lecithin cholesterol acyltransferase deficiency
alpha-lecithin:cholesterol acyltransferase deficiency
Frasier syndrome is characterised by the association of male pseudohermaphrodism and glomerular nephropathy. This syndrome is associated with a high risk of developing gonadoblastoma.
Renal cysts and diabetes syndrome (RCAD) is a rare form of maturity-onset diabetes of the young (MODY) characterized clinically by heterogeneous cystic renal disease and early-onset familial non-autoimmune diabetes. Pancreatic atrophy, liver dysfunction and genital tract anomalies are also features of the syndrome.
HNF1B-related renal cysts and diabetes syndrome
atypical familial juvenile hyperuricemic nephropathy
congenital anomalies of the kidney and urinary tract with diabetes
familial hypoplastic glomerulocystic kidney
hepatocyte nuclear Factor 1-beta-associated monogenic diabetes
hypoplastic type glomerulocystic kidney disease
maturity onset diabetes of the Young, type 5
renal cysts-maturity-onset diabetes of the young syndrome
renal dysfunction-early-onset diabetes syndrome
glomerulocystic kidney disease, hypoplastic type
glomerulocystic kidney, familial hypoplastic
hyperuricemic nephropathy, familial juvenile, atypical
maturity-onset diabetes of the Young, type 5
maturity-onset diabetes of the young type 5
Hypotrichosis - lymphedema - telangiectasia is an extremely rare syndromic lymphedema disorder characterized by early-onset hypotrichosis, childhood-onset lymphedema, and variable telangiectasia, particularly of the palms.
hypotrichosis lymphedema telangiectasia syndrome
hypotrichosis-lymphedema-telangiectasia syndrome (grouping)
Fibronectin glomerulopathy is a hereditary kidney disease characterized by proteinuria, type IV renal tubular acidosis, microscopic hematuria and hypertension that may lead to end-stage renal failure in the second to sixth decade of life.
glomerulopathy with fibronectin deposits
glomerular nephritis, familial, with fibronectin deposits
glomerulopathy with fibronectin deposits 1
glomerulopathy with fibronectin deposits 2
glomerulopathy with giant fibrillar deposits
Editor note: consider splitting out type 1, and also separate class for giant subtype
Congenital hydronephrosis is a renal urinary disease characterized by distension and dilation of the renal pelvis and calyces secondary to various congenital obstructive malformations of the kidneys and urinary tract that can evolve to renal atrophy.
Editor note: TODO check relationship to OMIM:143400
A condition caused by autosomal recessive loss-of-function mutation(s) in the CYP24A1 or SLC34A1 gene, encoding mitochondrial 1,25-dihydroxyvitamin D(3) 24-hydroxylase, and sodium-dependent phosphate transport protein 2A, respectively. This condition is characterized by vomiting, polyuria, dehydration, and failure to thrive, accompanied by hypercalcemia, suppressed parathyroid hormone, and nephrocalcinosis.
autosomal recessive hypercalcemia, infantile
familial infantile hypercalcemia with suppressed intact parathyroid hormone
hypercalcemia, infantile, autosomal recessive
autosomal recessive infantile hypercalcemia
An autosomal dominant inherited syndrome characterized by the development of parathyroid adenoma or carcinoma, ossifying fibroma of the mandible and maxilla, renal neoplasms, and renal cysts.
familial primary hyperparathyroidism with multiple ossifying jaw fibromas
hereditary hyperparathyroidism-jaw tumor syndrome
hyperparathyroidism, familial primary, with multiple ossifying jaw fibromas
hyperparathyroidism-jaw tumor syndrome, hereditary
parathyroid adenomatosis, familial cystic
Gordon hyperkalemia-hypertension syndrome
hyperpotassemia and hypertension, familial
An instance of essential hypertension that is caused by a modification of the individual's genome.
The HDR syndrome is an inherited condition consisting of hypoparathyroidism, sensorineural deafness and renal disease.
hypoparathyroidism, deafness, and renal anomalies syndrome
hypoparathyroidism, sensorineural deafness, and renal disease
hypoparathyroidism, sensorineural deafness, and renal dysplasia
hypoparathyroidism, sensorineural deafness, and renal dysplasia syndrome
nephrosis, nerve deafness, and hypoparathyroidism
hypoparathyroidism-deafness-renal disease syndrome
Pallister-Hall syndrome (PHS), a pleiotropic autosomal dominant malformative disorder, is characterized by hypothalamic hamartoma, pituitary dysfunction, bifid epiglottis, polydactyly, and, more rarely, renal abnormalities and genitourinary malformations.
hypothalamic hamartoblastoma, hypopituitarism, imperforate anus, and postaxial polydactyly
esophagogastric and vulvar leiomyomatosis
leiomyomatosis, esophagogastric and vulvar
Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a hereditary cancer syndrome characterized by a predisposition to cutaneous and uterine leiomyomas and, in some families, to renal cell cancer.
familial leiomyomatosis and renal cell cancer
familial leiomyomatosis with renal carcinoma
hereditary leiomyomatosis and renal cell cancer
hereditary leiomyomatosis and renal cell cancer syndrome
hereditary leiomyomatosis and renal cell carcinoma
hereditary leiomyomatosis with renal carcinoma
hereditary multiple cutaneous leiomyomas
multiple cutaneous and uterine leiomyomas
leiomyomatosis and renal cell cancer, hereditary
multiple cutaneous and uterine leiomyomata
multiple cutaneous and uterine leiomyomata 1, with or without renal cell carcinoma
An autoimmune multi-organ disease typically associated with vasculopathy and autoantibody production. Most patients have antinuclear antibodies (ANA). The presence of anti-dsDNA or anti-Smith antibodies are highly-specific.
excess lymphocyte low molecular weight DNA
Autosomal dominant primary hypomagnesemia with hypocalciuria (ADPHH) is a mild form of familial primary hypomagnesemia (FPH), characterized by extreme weakness, tetany and convulsions. Secondary disturbances in calcium excretion are observed.
familial primary hypomagnesemia caused by mutation in FXYD2
isolated autosomal dominant hypomagnesemia
primary hypomagnesemia caused by mutation in FXYD2
autosomal dominant primary hypomagnesemia with hypocalciuria
An autosomal dominant disorder characterized by the triad of thrombocytopenia, giant platelets, and characteristic inclusions in peripheral blood leukocytes. It is characterized by varying degrees of thrombocytopenia that may be associated with purpura and bleeding; it is associated with mutation of the MYH9 gene.
giant platelet syndrome with thrombocytopenia
macrothrombocytopenia and progressive sensorineural deafness
Alport syndrome with macrothrombocytopenia
Alport syndrome with macrothrombocytopenia, formerly
Dohle leukocyte inclusions with giant platelets
macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss
macrothrombocytopenia progressive deafness
macrothrombocytopenia with dispersed leukocytic inclusions
macrothrombocytopenia with leukocyte inclusions
macrothrombocytopenia, nephritis, and deafness
macrothrombocytopenia, nephritis, deafness, and leukocyte inclusions
Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a rare congenital disease characterized by massive abdominal distension caused by a largely dilated non-obstructed urinary bladder (megacystis), microcolon and decreased or absent intestinal peristalsis.
megacystis, microcolon, hypoperistalsis syndrome
megacystis, microcolon, intestinal hypoperistalsis syndrome
megacystis-microcolon-intestinal hypoperistalsis syndrome, MMIH
megacystis-microcolon-intestinal hypoperistalsis-hydronephrosis syndrome
megacystis microcolon intestinal hypoperistalsis syndrome
megacystis-microcolon-intestinal hypoperistalsis syndrome
Juvenile dermatomyositis (JDM) is the early-onset form of dermatomyositis (DM), a systemic, autoimmune inflammatory muscle disorder, characterized by proximal muscle weakness, evocative skin lesion, and systemic manifestations.
myopathy, familial idiopathic inflammatory
Nail-patella syndrome (NPS) is a rare hereditary patellar dysostosis characterized by nail hypoplasia or aplasia, aplastic or hypoplastic patellae, elbow dysplasia, and the presence of iliac horns as well as renal and ocular anomalies.
nephritis, familial, without deafness or ocular defect
renal failure, progressive, with hypertension
autosomal dominant progressive nephropathy with hypertension
Familial juvenile hyperuricemic nephropathy type 1 (FJHN1) is a rare kidney disorder characterized by hyperuricemia, progressive nephropathy, and gout occurring at an early age.
hyperuricemic nephropathy, familial juvenile
UMOD familial juvenile hyperuricemic nephropathy
UMOD-associated familial juvenile hyperuricemic nephropathy
familial juvenile hyperuricemic nephropathy caused by mutation in UMOD
hyperuricemic nephropathy, familial juvenile 1
hyperuricemic nephropathy, familial juvenile, 1
hyperuricemic nephropathy, familial juvenile, type 1
familial juvenile hyperuricaemic nephropathy
familial juvenile hyperuricemic nephropathy type 1
Noonan syndrome caused by mutations in the PTPN11 gene.
Idiopathic multicentric osteolysis is a very rare syndrome characterized by progressive loss of bone, usually the capsal and tarsal bones, resulting in deformity and disability, as well as chronic renal failure in many cases. The bone and renal disorders are sometimes associated with intellectual deficit and facial abnormalities.
idiopathic multicentric osteolysis with or without nephropathy
multicentric carpo-tarsal osteolysis with or without nephropathy
multicentric carpotarsal osteolysis syndrome
multicentric osteolysis, autosomal dominant
osteolysis, hereditary, of carpal bones with or without nephropathy
The presence of a calculus in the pelvis of the kidney; this is most often composed of mineral salts and proteins.
Any autosomal dominant polycystic kidney disease in which the cause of the disease is a mutation in the PKD1 gene.
PKD1 autosomal dominant polycystic kidney disease
autosomal dominant polycystic kidney disease caused by mutation in PKD1
polycystic kidney disease, adult, type I
Potter type 3 polycystic kidney disease, formerly
polycystic kidney disease 1 with or without polycystic liver disease
polycystic kidney disease, adult, type 1
A genetic kidney disease that causes progressive loss of kidney function caused by mutations in the genes encoding uromodulin (UMOD), hepatocyte nuclear factor-1β (HNF1B), renin (REN), or mucin-1 (MUC1).
autosomal dominant interstitial kidney disease
autosomal dominant medullary cystic kidney disease
autosomal dominant medullary cystic kidney disease with or without hyperuricemia
autosomal dominant tubulointerstitial kidney disease
Liddle syndrome is a rare inherited form of hypertension characterized by severe early-onset hypertension associated with decreased plasmatic levels of potassium, renin and aldosterone.
Renal pseudohypoaldosteronism type 1 (renal PHA1) is a mild form of primary mineralocorticoid resistance restricted to the kidney.
autosomal dominant pseudohypoaldosteronism type 1
pseudohypoaldosteronism type 1 autosomal dominant
pseudohypoaldosteronism type 1, dominant
pseudohypoaldosteronism, type I, autosomal dominant
Idiopathic and/or familial pulmonary arterial hypertension (IFPAH) is a form or pulmonary arterial hypertension (PAH, see his term) characterized by elevated pulmonary arterial resistance leading to right heart failure; it is progressive and potentially fatal. About 75% of heritable pulmonary arterial hypertension (HPAH) have an identified mutation. HPAH has been linked to mutations in BMPR2 in 75% of cases; other genes implicated in HPAH include ACVR1, BMPR1, CAV1, ENG and SMAD9 and CBLN2. (However, the majority of patients carrying an HPAH mutation do not develop PAH). Idiopathic pulmonary arterial hypertension (IFPAH) refers to those cases of pulmonary arterial hypertension in which etiology remains unknown.
idiopathic and/or familial pulmonary arterial hypertension
Autosomal dominant distal renal tubular acidosis (AD dRTA) is an inherited form of distal renal tubular acidosis (dRTA) characterized by hyperchloremic metabolic acidosis often but not always associated with hypokalemia.
autosomal dominant distal renal tubular acidosis (disease)
distal renal tubular acidosis (disease), autosomal dominant
autosomal dominant SLC4A1-associated distal renal tubular acidosis
renal tubular acidosis, distal, autosomal dominant
autosomal dominant distal renal tubular acidosis
Proximal renal tubular acidosis (pRTA) is a tubular kidney disease characterized by impaired ability of the proximal tubule to reabsorb bicarbonate from the glomerular filtrate leading to hyperchloremic metabolic acidosis.
Any Rubinstein-Taybi syndrome in which the cause of the disease is a mutation in the CREBBP gene.
Rubinstein-Taybi syndrome caused by mutation in CREBBP
broad thumbs and great toes, characteristic facies, and intellectual disability
broad thumbs and great toes, characteristic facies, and mental retardation
Rubinstein-Taybi syndrome due to CREBBP mutations
This syndrome is characterised by variable spastic paraplegia, bilateral sensorineural deafness, intellectual deficit and progressive nephropathy.
spastic paraplegia - nephritis - deafness
spastic paraplegia, bilateral sensorineural deafness, intellectual retardation, and progressive nephropathy
spastic paraplegia, sensorineural deafness, intellectual disability, and progressive nephropathy
spastic paraplegia, sensorineural deafness, mental retardation, and progressive nephropathy
spastic paraplegia-nephritis-deafness syndrome
Holoprosencephaly-radial heart renal anomalies syndrome is characterised by holoprosencephaly, predominantly radial limb deficiency (absent thumbs, phocomelia), heart defects, kidney malformations and absence of gallbladder.
holoprosencephaly radial heart renal anomalies
holoprosencephaly-radial heart renal anomalies syndrome
SupraValvar Aortic Stenosis (SVAS) is characterized by the narrowing of the aorta lumen (close to its origin) or other arteries (branch pulmonary arteries, coronary arteries). This narrowing of the aorta or pulmonary branches may impede blood flow, resulting in heart murmur and ventricular hypertrophy (in case of aorta involvement). The narrowing results from a thickening of the artery wall, which is not related to atherosclerosis.
supravalvar aortic stenosis, Eisenberg type
Giant cell arteritis (GCA) is a large vessel vasculitis predominantly involving the arteries originating from the aortic arch and especially the extracranial branches of the carotid arteries.
An autoimmune disorder in which the number of circulating platelets is reduced due to their antibody-mediated destruction. ITP is a diagnosis of exclusion and is heterogeneous in origin.
A congenital anomaly characterized by immunodeficiency, abnormal facies, congenital heart disease, hypocalcemia, and increased susceptibility to infections. Pathologic characteristics include conotruncal abnormalities and absence or hypoplasia of thymus and parathyroid glands. DiGeorge syndrome is associated with abnormalities of chromosome 22. Also known as DiGeorge anomaly.
third and fourth pharyngeal pouch syndrome
HELLP syndrome is a life-threatening condition that can potentially complicate pregnancy. It is named for 3 features of the condition: H emolysis, E levated L iver enzyme levels, and L ow P latelet levels. It typically occurs in the last 3 months of pregnancy (the third trimester) but can also start soon after delivery. A wide range of non-specific symptoms may be present in women with HELLP syndrome. Symptoms may include fatigue; malaise; fluid retention and excess weight gain; headache; nausea and vomiting; pain in the upper right or middle of the abdomen; blurry vision; and rarely, nosebleed or seizures. The cause of HELLP syndrome is not known, but certain risk factors have been associated with the condition. It is most common in women with preeclampsia or eclampsia. If not diagnosed and treated quickly, HELLP syndrome can lead to serious complications for the mother and baby.The main treatment is to deliver the baby as soon as possible, even if premature. Treatment may also includemedications needed for the mother or baby, and blood transfusion for severe bleeding problems.
hemolysis, elevated liver enzymes, low platelets in pregnancy
hemolysis-elevated liver enzymes-Low Platelet count syndrome
hemolysis-elevated liver enzymes-low platelets syndrome
hemolysis, elevated liver enzymes, and Low Platelet count
hemolysis, elevated liver enzymes, lowered platelets
Tuberous sclerosis mapped to chromosome 9q34 (TSC1 gene).
tuberous sclerosis caused by mutation in TSC1
Muckle-Wells syndrome (MWS) is an intermediate form of cryopyrin-associated periodic syndrome (CAPS) and is characterized by recurrent fever (with malaise and chills), recurrent urticaria-like skin rash, sensorineural deafness, general signs of inflammation (eye redness, headaches, arthralgia/myalgia) and potentially life-threatening secondary amyloidosis (AA type).
Cryopyrin-associated periodic syndrome 2
Double uterus, hemivagina and renal agenesis is a rare congenital urogenital anomaly characterized by the presence of double uterus (didelphys, bicornuate or septum-complete or partial), unilateral cervico-vaginal obstruction (obstructed hemivagina-communicant, not communicant or septate and unilateral cervical atresia) and ipsilateral renal anomalies (renal agenesis and/or other urinary tract anomalies). Patients are usually diagnosed at puberty after menarche due to recurrent severe dysmenorrhea, chronic pelvic pain, excessive foul smelling mucopurulent discharge, spotting and intermenstrual bleeding (depending on the existence of uterine or vaginal communications). fever, dyspareunia, and a palpable abdominal, pelvic or vaginal mass (mucocolpos or pyocolpos) may also be present.
Double uterus and obstructed hemivagina syndrome
obstructed hemivagina and ipsilateral renal anomaly
uterus BICORNIS BICOLLIS with partial vaginal septum and unilateral HEMATOCOLPOS with ipsilateral renal agenesis
double uterus-hemivagina-renal agenesis syndrome
Retinal vasculopathy and cerebral leukodystrophy (RVCL) is an inherited group of small vessel diseases comprised of cerebroretinal vasculopathy (CRV), hereditary vascular retinopathy (HRV) and hereditary endotheliopathy with retinopathy, nephropathy and stroke (HERNS); all exhibiting progressive visual impairment as well as variable cerebral dysfunction.
retinal vasculopathy and cerebral leukoencephalopathy
autosomal dominant retinal vasculopathy with cerebral leukodystrophy
retinal vasculopathy with cerebral leukodystrophy
retinopathy, vascular, with cerebral and renal involvement and Raynaud and migraine phenomena
vasculopathy, retinal, with cerebral leukodystrophy
Editor note: Orphanet:3421 is obsolete in the 2017 edition of ORDO, but the Orphanet website shows as active, see https://github.com/Orphanet/ORDO/issues/1
retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations
VACTERL/VATER is an association of congenital malformations typically characterized by the presence of at least three of the following: vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, renal anomalies, and limb abnormalities.
vertebral abnormalities, anal atresia, Cardiac abnormalities, tracheo-esophageal fistula, renal anomalies, limb defects syndrome
A chromosomal disease that has material basis in deletion polymorphisms at chromosome location 22q11 and is characterized by variable developmental problems and schizoid features.
Von Hippel-Lindau disease (VHL) is a familial cancer predisposition syndrome associated with a variety of malignant and benign neoplasms, most frequently retinal, cerebellar, and spinal hemangioblastoma, renal cell carcinoma (RCC), and pheochromocytoma.
Von Hippel-Lindau syndrome, Modifiers of
Williams syndrome is a rare genetic multisystemic neurodevelopmental disorder characterized by a distinct facial appearance, cardiac anomalies (most frequently supravalvular aortic stenosis), cognitive and developmental abnormalities, and connective tissue abnormalities (such as joint laxity)
chromosome 7Q11.23 deletion syndrome, 1.5- to 1.8-Mb
WAGR syndrome (Wilms tumor - aniridia - genitourinary anomalies - intellectual disability mental retardation) is a rare genetic disorder characterized by an unusual complex of congenital developmental abnormalities with intellectual disability, and an increased risk of developing Wilms tumor.
Wilms tumor, aniridia, genitourinary anomalies and developmental delay syndrome
Wilms tumor-aniridia-genitourinary anomalies-intellectual disability syndrome
Wilms tumor-aniridia-genitourinary anomalies-mental retardation syndrome
Wilms tumor, aniridia, genitourinary anomalies, and intellectual disability syndrome
Wilms tumor, aniridia, genitourinary anomalies, and mental retardation syndrome
Wilms tumor, aniridia, genitourinary anomalies, intellectual disability syndrome
Wilms tumor, aniridia, genitourinary anomalies, mental retardation syndrome
Wilms tumor-aniridia-gonadoblastoma-intellectual disability syndrome
Wilms tumor-aniridia-gonadoblastoma-mental retardation syndrome
Denys-Drash syndrome (DDS) is a rare urogenital disorder characterized by the association of diffuse mesangial sclerosis (DMS), male pseudohermaphroditism with a 46,XY karyotype, and nephroblastoma.
Wilms tumor and pseudo- or true hermaphroditism
nephropathy associated with male pseudohermaphroditism and Wilms' tumor
nephropathy, Wilms tumor, and genital anomalies
pseudohermaphroditism, nephron disorder and Wilms' tumor
Autosomal recessive form of acrorenal syndrome.
An instance of adrenal cortex carcinoma that is caused by an inherited modification of the individual's genome.
Pseudohypoparathyroidism type 2 (PHP2) is a type of pseudohypoparathyroidism (PHP) characterized by resistance to parathyroid hormone (PTH), which manifests with hypocalcemia, hyperphosphatemia and elevated PTH levels, absence of Albright's hereditary osteodystrophy (AHO), and normal expression of the Gs protein with a normal urinary cAMP response.
Autosomal recessive Alport syndrome isa genetic condition characterized by kidney disease, hearing loss, and eye abnormalities. Most affected individuals experience progressive loss of kidney function, usually resulting in end-stage kidney disease. People with Alport syndrome frequently develop sensorineural hearing loss in late childhood or early adolescence. The eye abnormalities seen in this condition seldom lead to vision loss. Alport syndrome can have different patterns of inheritance. About15 percentof Alport syndrome cases are inherited in an autosomal recessive pattern and are caused bymutations in both copies of the COL4A3 or COL4A4 genes. Treatment is based on the symptoms present and may include medications to delay the progression of kidney disease. In most cases, a kidney transplant is eventually needed.
AlstrC6m syndrome (AS) is a multisystemic disorder characterized by cone-rod dystrophy, hearing loss, obesity, insulin resistance and hyperinsulinemia, type 2 diabetes mellitus, dilated cardiomyopathy (DCM), and progressive hepatic and renal dysfunction.
Amelogenesis imperfecta-nephrocalcinosis, also called enamel-renal syndrome, is an extremely rare syndrome which is characterized by hypoplastic amelogenesis imperfecta (hypoplastic dental enamel) and nephrocalcinosis (precipitation of calcium salts in renal tissue). Oral manifestations include yellow and misshaped teeth, delayed tooth eruption, and intrapulpal calcifications. Nephrocalcinosis is often asymptomatic but can progress during late childhood or early adulthood to impaired renal function (e.g. recurrent urinary infections and renal tubular acidosis), and rarely to end-stage renal failure.
amelogenesis imperfecta and gingival fibromatosis syndrome
amelogenesis imperfecta caused by mutation in FAM20A
amelogenesis imperfecta hypoplastic with nephrocalcinosis
absent enamel, nephrocalcinosis and apparently normal calcium metabolism
amelogenesis imperfecta and nephrocalcinosis
amelogenesis imperfecta hypoplastic type, Ig
amelogenesis imperfecta nephrocalcinosis
amelogenesis imperfecta, hypoplastic, with nephrocalcinosis
amelogenesis imperfecta-nephrocalcinosis syndrome
generalized enamel hypoplasia and renal dysfunction
Aniridia - renal agenesis - psychomotor retardation is an extremely rare syndrome reported in two siblings of non consanguineous parents that is characterized by the association of ocular abnormalities (partial aniridia, congenital glaucoma, telecanthus) with frontal bossing, hypertelorism, unilateral renal agenesis and mild psychomotor delay. There have been no further descriptions in the literature since 1974.
aniridia partial with unilateral renal agenesis and psychomotor retardation
aniridia renal agenesis psychomotor retardation
aniridia, partial, with unilateral renal agenesis and psychomotor retardation
aniridia-renal agenesis-psychomotor retardation syndrome
AREDYLD stands for acral-renal-ectodermal-dysplasia-lipoatrophic-diabetes. This syndrome has been described in three individuals, one of whom was born to consanguineous parents. All patients had lipoatrophy, diabetes mellitus, generalized hypotrichosis, ectodermal dysplasia, renal alterations, dental abnormalities and other manifestations. It is probably transmitted as an autosomal recessive trait.
acrorenal defect-ectodermal dysplasia-diabetes syndrome
acral renal ectodermal dysplasia lipoatrophic diabetes
acrorenal Field defect, ectodermal dysplasia, and lipoatrophic diabetes
Any arthrogryposis-renal dysfunction-cholestasis syndrome in which the cause of the disease is a mutation in the VPS33B gene.
VPS33B arthrogryposis-renal dysfunction-cholestasis syndrome
arthrogryposis, renal dysfunction, and cholestasis 1
arthrogryposis, renal dysfunction, and cholestasis type 1
arthrogryposis-renal dysfunction-cholestasis syndrome caused by mutation in VPS33B
Neurogenic arthrogryposis multiplex congenita is a form of arthrogryposis multiplex congenita characterized by congenital immobility of the limbs with fixation of multiple joints and muscle wasting. This condition is secondary to neurogenic muscular atrophy.
arthrogryposis multiplex congenita neurogenic type
neurogenic arthrogryposis multiplex congenita
arthrogryposis multiplex congenita, neurogenic type
arthrogryposis multiplex congenita 2, neurogenic type
An asphyxiating thoracic dystrophy associated with variation in the region 15q13.
short-rib thoracic dysplasia 1 with or without polydactyly
A visceral heterotaxy characterized by complete atrioventricular septal defect with a common atrium and univentricular AV connection, total anomalous pulmonary drainage, and transposition or malposition of the great arteries and may be associated with bilateral trilobed lungs, midline liver, asplenia and situs inversus affecting other organs that has material basis in homozygous mutation in the GDF1 gene on chromosome 19p12.
heterotaxy, Visceroatrial, autosomal recessive
Any renal-hepatic-pancreatic dysplasia in which the cause of the disease is a mutation in the NPHP3 gene.
NPHP3 renal-hepatic-pancreatic dysplasia
renal-hepatic-pancreatic dysplasia caused by mutation in NPHP3
renal-hepatic-pancreatic dysplasia type 1
Atherosclerosis-deafness-diabetes-epilepsy-nephropathy syndrome is characterised by sensorineural deafness, diabetes mellitus, progressive neurological deterioration with photomyoclonic epilepsy, and progressive nephropathy. It has been described in two brothers. Premature atherosclerosis of renal, coronary, and cerebral arteries and the aorta was also observed.
atherosclerosis, premature, with deafness, nephropathy, diabetes mellitus, photomyoclonus, and degenerative neurologic disease
premature atherosclerosis with photomyoclonic epilepsy, deafness, diabetes mellitus, nephropathy, and neurodegenerative disorder
atherosclerosis-deafness-diabetes-epilepsy-nephropathy syndrome
A Bardet-Biedl syndrome that has material basis in homozygous mutation in the BBS1 gene on chromosome 11q13.
Buerger disease, also known as thromboangiitis obliterans (TAO), is a rare inflammatory non-necrotizing vascular disease affecting the small- and medium-sized arteries and veins of the upper and lower extremities characterized by endarteritis and vaso-occlusion due to occlusive thrombus development. The development and progression of the disease is consistently associated with exposure to tobacco.
thromboangiitis obliterans [Buerger's disease]
inflammatory occlusive peripheral vascular disease
A malignant neoplasm involving the lung.
Hepatic fibrosis-renal cysts-intellectual disability syndrome is a rare, syndromic intellectual disability characterized by early developmental delay with failure to thrive, intellectual disability, congenital hepatic fibrosis, renal cystic dysplasia, and dysmorphic facial features (bilateral ptosis, anteverted nostrils, high arched palate, and micrognathia). Variable additional features have been reported, including cerebellar anomalies, postaxial polydactyly, syndactyly, genital anomalies, tachypnea. There have been no further descriptions in the literature since 1987.
cerebellar vermis aplasia with associated features suggesting SMITH-Lemli-Opitz syndrome and Meckel syndrome
hepatic fibrosis-renal cysts-intellectual disability syndrome
peroxisome biogenesis disorder 1A (Zellweger)
peroxisome biogenesis disorder, complementation group 1
peroxisome biogenesis disorder, complementation group E
peroxisome biogenesis disorder 2A (Zellweger)
peroxisome biogenesis disorder, complementation group 2
CHARGE syndrome is a multiple congenital anomaly syndrome characterized by the variable combination of multiple anomalies, mainly Coloboma; Choanal atresia/stenosis; Cranial nerve dysfunction; Characteristic ear anomalies (known as the major 4 C's).
coloboInOwlma, heart defects, choanal atresia, retardation of Growth and development, genital abnormalities, and Ear anomalies association
coloboInOwlma, heart malformation, choanal atresia, retardation of Growth and development, genital abnormalities, and Ear malformations (CHARGE) association
coloboInOwlma-heart defects-atresia choanae-retardation of growth and development-genitourinary problems-ear abnormalities syndrome
Charge association--coloboInOwlma, heart anomaly, choanal atresia, retardation, genital and Ear anomalies
coloboInOwlma, heart anomaly, choanal atresia, retardation, genital and ear anomalies
Apparent mineralocorticoid excess (AME) is a rare form of pseudohyperaldosteronism characterized by very early-onset and severe hypertension, associated with low renin levels and hypoaldosteronism.
11 Beta-hydroxysteroid dehydrogenase type 2 deficiency
11-beta-hydroxysteroid dehydrogenase deficiency type 2
cortisol 11-beta-ketoreductase deficiency
Cranioectodermal dysplasia (CED) is a rare developmental disorder characterized by congenital skeletal and ectodermal defects associated with dysmorphic features, nephronophthisis, hepatic fibrosis and ocular anomalies (mainly retinitis pigmentosa).
A recessive syndrome characterized by craniosynostosis, mental retardation, seizures, choroidal coloboma, dysplastic kidneys, bat ears, cleft lip and palate, and beaked nose.
craniosynostosis-intellectual disability-clefting syndrome
craniosynostosis-mental retardation-clefting syndrome
craniosynostosis intellectual disability clefting syndrome
craniosynostosis mental retardation clefting syndrome
craniosynostosis, intellectual disability, seizures, choroidal coloboInOwlma, dysplastic kidneys, bat ears, cleft lip and palate, and beaked nose
craniosynostosis, mental retardation, seizures, choroidal coloboInOwlma, dysplastic kidneys, bat ears, cleft lip and palate, and beaked nose
Cataract - nephropathy - encephalopathy syndrome describes a lethal combination of manifestations including short stature, congenital cataracts, encephalopathy with epileptic fits, and postmortem confirmation of nephropathy (renal tubular necrosis). The combination of cataract - nephropathy - encephalopathy has been described in 2 female infant children of first cousin parents. The infants did not survive beyond 4 and 8 months respectively. There have been no further descriptions in the literature since 1963.
congenital cataracts, renal tubular necrosis and encephalopathy in two sisters
cataract-nephropathy-encephalopathy syndrome
Fraser syndrome is a rare clinical entity including as main characteristics cryptophthalmos and syndactyly.
cryptophthalmos with other malformations
congenital nephrosis-cerebral ventriculomegaly syndrome
ventriculomegaly with cystic kidney disease
Nephropathic juvenile cystinosis is the intermediate form, in regards to severity and age of onset, of cystinosis, a metabolic disease characterized by an accumulation of cystine inside the lysosomes that causes damage in different organs and tissues, particularly in the kidneys and eyes.
cystinosis, late-onset juvenile or adolescent nephropathic type
Cystinuria is a renal tubular amino acid transport disorder characterized by recurrent formation of kidneys cystine stones.
Hereditary renal hypouricemia (HRH) is a rare autosomal recessively inherited renal membrane transport disorder affecting urate reabsorption in the proximal tubules leading to usually asymptomatic hypouricemia and predisposing to urolithiasis and exercise induced acute renal failure (EIARF).
This syndrome is characterised by nephrogenic diabetes insipidus, intracerebral calcifications, intellectual deficit, short stature and facial dysmorphism.
diabetes insipidus nephrogenic intellectual disability and intracerebral calcification
diabetes insipidus nephrogenic mental retardation and intracerebral calcification
diabetes insipidus, nephrogenic, with intellectual disability and intracerebral calcification
diabetes insipidus, nephrogenic, with mental retardation and intracerebral calcification
nephrogenic diabetes insipidus-intracranial calcification syndrome
Ellis-van Creveld syndrome (EVC) is a skeletal and ectoderlam dysplasia characterized by a tetrad of short stature, postaxial polydactyly, ectodermal dysplasia, and congenital heart defects.
Faciocardiorenal syndrome is a very rare syndrome characterized by intellectual deficit, horseshoe kidney, and congenital heart defects.
Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.
Fanconi Anemia, complementation group type C
Fanconi anemia complementation group type C
Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.
Fanconi anemia, complementation group D2
Fanconi anemia caused by mutations of the FANCA gene. FANCA gene mutations are the most common cause of Fanconi anemia. This gene provides instructions for making a protein that is involved in the Fanconi anemia (FA) pathway.
Fanconi Anemia, complementation group type a
Fanconi anemia caused by mutation in FANCA
Fanconi anemia complementation group type A
Estren-Dameshek variant of Fanconi Anemia
Estren-Dameshek variant of Fanconi pancytopenia
Fanconi-Bickel glycogenosis (FBG) is a rare glycogen storage disease characterized by hepatorenal glycogen accumulation, severe renal tubular dysfunction and impaired glucose and galactose metabolism.
Fanconi syndrome with intestinal malabsorption and galactose intolerance
glycogen storage disease due to GLUT2 deficiency
hepatic glycogenosis with Fanconi nephropathy
hepatic glycogenosis with amino aciduria and glucosuria
hepatorenal glycogenosis with renal Fanconi syndrome
Fibulo-ulnar hypoplasia-renal anomalies syndrome is characterized by fibuloulnar dysostosis with renal anomalies. It has been described in two sibs born to nonconsanguinous parents. The syndrome is lethal at birth (respiratory failure). Clinical manifestations include ear and facial anomalies (including micrognathia), symmetrical shortness of long bones, fibular agenesis and hypoplastic ulna, oligosyndactyly, congenital heart defects, and cystic or hypoplastic kidney. It is transmitted as an autosomal recessive trait.
FIBULOULNAR aplasia or hypoplasia with renal abnormalities
Fibulo-ulnar hypoplasia-renal anomalies syndrome
Hereditary fructose intolerance (HFI) is an autosomal recessive disorder of fructose metabolism, resulting from a deficiency of hepatic fructose-1-phosphate aldolase activity and leading to gastrointestinal disorders and postprandial hypoglycemia following fructose ingestion. HFI is a benign condition when treated, but it is life-threatening and potentially fatal if left untreated.
fructose-1,6-bisphosphate aldolase B deficiency
hereditary fructose intolerance syndrome
hereditary fructose-1-phosphate aldolase deficiency
fructose-1-phosphate aldolase deficiency
Galactokinase deficiency is a rare mild form of galactosemia characterized by early onset of cataract and an absence of the usual signs of classic galactosemia, i.e. feeding difficulties, poor weight gain and growth, lethargy, and jaundice.
Galactose epimerase deficiency is a very rare, moderate to severe form of galactosemia characterized by moderate to severe signs of impaired galactose metabolism.
uridine diphosphate galactose-4-epimerase deficiency
Classic galactosemia is a life-threatening metabolic disease with onset in the neonatal period. Infants usually develop feeding difficulties, lethargy, and severe liver disease.
galactose-1-phosphate uridyltransferase deficiency
classical galactosemia, homozygous duarte-type
galactose-1-phosphate uridylyltransferase deficiency
Glycogenosis due to glucose-6-phosphatase deficiency (G6P) type a, or glycogen storage disease (GSD) type 1a, is a type of glycogenosis due to G6P deficiency.
glycogen storage disease caused by mutation in G6PC
glycogen storage disease due to G6P deficiency type Ia
glycogenosis due to glucose-6-phosphatase deficiency type 1a
glycogenosis due to glucose-6-phosphatase deficiency type Ia
glucose-6-phosphatase deficiency glycogen storage disease
hepatorenal form of glycogen storage disease
glycogen storage disease due to glucose-6-phosphatase deficiency type IA
Glycogenosis due to glucose-6-phosphatase deficiency (G6P) type b, or glycogen storage disease (GSD) type 1b, is a type of glycogenosis due to G6P deficiency.
glycogen storage disease due to G6P deficiency type IB
glycogenosis due to glucose-6-phosphatase deficiency type 1b
glycogenosis due to glucose-6-phosphatase transport defect type IB
Editor note: TODO decide whether to merge Ic
glycogen storage disease due to glucose-6-phosphatase deficiency type IB
Familial Renal Glucosuria (FRG) is characterized by the presence of persistent isolated glucosuria in the absence of both generalized proximal tubular dysfunction and hyperglycemia. FRG is usually considered a benign entity as most patients are not affected by severe clinical consequences. Polyuria and enuresis and later a mild growth and pubertal maturation delay are the only manifestations that have been reported during a follow-up period of 30 years. Episodic dehydration and ketosis during pregnancy and starvation and an increased incidence of urinary tract infections have occasionally been reported in severe cases. FRG is caused by loss-of-function mutations in the gene SLC5A2 (16p11.2).
Goodpasture syndrome is an autoimmune disease that affects the lungs and kidneys and is characterized by pulmonary alveolar hemorrhage (bleeding in the lungs) and a kidney disease known as glomerulonephritis. Some use the term 'Goodpasture syndrome' for the findings of glomerulonephritis and pulmonary hemorrhage and the term 'Goodpasture disease' for those patients with glomerulonephritis, pulmonary hemorrhage, and anti-GBM antibodies. Currently, the preferred term for both conditions is “ anti-GBM antibody disease ”. Circulating antibodies are directed against the collagen of the part of the kidney known as the glomerular basement membrane (GBM), resulting in acute or rapidly progressive glomerulonephritis. Antibodies also attack the collagen of the air sacs of the lung (alveoli) resulting in bleeding of the lung (pulmonary hemorrhage). Symptoms may include general body discomfort or pain, bleeding from the nose and/or blood in the urine, respiratory problems, anemia, chest pain, and kidney failure. Anti-GBM disease is thought to result from an environmental insult (smoking, infections, exposure to certain drugs) in a person with genetic susceptibility, such as a specific human leukocyte antigen (HLA) type. Diagnosis is confirmed with the presence of anti-GBM antibody in the blood or in the kidney. The treatment of choice is plasmapheresis in conjunction with prednisone and cyclophosphamide.
anti-glomerular basement membrane disease
glomerulonephritis - pulmonary hemorrhage
rapidly progressive glomerulonephritis with pulmonary hemorrhage
Hartnup disease is a rare metabolic disorder belonging to the neutral aminoacidurias and characterized by abnormal renal and gastrointestinal transport of neutral amino acids (tryptophan, alanine, asparagine, glutamine, histidine, isoleucine, leucine, phenylalanine, serine, threonine, tyrosine and valine).
A rare form of pulmonary arterial hypertension (PAH) characterized by a capillary infiltration of the pulmonary interstitium, bronchioles and pleura leading to elevated pulmonary arterial resistance and right heart failure. PCH is potentially fatal.
familial pulmonary capillary hemangiomatosis
hemangiomatosis, familial pulmonary capillary
pulmonary venoocclusive disease 2, autosomal recessive
Editor note: check ORDO class - not clear if it intends to be the same as PVOD2
A disorder of the blood that is present at birth.
hemolytic uremic syndrome, atypical, susceptibility to, 1
hemolytic uremic syndrome, atypical, susceptibility to, type 1
susceptibility to atypical hemolytic uremic syndrome 1
hydranencephaly with renal aplasia-dysplasia
multinucleated neurons, anhydramnios, renal dysplasia, cerebellar Hypoplasia, and hydranencephaly
multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome
facial palsy, partial, with urinary abnormalities
Non-immune hydrops fetalis (NIHF), a form of HF, is a severe fetal condition defined as the excessive accumulation of fetal fluid within the fetal extravascular compartments and body cavities, and is the end-stage of a wide variety of disorders.
hydrops fetalis, Alpha-thalassemia-related
Any Bartter syndrome in which the cause of the disease is a mutation in the KCNJ1 gene.
Bartter syndrome caused by mutation in KCNJ1
hypokalemic alkalosis with hypercalciuria 2 antenatal
hypokalemic alkalosis with hypercalciuria 2, antenatal
hypokalemic alkalosis with hypercalciuria antenatal 2
hypokalemic alkalosis with hypercalciuria, antenatal, 2
Hypothalamic hamartomas (HH) are rare, tumor-like malformations that occur during fetal development and are present at birth. The lesions usually do not change in size or spread to other locations. Both the type and severity of symptoms vary greatly among patients with hypothalamic hamartomas. Common symptoms include frequent gelastic seizures (spontaneous laughing, giggling and/or smirking) or dacrystic seizures (crying or grunting); developmental delays; and/or precocious puberty. Additional symptoms may include cognitive impairment; emotional and behavioral difficulties; and endocrine disturbances. These symptoms often start early in life but are frequently misdiagnosed. For some patients, endocrine (hormonal) disturbances such as central precocious puberty may be the only symptom. These patients can often be treated successfully with medications. For some, however, HH can be disabling. For those with HH and epilepsy, it is common for the disorder to progress and for different types of seizures to develop. The seizures associated with HH often cannot be well-controlled with the standard seizure medications. For some, additional treatment such as surgical removal, radiosurgery, or thermoablation may be indicated. Though hypothalamic hamartomas can occur in patients with certain genetic disorders (such as Pallister-Hall syndrome), the majority of cases are sporadic.
congenital hypothalamic hamartoma syndrome
hypouricemia, hypercalcinuria, and decreased bone density
Ichthyosis-intellectual disability-dwarfism-renal impairment syndrome is characterised by nonbullous congenital ichthyosis, intellectual deficit, dwarfism and renal impairment. It has been described in four members of one Iranian family. Transmission is autosomal recessive.
ichthyosis intellectual deficit dwarfism renal impairment
ichthyosis, intellectual disability, dwarfism and renal impairment
ichthyosis, intellectual disability, dwarfism, and renal impairment
ichthyosis, mental retardation, dwarfism and renal impairment
ichthyosis, mental retardation, dwarfism, and renal impairment
ichthyosis-intellectual disability-dwarfism-renal impairment syndrome
Schimke immuno-osseous dysplasia (SIOD) is a multisystem disorder characterized by spondyloepiphyseal dysplasia and disproportionate short stature, facial dysmorphism, T-cell immunodeficiency, and glomerulonephritis with nephrotic syndrome.
spondyloepiphyseal dysplasia - nephrotic syndrome
spondyloepiphyseal dysplasia-nephrotic syndrome
spondyloepiphyseal dysplasia nephrotic syndrome
Stromme syndrome is an autosomal recessive congenital disorder affecting multiple systems with features of a ciliopathy. Affected individuals typically have some type of intestinal atresia, variable ocular abnormalities, microcephaly, and sometimes involvement of other systems, including renal and cardiac. In some cases, the condition is lethal in early life, whereas other patients show normal survival with or without mild cognitive impairment (summary by Filges et al., 2016).
apple peel syndrome with microcephaly and ocular anomalies
apple-peel intestinal atresia-ocular anomalies-microcephaly syndrome
jejunal atresia with microcephaly and ocular anomalies
jejunal atresia-microcephaly-ocular anomalies syndrome
lethal fetal brain malformation-duodenal atresia-bilateral renal hypoplasia syndrome
ciliary dyskinesia, primary, 31, formerly
Familial LCAT (lecithin-cholesterol acyltransferase) deficiency (FLD) is a form of lecithin-cholesterol acyltransferase deficiency (LCAT) characterized clinically by corneal opacities, hemolytic anemia, and renal failure, and biochemically by severely decreased HDL cholesterol and complete deficiency of the LCAT enzyme.
lecithin:cholesterol acyltransferase deficiency
Familial primary hypomagnesemia with hypercalciuria and nephrocalcinosis with severe ocular involvement (FHHNCOI) is a form of familial primary hypomagnesemia (FPH), characterized by excessive magnesium and calcium renal wasting, bilateral nephrocalcinosis, progressive renal failure and severe ocular abnormalities.
bilateral macular coloboInOwlma with hypercalciuria
familial hypomagnesemia with hypercalciuria, nephrocalcinosis and severe ocular involvement
hypercalciuria-bilateral macular coloboInOwlma syndrome
familial primary hypomagnesemia with hypercalciuria and nephrocalcinosis with severe ocular involvement
hypomagnesemia 5, renal, with ocular involvement
hypomagnesemia, familial, with hypercalciuria, nephrocalcinosis, and severe ocular involvement
hypomagnesemia, renal, with ocular involvement
idiopathic hypercalciuria with bilateral macular coloboInOwlmata
macular coloboInOwlma, bilateral, with hypercalciuria
renal hypomagnesemia 5 with ocular involvement
Familial primary hypomagnesemia with hypercalciuria and nephrocalcinosis without severe ocular involvement (FHHN) is a form of familial primary hypomagnesemia (FPH), characterized by recurrent urinary tract infections, nephrolithiasis, bilateral nephrocalcinosis, renal magnesium (Mg) wasting, hypercalciuria and kidney failure.
familial primary hypomagnesemia caused by mutation in CLDN16
familial primary hypomagnesemia with hypercalciuria and nephrocalcinosis without severe ocular involvement
primary hypomagnesemia caused by mutation in CLDN16
primary hypomagnesemia due to defect in renal tubular transport of magnesium
hypercalciuria, childhood, self-limiting
hypomagnesemia, familial, with hypercalciuria and nephrocalcinosis
hypomagnesemia, familial, with hypercalciuria and nephrocalcinosis hypercalciuria, childhood, self-limiting, included
hypomagnesemia, primary, due to defect in renal tubular Transport Of magnesium
magnesium, defect in renal tubular transport of
Any Meckel syndrome in which the cause of the disease is a mutation in the MKS1 gene.
Meckel syndrome caused by mutation in MKS1
Autosomal recessive form of familial Mediterranean fever.
familial Mediterranean fever, autosomal recessive
autosomal recessive familial Mediterranean fever
Methylcobalamin deficiency cbl G type is a rare condition that occurs when the body is unable to process certain amino acids (building blocks of protein) properly. In most cases, signs and symptoms develop during the first year of life; however, the age of onset can range from infancy to adulthood. Common features of the condition include feeding difficulties, lethargy, seizures, poor muscle tone (hypotonia), developmental delay, microcephaly (unusually small head size), and megaloblastic anemia. Methylcobalamin deficiency cbl G type is caused by changes (mutations) in the MTR gene and is inherited in an autosomal recessive manner. Treatment generally includes regular doses of hydroxycobalamin (vitamin B12). Some affected people may also require supplementation with folates and betaine.
functional methionine synthase deficiency type cblG
homocystinuria due to defect in methylation Cbl g
homocystinuria-megaloblastic Anemia due to defect in cobalamin metabolism, cblG complementation type
homocystinuria-megaloblastic anemia, cblG complementation type
methylmalonic aciduria and homocystinuria type cblG
Vitamin B12-unresponsive methylmalonic acidemia is an inborn error of vitamin B12 (cobalamin) metabolism characterized by recurrent ketoacidotic crises or transient vomiting, dehydration, hypotonia and intellectual deficit, which does not respond to administration of vitamin B12. There are two types of vitamin B12-unresponsive methylmalonic acidemia: mut0 and mut-.
methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency
methylmalonyl-Coenzyme A mutase deficiency
vitamin B12-unresponsive methylmalonic aciduria
methylmalonic acidemia due to methylmalonyl-Coa mutase deficiency MMA due to MCM deficiency
vitamin B12-unresponsive methylmalonic acidemia
An autosomal recessive form of methylmalonic aciduria, caused by mutation(s) in the MMAA gene, encoding MMAA protein.
methylmalonic aciduria, vitamin B12-responsive due to a defect in synthesis of adenosylcobalamin cb1A type
methylmalonic aciduria, vitamin B12-responsive due to a defect in synthesis of adenosylcobalamin cblA type
vitamin B12-responsive methylmalonic acidemia type cblA
vitamin B12-responsive methylmalonic aciduria type cblA
methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblA complementation type
An autosomal recessive form of methylmalonic aciduria, caused by mutation(s) in the MMAB gene, encoding cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial.
methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblB complementation type
vitamin B12-responsive methylmalonic acidemia type cblB
vitamin B12-responsive methylmalonic aciduria, type cblB
Galloway syndrome is characterized by the association of nephrotic syndrome and central nervous system anomalies.
microcephaly, hiatal hernia and nephrotic syndrome
microcephaly-hiatus hernia-nephrotic syndrome
nephrosis-neuronal dysmigration syndrome
spinocerebellar ataxia, autosomal recessive 5
cerebellar ataxia with intellectual disability, optic atrophy, and skin abnormalities
cerebellar ataxia with mental retardation, optic atrophy, and skin abnormalities
hiatal hernia-microcephaly-nephrosis, Galloway type
microcephaly, hiatal hernia, and nephrotic syndrome
nephrosis neuronal dysmigration syndrome
spinocerebellar ataxia, autosomal recessive 5, formerly
Action myoclonus-renal failure syndrome (AMRF) is a rare epilepsy syndrome characterized by progressive myoclonus epilepsy in association with primary glomerular disease. Patients present with neurologic symptoms (including tremor, action myoclonus, tonic-clonic seizures, later ataxia and dysarthria) that may precede, occur simultaneously or be followed by renal manifestations including proteinuria that progresses to nephrotic syndrome and end-stage renal disease. In some patients, sensorimotor peripheral neuropathy, sensorineural hearing loss and dilated cardiomyopathy are associated symptoms.
epilepsy, progressive myoclonic, 4, with or without renal failure
Nail-patella-like renal disease is a severe nephropathy characterised by renal dysfunction, proteinuria, oedema and microscopic haematuria. It has been described in three brothers, two of which died from end-stage renal insufficiency.
glomerular basement Membrane disease, nail-patella syndrome type
Progressive tubulointerstitial nephritis inherited in an autosomal recessive manner. It is caused by mutations in the NPHP1 gene. Patients present with anemia, polyuria, and polydipsia during childhood. The progressive bilateral kidney damage results in renal failure.
nephronophthisis (disease) caused by mutation in NPHP1
Nephrosis-deafness-urinary tract-digital malformations syndrome is characterised by anomalies of the urinary tract, thumbs and big toes, deafness and nephrosis. It has been described in five brothers. The mode of transmission has not been clearly established but seems to be either autosomal recessive or X-linked dominant.
nephrosis deafness urinary tract digital malformation
nephrosis with deafness and urinary tract and digital malformations
nephrosis-deafness-urinary tract-digital malformations syndrome
Congenital nephrotic syndrome, Finnish type is characterised by protein loss beginning during foetal life.
congenital nephrotic syndrome - Finnish type
congenital nephrotic syndrome Finnish type
congenital nephrotic syndrome, Finnish type
Nephrotic syndrome within the first three motnhs of life, characterized initially by increased mesangial matrix, with or without hypertrophy and hyperplasia of podocytes, and eventual glomerular sclerosis.
congenital nephrotic syndrome - diffuse mesangial sclerosis
nephrotic syndrome caused by mutation in WT1
nephrotic syndrome, early onset with diffuse mesangial sclerosis
Sialidosis type 2 (ST-2) is a rare lysosomal storage disease, and the severe, early onset form of sialidosis characterized by a progressively severe mucopolysaccharidosis-like phenotype (coarse facies, dysostosis multiplex, hepatosplenomegaly), macular cherry-red spots as well as psychomotor and developmental delay. ST-2 displays a broad spectrum of clinical severity with antenatal/congenital, infantile and juvenile presentations.
dysmorphic sialidosis with renal involvement
See https://github.com/monarch-initiative/monarch-disease-ontology/issues/227
Neurofaciodigitorenal syndrome is a rare, multiple developmental anomalies syndrome characterized by neurological abnormalities (including megalencephaly, hypotonia, intellectual disability, abnormal EEG), dysmorphic facial features (high prominent forehead, grooved nasal tip, ptosis, ear anomalies) and acrorenal defects (such as triphalangism, broad halluces, unilateral renal agenesis). Additionally, intrauterine growth restriction, short stature and congenital heart defects may be associated. There have been no further descriptions in the literature since 1997.
absence of the cerebellar granular layer, intellectual disability, tapetoretinal degeneration and progressive glomerulopathy
absence of the cerebellar granular layer, mental retardation, tapetoretinal degeneration and progressive glomerulopathy
Cloacal exstrophy (EC) is a major birth defect representing the severe end of the spectrum of the exstrophy-epispadias complex (EEC) characterized by omphalocele, exstrophy, imperforate anus and spinal defects (also referred to as the OEIS complex), often associated with other malformations.
omphalocele-cloacal exstrophy-imperforate anus-spinal defect syndrome
omphalocele - cloacal exstrophy - imperforate anus - spinal defect
omphalocele, exstrophy of the cloaca, imperforate anus, and spinal defects
omphalocele, exstrophy of the cloaca, imperforate anus, and spinal defects complex
omphalocele-exstrophy-imperforate anus-spinal defects
A usually aggressive malignant bone-forming mesenchymal neoplasm, predominantly affecting adolescents and young adults. It usually involves bones and less frequently extraosseous sites. It often involves the long bones (particularly distal femur, proximal tibia, and proximal humerus). Pain with or without a palpable mass is the most frequent clinical symptom. It may spread to other anatomic sites, particularly the lungs.
Osteopetrosis with renal tubular acidosis is a rare disorder characterized by osteopetrosis, renal tubular acidosis (RTA), and neurological disorders related to cerebral calcifications.
Autosomal Recessive osteopetrosis, type 3
autosomal recessive osteopetrosis 3 with renal tubular acidosis
autosomal recessive osteopetrosis type 3
osteopetrosis (disease) caused by mutation in CA2
osteopetrosis with renal tubular acidosis
osteopetrosis, autosomal recessive type 3
Primary hyperoxaluria type 1 (PH1) is a rare disorder of glyoxylate metabolism characterized by the accumulation of oxalate due to a deficiency of the peroxisomal hepatic enzyme L-alanine: glyoxylate aminotransferase (AGT). Clinical presentation is variable, ranging from occasional symptomatic nephrolithiasis to nephrocalcinosis and end-stage renal disease with systemic involvement.
peroxisomal alanine-glyoxylate aminotransferase deficiency
primary hyperoxaluria caused by mutation in AGXT
alanine-glyoxylate aminotransferase deficiency
peroxisomal alanine glyoxylate aminotransferase deficiency
peroxisomal alanine:glyoxylate aminotransferase deficiency
serine pyruvate aminotransferase deficiency
serine:pyruvate aminotransferase deficiency
Primary hyperoxaluria (PH) type 2 is a rare disorder of glyoxylate metabolism caused by the deficiency of the enzyme glyoxylate reductase/hydropyruvate reductase (GR/HPR) characterized by a childhood onset with clinical manifestations that include recurrent nephrolithiasis, nephrocalcinosis and end-stage renal disease with subsequent systemic oxalosis.
primary hyperoxaluria caused by mutation in GRHPR
glyoxylate reductase/hydroxypyruvate reductase deficiency
Imerslund-Grasbeck syndrome (IGS) or selective vitamin B12 (cobalamin) malabsorption with proteinuria is a rare autosomal recessive disorder characterized by vitamin B12 deficiency commonly resulting in megaloblastic anemia, which is responsive to parenteral vitamin B12 therapy and appears in childhood.
selective cobalamin malabsorption with proteinuria
defect of enterocyte intrinsic factor receptor
Autosomal recessive polycystic kidney disease (ARPKD) is an inherited disorder characterised by the development of cysts affecting the collecting ducts. It is frequently associated with hepatic involvement.
polycystic kidney disease, autosomal recessive
polycystic kidney disease, infantile type
polycystic kidney disease, infantile, type I
autosomal recessive polycystic kidney disease
A group of rare, autosomal recessive inherited disorders characterized by a constricted thoracic cage, short ribs, and a 'trident' appearance of the acetabular roof. Polydactyly may or may not be present. Other abnormalities include cleft lip and palate and abnormalities of the brain, eye, heart, liver, pancreas, intestine, kidney, and genitalia.
polydactyly with neonatal chondrodystrophy type II
polydactyly with neonatal chondrodystrophy, type II
short-rib thoracic dysplasia 6 with or without polydactyly
polydactyly with neonatal chondrodystrophy, type 2
Gitelman syndrome (GS), also referred to as familial hypokalemia-hypomagnesemia, is characterized by hypokalemic metabolic alkalosis in combination with significant hypomagnesemia and low urinary calcium excretion.
hypomagnesemia-hypokalemia, primary renotubular, with hypocalciuria
primary renal tubular hypokalemic hypomagnesemia with hypocalciuria
Generalized pseudohypoaldosteronism type 1 (generalized PHA1) is a severe form of primary mineralocorticoid resistance with systemic involvement and salt loss in multiple organs.
autosomal recessive pseudohypoaldosteronism type 1
generalized pseudohypoaldosteronism type 1
pseudohypoaldosteronism type 1 autosomal recessive
pseudohypoaldosteronism type 1, recessive
pseudohypoaldosteronism, type I, autosomal recessive
pseudoxanthoma elasticum, modifier of severity of
autosomal recessive inherited pseudoxanthoma elasticum
A disorder characterized by pulmonary venous constriction or occlusion, resulting in pulmonary hypertension.
obstructive disease of the pulmonary veins
A very rare, clinically variable, multisystemic metabolic disease, characterized by anosmia, early-onset retinitis pigmentosa and possible neurological manifestations, including neuropathy, and cerebellar ataxia, deafness, ichthyosis, skeletal abnormalities, and cardiac arrhythmia. It is characterized biochemically by accumulation of phytanic acid in plasma and tissues.
Refsum disease with increased pipecolic acidemia
hereditary motor and sensory neuropathy type 4
disorder of cornification 11 (phytanic acid type)
hereditary motor and sensory neuropathy 4
hereditary sensory and motor neuropathy type 4
Curator note: do not confuse with Infantial Refsum, see https://omim.org/entry/266500
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the NPHP1 gene.
Senior-Loken syndrome caused by mutation in NPHP1
juvenile nephronophthisis with Leber amaurosis
Ulbright-Hodes syndrome is characterised by renal dysplasia, growth retardation, phocomelia or mesomelia, radiohumeral fusion, rib abnormalities, anomalies of the external genitalia and a potter-like facies. The syndrome has been described in three infants (one pair of sibs and an unrelated case), all of whom died shortly after birth from respiratory distress resulting from pulmonary hypoplasia and oligohydramnios caused by renal dysplasia. The mode of transmission appears to be autosomal recessive.
renal dysplasia-mesomelia-radiohumeral fusion syndrome
renal dysplasia, mesomelia, and radiohumeral fusion
An asphyxiating thoracic dystrophy that has material basis in homozygous or compound heterozygous mutation in the IFT140 gene on chromosome 16p13.
renal dysplasia, retinal pigmentary dystrophy, cerebellar ataxia and skeletal dysplasia
renal dysplasia-retinal pigmentary dystrophy-cerebellar ataxia-skeletal dysplasia syndrome
short-rib thoracic dysplasia 9 with or without polydactyly
renal dysplasia, retinal pigmentary dystrophy, cerebellar ataxia, and skeletal dysplasia
Perlman syndrome is characterized principally by polyhydramnios, neonatal macrosomia, bilateral renal tumours (hamartomas with or without nephroblastomatosis), hypertrophy of the islets of Langerhans and facial dysmorphism.
nephroblastomatosis - fetal ascites - macrosomia - Wilms tumor
nephroblastomatosis, fetal ascites, macrosomia and Wilms tumor
nephroblastomatosis-fetal ascites-macrosomia-Wilms tumor syndrome
renal hamartomas, nephroblastomatosis and fetal gigantism
nephroblastomatosis fetal ascites macrosomia and Wilms tumor
nephroblastomatosis, fetal ascites, macrosomia, and Wilms tumor
renal hamartomas, nephroblastomatosis, and fetal gigantism
renal-hepatic-pancreatic dysplasia-Dandy-Walker cysts syndrome
Dandy-Walker cyst with renal-hepatic-pancreatic dysplasia
renal-hepatic-pancreatic dysplasia with Dandy-Walker cyst
distal renal tubular acidosis co-occurrent with sensorineural deafness
renal tubular acidosis, distal, with progressive nerve deafness
autosomal recessive distal renal tubular acidosis with deafness
autosomal recessive distal renal tubular acidosis with hearing loss
renal tubular acidosis progressive nerve deafness
renal tubular acidosis with progressive nerve deafness
renal tubular acidosis, autosomal recessive, with progressive nerve deafness
renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss
renal, genital, and middle EAR anomalies
An instance of renal tubular dysgenesis that is caused by a modification of the individual's genome.
renal tubular dysgenesis with choanal atresia and athelia
renal tubular dysgenesis of genetic origin
EEC syndrome is a genetic developmental disorder characterized by ectrodactyly, ectodermal dysplasia, and orofacial clefts (cleft lip/palate).
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome
ectrodactyly-ectodermal dysplasia-cleft lip/palate syndrome
ectrodactyly-ectodermal dysplasia-cleft syndrome
ectrodactyly-ectodermal dysplasia-clefting syndrome
ectrodactyly-ectodermal dysplasia-cleft lip/cleft palate
ectrodactyly-ectodermal dysplasia-clefting (EEC) syndrome
Schinzel-Giedion syndrome (SGS) is an ectodermal dysplasia syndrome chiefly characterized by a distinctive facial dysmorphism, hydronephrosis, severe developmental delay, typical skeletal malformations, and genital and cardiac anomalies.
Schinzel-Giedion midface-retraction syndrome
Schinzel Giedion midface-retraction syndrome
Schinzel-Giedion midface retraction syndrome
Short rib-polydactyly syndrome (SRPS), Beemer-Langer type is an extremely rare type of SRPS developing prenatally or immediately after birth and characterized by short and narrow thorax with horizontally oriented ribs. Other bone features include small iliac bones, short tubular bones, bowing of long bones and rarely pre- and post-axial polydactyly. Brain defects are common and some cases of cleft lip, absent internal genitalia and renal, biliary and pancreatic cysts have been reported. The course is rapidly fatal.
short rib polydactyly syndrome Beemer-Langer type
short rib-polydactyly syndrome Beemer type
short rib-polydactyly syndrome, Beemer-Langer type
A congenital condition in which there is complete right-to-left reversal of the position of the major thoracic and abdominal organs (that is, they are arranged in a mirror image of the normal positioning).
complete transposition (morphologic abnormality)
Smith-Lemli-Opitz syndrome (SLOS) is characterized by multiple congenital anomalies, intellectual deficit, and behavioral problems.
7-dehydrocholesterol reductase deficiency
Rutledge lethal multiple congenital anomaly syndrome
polydactyly, sex reversal, renal hypoplasia, and unilobar lung
polydactyly, sex reversal, renal hypoplasia, and unilobular lung
Congenital thrombotic thrombocytopenic purpura is the hereditary form of thrombotic thrombocytopenic purpura (TTP) characterized by profound peripheral thrombocytopenia, microangiopathic hemolytic anemia (MAHA) and single or multiple organ failure of variable severity.
hereditary thrombotic thrombocytopenic purpura
Microangiopathic hemolytic Anemia, congenital
thrombotic thrombocytopenic purpura, congenital
thrombotic thrombocytopenic purpura, familial
congenital thrombotic thrombocytopenic purpura
Thyrocerebrorenal syndrome is characterized by renal, neurologic, thyroid disease, associated with thrombocytopenia. It has been described in a brother and his sister. Intelligence was normal. It is transmitted as an autosomal recessive trait.
This syndrome is characterised by intrauterine growth retardation, renal dysgenesis and a unilobed or absent thymus.
syndrome of unilobed or absent thymus, renal and ureter agenesis/dysgenesis, and intrauterine growth retardation (IUGR)
Tyrosinemia type 1 (HTI) is an inborn error of tyrosine catabolism caused by defective activity of fumarylacetoacetate hydrolase (FAH) and is characterized by progressive liver disease, renal tubular dysfunction, porphyria-like crises and a dramatic improvement in prognosis following treatment with nitisinone.
fumarylacetoacetate hydrolase deficiency
VACTERL is an acronym for Vertebral anomalies, Anal atresia, Congenital cardiac disease, tracheoesophageal fistula, Renal anomalies, and Limb defects. VACTERL associated with hydrocephalus has rarely been reported and is thought to be an autosomal recessive anomaly. The condition is described as a uniformly lethal or developmentally devastating disorder distinct from the VATER association.
Vater association with macrocephaly and ventriculomegaly
vertebral (V), anal (A), cardiac (C), tracheoesophageal (te), renal (R) and limb (L) anomalies and hydrocephaly
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome type 1, a form of MRKH syndrome, is an isolated form of congenital aplasia of the uterus and 2/3 of the vagina occurring in otherwise phenotypically normal females.
Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH)
Mayer-Rokitansky-Küster-Hauser syndrome type 1
congenital absence of the uterus and vagina (CAUV)
uterus Bipartitus solidus Rudimentarius cum vagina Solida
Mayer-Rokitansky-Kuster-Hauser syndrome type 1
Wilson disease is a very rare inherited multisystemic disease presenting non-specific neurological, hepatic, psychiatric or osseo-muscular manifestations due to excessive copper deposition in the body.
Type I xanthinuria, a type of classical xanthinuria, is a rare autosomal recessive disorder of purine metabolism characterized by the isolated deficiency of xanthine dehydrogenase, causing hyperxanthinemia with low or absent uric acid and xanthinuria, leading to urolithiasis, hematuria, renal colic and urinary tract infections, while some patients are asymptomatic and others suffer from kidney failure. Less common manifestations include arthropathy, myopathy and duodenal ulcer.
Dent disease type 1 is a type of Dent disease with predominantly renal manifestations.
Dent disease caused by mutation in CLCN5
nephrolithiasis, hypercalciuric, X-linked
Simpson-Golabi-Behmel syndrome (SGBS) type 2 is an extremely rare and severe, early-lethal form of SGBS, an overgrowth-multiple anomalies syndrome, characterized by hydrops fetalis, macrocephaly, facial dysmorphism (hypertelorism, low-set, posteriorly angulated ears, short and broad nose with anteverted nares, prominent philtrum, large mouth with thin upper vermilion border, high-arched and cleft palate), short neck, redundant skin, skeletal defects (involving upper and lower limbs), hypoplastic nails, gastrointestinal and genitourinary anomalies, hypotonia and neurologic impairment. Severe intellectual disability, obesity and infections (pneumonia, sepsis) have been reported.
Simpson-Golabi-Behmel syndrome caused by mutation in OFD1
lethal variant of Simpson-Golabi-Behmel syndrome
Lesch-Nyhan syndrome (LNS) is the most severe form of hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency, a hereditary disorder of purine metabolism, and is associated with uric acid overproduction (UAO), neurological troubles, and behavioral problems.
hypoxanthine guanine phosphoribosyltransferase deficiency
hypoxanthine-guanine phosphoribosyltransferase deficiency (disorder) [ambiguous]
X-linked hyperuricemia (disorder) [ambiguous]
complete hypoxanthine-guanine phosphoribosyltransferase deficiency
hypoxanthine guanine phosphoribosyltransferase complete deficiency
hypoxanthine guanine phosphoribosyltransferase deficiency, grade IV
hypoxanthine-guanine phosphoribosyltransferase deficiency
hypoxanthine-guanine-phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome, neurologic variant
hypoxanthine guanine phospho-ribosyltransferase 1 deficiency
hypoxanthine guanine phosphoribosyltransferase 1 deficiency
hypoxanthine-guanine-phosphoribosyltransferase deficiency (& [Lesch - Nyhan syndrome])
Kelley-Seegmiller syndrome (KSS) is the mildest form of hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency, a hereditary disorder of purine metabolism, and is associated with uric acid overproduction (UAO) leading to urolithiasis, and early-onset gout.
hypoxanthine guanine phosphoribosyltransferase 1 partial deficiency
hypoxanthine guanine phosphoribosyltransferase deficiency, grade I
hypoxanthine guanine phosphoribosyltransferase 1 deficiency, partial
hypoxanthine guanine phosphoribosyltransferase partial deficiency
Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.
Fanconi Anemia, complementation group type B
Fanconi anemia complementation group type B
Nephrogenic syndrome of inappropriate antidiuresis (NSIAD) is a rare genetic disorder of water balance, closely resembling the far more frequent syndrome of inappropriate antidiuretic secretion (SIAD), and characterized by euvolemic hypotonic hyponatremia due to impaired free water excretion and undetectable or low plasma arginine vasopressin (AVP) levels.
nephrogenic syndrome of inappropriate antidiuresis
Dent disease type 2 is a type of Dent disease in which patients have the manifestations of Dent disease type 1 associated with extra-renal features.
Phosphoribosylpyrophosphate (PRPP) synthetase superactivity is an X-linked disorder of purine metabolism associated with hyperuricemia and hyperuricosuria, comprised of two forms: an early-onset severe form characterized by gout, urolithiasis, and neurodevelopmental anomalies (severe PRPP synthetase superactivity) and a mild late-onset form with no neurologic involvement (mild PRPP synthetase superactivity).
phosphoribosylpyrophosphate synthetase superactivity
Any paroxysmal nocturnal hemoglobinuria in which the cause of the disease is a mutation in the PIGA gene.
PIGA paroxysmal nocturnal hemoglobinuria
paroxysmal nocturnal hemoglobinuria caused by mutation in PIGA
paroxysmal nocturnal hemoglobinuria type 1
Any Bartter syndrome in which the cause of the disease is a mutation in the MAGED2 gene.
Bartter syndrome caused by mutation in MAGED2
Bartter syndrome, type 5, antenatal, transient
Fabry disease (FD) is a progressive, inherited, multisystemic lysosomal storage disease characterized by specific neurological, cutaneous, renal, cardiovascular, cochleo-vestibular and cerebrovascular manifestations.
diabetes insipidus, nephrogenic, X-linked
membranoproliferative glomerulonephritis, X-linked
Mesangiocapillary glomerulonephritis, X-linked
hypouricemia, familial renal, due to tubular hypersecretion
The association of X-linked Alport syndrome with leiomyomatosis of the esophagus, tracheobronchial tree or female genitals has been reported in more than 30 families.
Alport syndrome and diffuse leiomyomatosis
Alport syndrome with diffuse leiomyomatosis
chromosome Xq22.3 centromeric deletion syndrome
diffuse leiomyomatosis in Alport syndrome
leiomyomatosis, diffuse, with Alport syndrome
leiomyomatosis, esophageal and vulval, with nephropathy
X-linked diffuse leiomyomatosis-Alport syndrome
proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
Editor note: ORDO inclides a btnt xref to this from Dent disease type 1, presumably due to the fact proteinuria is sometimes a feature of dent disease. We capture this separately in annotations
Oculocerebrorenal syndrome of Lowe (OCRL) is a multisystem disorder characterized by congenital cataracts, glaucoma, intellectual disabilities, postnatal growth retardation and renal tubular dysfunction with chronic renal failure.
phosphatidylinositol 4,5-biphosphate 5-phosphatase deficiency
phosphatidylinositol 4,5-bisphosphate 5-phosphatase deficiency
nephrolithiasis, X-linked recessive, with renal failure
nephrolithiasis, X-linked recessive, type 1
urolithiasis, X-linked recessive, type 1
Editor note: ORDO inclides a btnt xref to this from Dent disease type 1, presumably due to the fact nephrolithiasis is sometimes a feature of dent disease. We capture this separately in annotations
Oral-facial-digital syndrome type 1 (OFD1) is a rare neurodevelopmental disorder in the ciliopathy group that is lethal in males and characterized by variable anomalies including external malformations (craniofacial and digital), and possible involvement of the central nervous system (CNS) and of viscera (kidneys, pancreas and ovaries) in females.
Papillon-league-Psaume syndrome (formerly)
Simpson-Golabi-Behmel syndrome is a rare X-linked multiple congenital anomalies syndrome, characterized by pre- and postnatal overgrowth, distinctive craniofacial features, variable congenital malformations, organomegaly and an increased tumor risk.
VACTERL association, X-linked, with or without hydrocephalus
VACTERL association with hydrocephaly, X-linked
A usually benign neoplasm composed of large cells with abundant eosinophilic granular cytoplasm. Representative examples include oncocytic neoplasms of the thyroid gland, and kidney. (NCI05)
Proximal tubulopathy-diabetes mellitus-cerebellar ataxia syndrome is characterised by onset of proximal tubulopathy in the first year of life, followed by progressive development during childhood of skin anomalies (erythrocyanosis and abnormal pigmentation), blindness, osteoporosis, cerebellar ataxia, mitochondrial myopathy, deafness and diabetes mellitus.
proximal tubulopathy, diabetes mellitus and cerebellar ataxia
renal tubulopathy, diabetes mellitus, and cerebellar ataxia
renal tubulopathy, diabetes mellitus, and cerebellar ataxia due to duplication of mitochondrial DNA
proximal tubulopathy-diabetes mellitus-cerebellar ataxia syndrome
Bladder exstrophy (or classic bladder exstrophy; CEB) is a congenital genitourinary malformation belonging to the spectrum of the exstrophy-epispadias complex (EEC) and is characterized by an evaginated bladder plate, epispadias and an anterior defect of the pelvis, pelvic floor and abdominal wall.
bladder exstrophy and epispadias Complex
Hyperfunction of the parathyroid glands resulting in the overproduction of parathyroid hormone. It is caused by parathyroid adenoma, parathyroid hyperplasia, parathyroid carcinoma, and multiple endocrine neoplasia. It is associated with hypercalcemia and hypophosphatemia. Signs and symptoms include weakness, fatigue, nausea, vomiting, constipation, depression, bone pain, osteoporosis, cystic bone lesions, and kidney stones.
Editor note: check relationship to parent and familiar form
Polycystic kidney disease with tuberous sclerosis (PKD-TSC) is characterised by early-onset and severe polycystic kidney disease with various manifestations of tuberous sclerosis (multiple angiomyolipomas, lymphangioleiomyomatosis and periventricular calcifications of the central nervous system).
tuberous sclerosis/polycystic kidney disease contiguous gene syndrome
chromosome 16P13.3 deletion syndrome, distal
polycystic kidney disease, infantile severe, with tuberous sclerosis
polycystic kidneys, severe infantile with tuberous sclerosis
tuberous sclerosis polycystic kidney disease contiguous gene syndrome
autosomal dominant polycystic kidney disease type 1 with tuberous sclerosis
Any autosomal dominant polycystic kidney disease in which the cause of the disease is a mutation in the GANAB gene.
GANAB autosomal dominant polycystic kidney disease
autosomal dominant polycystic kidney disease caused by mutation in GANAB
polycystic kidney disease 3 with or without polycystic liver disease
polycystic kidney disease 3, autosomal dominant
polycystic kidney disease, adult, type 3
polycystic kidney disease, adult, type III
Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.
Fanconi Anemia, complementation group type E
Fanconi anemia caused by mutation in FANCE
Fanconi anemia complementation group type E
Infundibulopelvic stenosis-multicystic kidney syndrome is a rare, genetic renal malformation syndrome characterized by variable degrees of malformation in the pelvicalyceal system (including unilateral or bilateral calyceal dilatation, infundibular stenosis, hypoplasia or stenosis of the renal pelvis) which lead to multicystic kidney. Clinically it exhibits abdominal, lumbar or flank pain, recurrent urinary tract infections, hypertension, proteinuria and often progresses to renal insufficiency. Calyceal dilatation and hydronephrosis are frequently seen on imaging.
infundibulopelvic stenosis-multicystic kidney syndrome
Any nephrotic syndrome in which the cause of the disease is a mutation in the NPHS2 gene.
nephrotic syndrome caused by mutation in NPHS2
nephrotic syndrome, idiopathic, steroid-resistant
nephrotic syndrome, steroid-resistant, autosomal recessive
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome type 2, a form of MRKH syndrome, is characterized by congenital aplasia of the uterus and upper 2/3 of the vagina that is associated with at least one other malformation such as renal, vertebral, or, less commonly, auditory and cardiac defects. The acronym MURCS (MCllerian duct aplasia, Renal dysplasia, Cervical Somite anomalies) is also used.
Mayer-Rokitansky-Küster-Hauser syndrome type 2
Mullerian duct aplasia-renal dysplasia-cervical somite anomalies syndrome
Müllerian duct aplasia-renal dysplasia-cervical somite anomalies syndrome
Klippel-Feil deformity, conductive deafness, and absent vagina
MULLERIAN duct aplasia, unilateral renal agenesis, and cervicothoracic somite anomalies
Mayer-Rokitansky-Kuster-Hauser syndrome, type 2
adrenoleukodystrophy, autosomal neonatal
peroxisome biogenesis disorder (NALD/Ird)
peroxisome biogenesis disorder (neonatal adrenoleukodystrophy/infantile Refsum disease)
Any Wilms tumor in which the cause of the disease is a mutation in the POU6F2 gene.
Wilms tumor and radial bilateral aplasia
bilateral radial aplasia with Wilms tumor
Editor note: see https://github.com/monarch-initiative/mondo/issues/203; this groups IRID1 and IRID2
A disorder involving an excessive amount of body fat.
Obesity is a complex disease that may involve multiple environmental and genetic causes. See the subclass monogenic disease for genetic subtypes
Antenatal Bartter syndrome is a phenotypic variant of Bartter syndrome presenting antenatally with maternal polyhydramnios, pre-term delivery and postnatally with polyuria, and nephrocalcinosis. hypokalemic alkalosis, increased levels of plasma renin and aldosterone, low blood pressure and vascular resistance to angiotensin II are characteristically associated. Genotypically they comprise Type 1 and Type 2 Bartter syndrome
Bartter syndrome caused by mutation in SLC12A1
Bartter syndrome, furosemide-amiloride type
hypokalemic alkalosis with hypercalciuria 1 antenatal
hypokalemic alkalosis with hypercalciuria 1, antenatal
hypokalemic alkalosis with hypercalciuria antenatal 1
hypokalemic alkalosis with hypercalciuria, antenatal, 1
Ehlers-Danlos syndrome, musculocontractural type is a congenital form of Ehlers-Danlos syndrome characterized by distinct craniofacial features, multiple contractures, progressive joint and skin laxity, adduction-flexion contractures of the thumbs, talipes equinovarus, bruisability and multisystem fragility-related manifestations.
Ehlers-Danlos syndrome, arthrogryposic type
adducted thumbs-arthrogryposis syndrome, Dundar type
musculocontractural Ehlers-Danlos syndrome
Ehlers-Danlos syndrome, musculocontractural type 1
Ehlers-Danlos syndrome, musculocontractural type, 1
Ehlers-Danlos syndrome, type VIB, formerly
adducted thumb, clubfoot, and progressive joint and skin laxity syndrome
arthrogryposis, distal, with peculiar facies and hydronephrosis
autosomal recessive adducted thumb-club foot syndrome
Ehlers-Danlos syndrome, musculocontractural type
Any fibronectin glomerulopathy in which the cause of the disease is a mutation in the FN1 gene.
fibronectin glomerulopathy caused by mutation in FN1
glomerulopathy with fibronectin deposits type 2
glomerular nephritis familial with fibronectin deposits
Primary hypomagnesemia with secondary hypocalcemia (PHSH) is a form of familial primary hypomagnesemia (FPH), characterized by severe hypomagnesemia and secondary hypocalcemia associated with neurological symptoms, including generalized seizures, tetany and muscle spasms. PHSH may be fatal or may result in chronic irreversible neurological complications.
familial primary hypomagnesemia caused by mutation in TRPM6
hypomagnesemia caused by selective magnesium malabsorption
intestinal hypomagnesemia with secondary hypocalcemia
primary hypomagnesemia caused by mutation in TRPM6
primary hypomagnesemia with secondary hypocalcemia
hypomagnesemia with secondary hypocalcemia
hypomagnesemia, intestinal, with secondary hypocalcemia
Any nephronophthisis in which the cause of the disease is a mutation in the INVS gene.
nephronophthisis (disease) caused by mutation in INVS
RHYNS syndrome is characterised by the association of retinitis pigmentosa, hypopituitarism, nephronophthisis, and skeletal dysplasia.
retinitis pigmentosa-hypopituitarism-nephronophthisis-skeletal dysplasia syndrome
retinitis pigmentosa, hypopituitarism, nephronophthisis, and mild skeletal dysplasia
Any Bartter syndrome in which the cause of the disease is a mutation in the BSND gene.
Bartter syndrome caused by mutation in BSND
neonatal Bartter syndrome with sensorineural deafness
Bartter syndrome, neonatal, with sensorineural deafness
Bartter syndrome, type 4A, neonatal, with sensorineural deafness
sensorineural deafness with mild renal dysfunction
renal tubular acidosis, distal, autosomal recessive
renal tubular acidosis, autosomal recessive with preserved hearing
renal tubular acidosis, autosomal recessive, with preserved hearing
renal tubular acidosis, distal, autosomal recessive, with late-onset sensorineural hearing loss
renal tubular acidosis, distal, autosomal recessive, with late-onset sensorineural hearing loss, included
renal tubular acidosis, distal, 3, with or without sensorineural hearing loss
Any Meckel syndrome in which the cause of the disease is a mutation in the TMEM216 gene.
Meckel syndrome caused by mutation in TMEM216
Pseudohypoparathyroidism type 1B (PHP-1b) is a type of pseudohypoparathyroidism (PHP) characterized by localized resistance to parathyroid hormone (PTH) mainly in the renal tissues which manifests with hypocalcemia, hyperphosphatemia and elevated PTH levels. About 60-70% of patients also present with elevated TSH levels due to TSH resistance.
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the ACTN4 gene.
ACTN4 focal segmental glomerulosclerosis
familial idiopathic steroid-resistant nephrotic syndrome with focal segmental glomerulosclerosis
focal segmental glomerulosclerosis caused by mutation in ACTN4
focal segmental glomerulosclerosis type 1
familial idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis
Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.
Fanconi Anemia, complementation group type F
Fanconi anemia complementation group type F
SLC35A1-CDG is an extremely rare form of CDG syndrome characterized clinically in the single reported case by repeated hemorrhagic incidents, including severe pulmonary hemorrhage.
carbohydrate deficient glycoprotein syndrome type IIf
congenital disorder of glycosylation type 2f
congenital disorder of glycosylation type IIf
congenital disorder of glycosylation, type IIf
Type II xanthinuria, a type of classical xanthinuria, is a rare autosomal recessive disorder of purine metabolism characterized by the deficiency of both xanthine dehydrogenase and aldehyde oxidase, leading to the formation of urinary xanthine urolithiasis and leading, in some patients, to kidney failure. Other less common manifestations include arthropathy, myopathy and duodenal ulcer, while some patients remain asymptomatic.
xanthine dehydrogenase and aldehyde oxidase, combined deficiency of
xanthine dehydrogenase and xanthine aldehyde oxidase dual deficiency
xanthine dehydrogenase and aldehyde oxidase combined deficiency of
An inherited form of cystic kidney disease leading to fibrosis and impaired renal function that is caused by mutations in the UMOD gene, which encodes uromodulin/Tamm-Horsfall mucoprotein.
medullary cystic kidney disease 2, autosomal dominant
Dominant beta-thalassemia is a form of beta-thalassemia resulting in moderate to severe anemia.
BETA-thalassemia, dominant inclusion body type
dyserythropoietic Anemia, congenital, Irish or Weatherall type
Sickle cell anemias are chronic hemolytic diseases that may induce three types of acute accidents: severe anemia, severe bacterial infections, and ischemic vasoocclusive accidents (VOA) caused by sickle-shaped red blood cells obstructing small blood vessels and capillaries. Many diverse complications can occur.
hypertension, essential, susceptibility to, 1
hypertension, essential, susceptibility to, type 1
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the TRPC6 gene.
TRPC6 focal segmental glomerulosclerosis
focal segmental glomerulosclerosis caused by mutation in TRPC6
focal segmental glomerulosclerosis type 2
Alpha-thalassemia is an inherited hemoglobinopathy characterized by impaired synthesis of alpha-globin chains leading to a variable clinical picture depending on the number of affected alleles.
Autosomal recessive proximal renal tubular acidosis (AR pRTA) is a rare form of proximal renal tubular acidosis (pRTA) characterized by an isolated defect in the proximal tubule leading to the decreased reabsorption of bicarbonate and consequentially to urinary bicarbonate wastage along with additional characteristic clinical features.
proximal renal tubular acidosis with ocular abnormalities and intellectual disability
proximal renal tubular acidosis, autosomal recessive
renal tubular acidosis, proximal, with ocular abnormalities and intellectual disability
renal tubular acidosis, proximal, with ocular abnormalities and mental retardation
autosomal recessive proximal renal tubular acidosis
Any EEC syndrome in which the cause of the disease is a mutation in the TP63 gene.
ectrodactyly, ectodermal dysplasia, and cleft Lip/palate syndrome type 3
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome type 3
ectrodactyly, ectodermal dysplasia, and cleft LIP/palate syndrome 3
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3
hypertension, essential, susceptibility to, 2
hypertension, essential, susceptibility to, type 2
Any nephronophthisis in which the cause of the disease is a mutation in the NPHP3 gene.
nephronophthisis (disease) caused by mutation in NPHP3
Hypertension due to gain-of-function mutations in the mineralocorticoid receptor is a rare genetic hypertension characterized by a familial severe hypertension with an onset before age 20 years, associated with suppressed plasma renin and low aldosterone levels in the presence of low or normal levels of the mineralocorticoid aldosterone, that is highly resistant to antihypertensive medication. During pregnancy, there is a marked exacerbation of hypertension, accompanied by low serum potassium levels and undetectable aldosterone levels, but without signs of preeclampsia, requiring early delivery.
early-onset hypertension with exacerbation in pregnancy
hypertension due to gain-of-function mutations in the mineralocorticoid receptor
hypertension, early-onset, autosomal dominant, with Severe exacerbation in pregnancy
Familial papillary thyroid carcinoma with renal papillary neoplasia (fPTC/PRN) is an extremely rare inherited tumor syndrome within the familial nonmedullary thyroid cancer group (fNMTC).
thyroid carcinoma, papillary, with papillary renal neoplasia
Editor note: check MONDO:0000201 thyroid cancer, nonmedullary
familial papillary thyroid carcinoma with renal papillary neoplasia
Inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations is a rare cancer-predisposing syndrome, associated with the D1 subgroup of Fanconi anemia (FA), characterized by progressive bone marrow failure, cardiac, brain, intestinal or skeletal abnormalities and predisposition to various malignancies. Bone marrow suppression and the incidence of developmental abnormalities are less frequent than in other FA, but cancer risk is very high with the spectrum of childhood cancers including Wilms tumor, brain tumor (often medulloblastoma) and ALL/AML.
Fanconi anemia, complementation group D1
inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations
Hypotonia-Cystinuria syndrome (HCS) is a rare syndrome including neonatal and infantile hypotonia and failure to thrive, cystinuria type 1 and nephrolithiasis, growth retardation due to growth hormone deficiency, and minor facial dysmorphism.
homozygous 2P16 deletion syndrome, formerly
Editor note: check this. ORDO has type 1 as a superclass
Autosomal recessive form of craniosynostosis.
craniosynostosis syndrome, autosomal recessive
Any nephronophthisis in which the cause of the disease is a mutation in the NPHP4 gene.
nephronophthisis (disease) caused by mutation in NPHP4
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the NPHP4 gene.
Senior-Loken syndrome caused by mutation in NPHP4
hypertension, essential, susceptibility to, 3
hypertension, essential, susceptibility to, type 3
Any Meckel syndrome in which the cause of the disease is a mutation in the TMEM67 gene.
Meckel syndrome caused by mutation in TMEM67
Classic Bartter syndrome is a type of Bartter syndrome, characterized by a milder clinical picture than the antenatal/infantile subtype, and presenting with failure to thrive, hypokalemic alkalosis, increased levels of plasma renin and aldosterone, low blood pressure and vascular resistance to angiotensin II.
Bartter syndrome, type 3, with hypocalciuria
An autoimmune disorder comprising tubulointerstitial nephritis and uveitis.
Tubulointerstitial nephritis and uveitis
acute tubulointerstitial nephritis and uveitis syndrome
TUBULOINTERSTITIAL nephritis with uveitis
tubulointerstitial nephritis and uveitis syndrome
(11q14.1), resulting in a block in the initial step of protein glycosylation.
carbohydrate deficient glycoprotein syndrome type Ih
congenital disorder of glycosylation type 1h
congenital disorder of glycosylation type Ih
congenital disorder of glycosylation, type Ih
Braddock syndrome is a rare malformation syndrome with multiple congenital abnormalities, described in 2 siblings, that is characterized by VACTERL -like association in combination with pulmonary hypertension, laryngeal webs, blue sclerae, abnormal ears, persistent growth deficiency and normal intellect.
Vater-like syndrome with pulmonary hypertension, abnormal ears and growth deficiency
VATER-like defects with pulmonary hypertension, laryngeal webs, and growth deficiency
A small-vessel necrotizing vasculitis characterised by the association of inflammation of the vessel wall and peri- and extravascular granulomatosis.
pauci-immune glomerulonephritis associated with granulomatosis with polyangiitis
hypertension, essential, susceptibility to, 4
hypertension, essential, susceptibility to, type 4
BNAR syndrome is a very rare multiple congenital anomaly syndrome characterized by a bifid nose (with bulbous nasal tip but not associated with hypertelorism) with or without the presence of anal defects (i.e. anteriorly placed anus, rectal stenosis or atresia) and renal dysplasia (unilateral or bilateral renal agenesis) and without intellectual disability. BNAR syndrome is phenotypically related to Fraser syndrome and oculotrichoanal syndrome.
bifid nose with or without anorectal and renal anomalies
Pierson syndrome is characterised by the association of congenital nephrotic syndrome and ocular anomalies with microcoria.
microcoria-congenital nephrosis syndrome
microcoria - congenital nephrotic syndrome
microcoria-congenital nephrotic syndrome
Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.
Fanconi Anemia, complementation group type 1
Fanconi anemia complementation group type I
Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.
Fanconi Anemia, complementation group type J
Fanconi anemia complementation group type J
nephrotic syndrome-hearing loss-pretibial epidermolysis bullosa syndrome
nephropathy with pretibial epidermolysis bullosa and deafness
nephrotic syndrome - deafness - pretibial epidermolysis bullosa syndrome
Familial non-autoimmune autosomal dominant hyperthyroidism (FNAH) is a rare hyperthyroidism characterized by mild to severe hyperthyroidism, presence of goiter, absence of features of autoimmunity, frequent relapses while on treatment and a positive family history.
resistance to thyroid stimulating hormone
hyperthyroidism, Nonautoimmune, autosomal dominant
hyperthyroidism, congenital Nonautoimmune
toxic thyroid hyperplasia, autosomal dominant
familial hyperthyroidism due to mutations in TSH receptor
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the IQCB1 gene.
Senior-Loken syndrome caused by mutation in IQCB1
CEREBRORENODIGITAL syndrome with limb malformations and triradiate acetabula
Any preeclampsia in which the cause of the disease is a mutation in the STOX1 gene.
preeclampsia caused by mutation in STOX1
Joubert syndrome with renal defect is a rare subtype of Joubert syndrome and related disorders (JSRD) characterized by the neurological features of JS associated with renal disease, in the absence of retinopathy.
glomerulocystic kidney disease with hyperuricemia and isosthenuria
Any Noonan syndrome in which the cause of the disease is a mutation in the KRAS gene.
Noonan syndrome caused by mutation in KRAS
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the CEP290 gene.
Senior-Loken syndrome caused by mutation in CEP290
A rare genetic disease characterized by intrauterine growth retardation, permanent neonatal diabetes mellitus, and congenital hypothyroidism. Additional manifestations include congenital glaucoma, hepatic disease (hepatitis, fibrosis, and cirrhosis), polycystic kidneys, exocrine pancreatic dysfunction, sensorineural hearing impairment, developmental delay, and mild facial dysmorphism (such as flat nasal bridge, epicanthal folds, long philtrum, and low-set ears), among others
diabetes mellitus, neonatal, with congenital hypothyroidism
neonatal diabetes-congenital hypothyroidism-congenital glaucoma-hepatic fibrosis-polycystic kidneys syndrome
neonatal diabetes mellitus with congenital hypothyroidism
Alagille-Watson syndrome due to a NOTCH2 point mutation
Arteriohepatic dysplasia due to a NOTCH2 point mutation
syndromic bile duct paucity due to a NOTCH2 point mutation
Alagille syndrome due to a NOTCH2 point mutation
hypertension, essential, susceptibility to, 5
hypertension, essential, susceptibility to, type 5
hypertension, essential, body Mass-related
hypertension, essential, susceptibility to, 6
hypertension, essential, susceptibility to, type 6
hypertension, essential, kidney function-related
Chromosome 16p13.3deletion syndrome is a chromosome abnormality that can affect many parts of the body. People with this condition are missing a small piece (deletion) of chromosome 16 at a location designated p13.3. Although once thought to be a severe form of Rubinstein-Taybi syndrome, it is now emerging as a unique syndrome. Signs and symptoms may include failure to thrive, hypotonia (reduced muscle tone), short stature, microcephaly (unusually small head), characteristic facial features, mild to moderate intellectual disability, organ anomalies (i.e. heart and/or kidney problems), and vulnerability to infections. Chromosome testing of both parents can provide information about whether the deletion was inherited. In most cases, parents do not have any chromosome abnormalities. However, sometimes one parent has a balanced translocation where a piece of a chromosome has broken off and attached to another one with no gain or loss of genetic material. The balanced translocation normally does not cause signs or symptoms, but it increases the risk for having a child with a chromosome abnormality like a deletion. Treatment is based on the signs and symptoms present in each person.To learn more about chromosome abnormalities in general, view our GARD fact sheet on Chromosome Disorders.
chromosome 16p13.3 deletion syndrome, proximal
Rubinstein-Taybi syndrome due to 16p13.3 microdeletion
Any nephrotic syndrome in which the cause of the disease is a mutation in the PLCE1 gene.
nephrotic syndrome caused by mutation in PLCE1
Any Noonan syndrome in which the cause of the disease is a mutation in the SOS1 gene.
Noonan syndrome caused by mutation in SOS1
Any congenital anomaly of kidney and urinary tract in which the cause of the disease is a mutation in the DSTYK gene.
DSTYK congenital anomaly of kidney and urinary tract
congenital anomalies of kidney and urinary tract 1
congenital anomaly of kidney and urinary tract caused by mutation in DSTYK
Any Fanconi anemia in which the cause of the disease is a mutation in the PALB2 gene.
Fanconi Anemia, complementation group type N
Fanconi anemia caused by mutation in PALB2
Fanconi anemia complementation group type N
Any branchio-oto-renal syndrome in which the cause of the disease is a mutation in the SIX5 gene.
branchio-oto-renal syndrome caused by mutation in SIX5
hypertension, essential, susceptibility to, 7
hypertension, essential, susceptibility to, type 7
hypertension, essential, susceptibility to, 8
Any Meckel syndrome in which the cause of the disease is a mutation in the CEP290 gene.
Meckel syndrome caused by mutation in CEP290
Any Jeune syndrome in which the cause of the disease is a mutation in the IFT80 gene.
Jeune syndrome caused by mutation in IFT80
short-rib thoracic dysplasia 2 with or without polydactyly
Any nephronophthisis in which the cause of the disease is a mutation in the GLIS2 gene.
nephronophthisis (disease) caused by mutation in GLIS2
Any Noonan syndrome in which the cause of the disease is a mutation in the RAF1 gene.
Noonan syndrome caused by mutation in RAF1
Any Meckel syndrome in which the cause of the disease is a mutation in the RPGRIP1L gene.
Meckel syndrome caused by mutation in RPGRIP1L
Distal renal tubular acidosis (dRTA) with anemia is a very rare form of distal renal tubular acidosis (dRTA) characterized by a defect in renal acidification and hereditary hemolytic anemia.
distal renal tubular acidosis with anemia
RTA, distal, autosomal recessive, with hemolytic Anemia
renal tubular acidosis, distal, with hemolytic anemia
renal tubular acidosis, distal, with normal Red cell morphology
renal tubular acidosis, distal, 4, with hemolytic anemia
Any primary hypomagnesemia in which the cause of the disease is a mutation in the EGF gene.
familial primary hypomagnesemia caused by mutation in EGF
primary hypomagnesemia caused by mutation in EGF
Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome is characterised by the association of hematuria (without proteinuria) with extrarenal manifestations: retinal arterial tortuosities responsible for retinal haemorrhages, cardiac arrhythmia, Raynaud phenomena and congenital muscular contractures.
hereditary angiopathy-nephropathy-aneurysms-muscle cramps syndrome
angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps
hereditary angiopathy with nephropathy, aneurysms, and muscle cramps syndrome
autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome
Juvenile cataract - microcornea - renal glucosuria is an extremely rare autosomal dominant association reported in a single Swiss family and characterized clinically by juvenile cataract associated with bilateral microcornea, and renal glucosuria without other renal tubular defects.
cataract, juvenile, with microcornea and glucosuria
cataract, juvenile, with microcornea and glucosuria, formerly
juvenile cataract-microcornea-renal glucosuria syndrome
uric acid concentration, serum, quantitative trait locus 2
The metabolic condition resulted from uncontrolled diabetes mellitus, in which the shift of acid-base status of the body toward the acid side because of loss of base or retention of acids other than carbonic acid is accompanied by the accumulation of ketone bodies in body tissues and fluids.
Crouzon syndrome with acanthosis nigricans (CAN) is a very rare, clinically heterogeneous form of faciocraniostenosis with Crouzon-like features and premature synostosis of cranial sutures (Crouzon disease), associated with acanthosis nigricans (AN).
Crouzon syndrome with acanthosis nigricans
Crouzon syndrome-acanthosis nigricans syndrome
Any Meckel syndrome in which the cause of the disease is a mutation in the CC2D2A gene.
Meckel syndrome caused by mutation in CC2D2A
hypophosphatemic nephrolithiasis/osteoporosis type 1
nephrolithiasis/osteoporosis, hypophosphatemic, type 1
nephrolithiasis/osteoporosis, hypophosphatemic, 1
hypophosphatemic nephrolithiasis/osteoporosis 1
hypophosphatemic nephrolithiasis/osteoporosis type 2
nephrolithiasis/osteoporosis, hypophosphatemic, type 2
nephrolithiasis/osteoporosis, hypophosphatemic, 2
hypophosphatemic nephrolithiasis/osteoporosis 2
Pseudohypoparathyroidism type 1c (PHP1c) is a rare type of pseudohypoparathyroidism (PHP) characterized by resistance to parathyroid hormone (PTH) and other hormones, which manifests with hypocalcemia, hyperphosphatemia and elevated PTH levels, a constellation of clinical features collectively termed Albright's hereditary osteodystrophy (AHO), but normal activity of the stimulatory protein G (Gs alpha).
Pseudopseudohypoparathyroidism (pseudo-PHP) is a disease characterized by a constellation of clinical features collectively termed Albright hereditary osteodystrophy (AHO) but no evidence of resistance to parathyroid hormone (PTH), which is seen in other forms of pseudohypoparathyroidism (PHP).
Albright hereditary osteodystrophy-PPHP syndrome
Normocalcemic pseudohypoparathyroidism (disorder) [ambiguous]
Albright hereditary osteodystrophy without multiple hormone resistance
A sub-phenotype of WAGR that includes obesity, and is associated with mutation(s) in the BDNF gene.
Wilms tumor, aniridia, genitourinary anomalies, intellectual disability, and obesity syndrome
Wilms tumor, aniridia, genitourinary anomalies, mental retardation, and obesity syndrome
Wilms tumor-aniridia-genitourinary anomalies-intellectual disability-obesity syndrome
Wilms tumor-aniridia-genitourinary anomalies-mental retardation-obesity syndrome
SeSAME syndrome is characterized by seizures, sensorineural deafness, ataxia, intellectual deficit, and electrolyte imbalance (hypokalemia, metabolic alkalosis, and hypomagnesemia).
epilepsy, ataxia, sensorineural deafness and tubulopathy
seizures, sensorineural deafness, ataxia, intellectual disability and electrolyte imbalance
seizures, sensorineural deafness, ataxia, mental retardation and electrolyte imbalance
seizures-sensorineural deafness-ataxia-intellectual disability-electrolyte imbalance syndrome
epilepsy, ataxia, sensorineural deafness, and tubulopathy
seizures - sensorineural deafness - ataxia - intellectual disability - electrolyte imbalance
seizures, sensorineural deafness, ataxia, intellectual disability, and electrolyte imbalance
seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance
hemolytic uremic syndrome, atypical, susceptibility to, type 2
hemolytic-uremic syndrome without diarrhea with MCP/CD46 anomaly
hemolytic uremic syndrome, atypical, susceptibility to, 2
susceptibility to atypical hemolytic uremic syndrome 2
atypical hemolytic-uremic syndrome with MCP/CD46 anomaly
hemolytic uremic syndrome, atypical, susceptibility to, type 3
hemolytic-uremic syndrome without diarrhea with I factor anomaly
hemolytic uremic syndrome, atypical, susceptibility to, 3
susceptibility to atypical hemolytic uremic syndrome 3
atypical hemolytic-uremic syndrome with I factor anomaly
hemolytic uremic syndrome, atypical, susceptibility to, type 4
hemolytic-uremic syndrome without diarrhea with B factor anomaly
hemolytic uremic syndrome, atypical, susceptibility to, 4
susceptibility to atypical hemolytic uremic syndrome 4
atypical hemolytic-uremic syndrome with B factor anomaly
hemolytic uremic syndrome, atypical, susceptibility to, type 5
hemolytic-uremic syndrome without diarrhea with C3 anomaly
hemolytic uremic syndrome, atypical, susceptibility to, 5
susceptibility to atypical hemolytic uremic syndrome 5
atypical hemolytic-uremic syndrome with C3 anomaly
atypical HUS with thrombomodulin anomaly
hemolytic uremic syndrome, atypical, susceptibility to, type 6
hemolytic-uremic syndrome without diarrhea with thrombomodulin anomaly
hemolytic uremic syndrome, atypical, susceptibility to, 6
susceptibility to atypical hemolytic uremic syndrome 6
atypical hemolytic-uremic syndrome with thrombomodulin anomaly
An asphyxiating thoracic dystrophy that has material basis in homozygous or compound heterozygous mutation in the DYNC2H1 gene on chromosome 11q22.
polydactyly with neonatal chondrodystrophy, type I
polydactyly with neonatal chondrodystrophy, type III
short rib-polydactyly syndrome, type IIB
short-rib thoracic dysplasia 3 with or without polydactyly
polydactyly with neonatal chondrodystrophy, type 1
polydactyly with neonatal chondrodystrophy, type 3
Familial juvenile hyperuricemic nephropathy type 2 is a rare autosomal dominantly inherited disease of childhood characterized by hypoproliferative anemia, hyperuricemia and slowly progressing kidney failure due to dysregulation of the renin-angiotensin system (RAS).
REN familial juvenile hyperuricemic nephropathy
REN-associated familial juvenile hyperuricemic nephropathy
autosomal dominant tubulointerstitial kidney disease due to mutations in REN
familial juvenile hyperuricemic nephropathy caused by mutation in REN
familial juvenile hyperuricemic nephropathy type 2
hyperuricemic nephropathy, familial juvenile, type 2
REN-related autosomal dominant tubulointerstitial kidney disease
early-onset hyperuricemia, Anemia, and progressive kidney failure
hyperuricemic nephropathy, familial juvenile, 2
Autosomal dominant polycystic kidney disease caused by a mutation in PKD2.
Autosomal dominant polycystic kidney disease type 2
PKD2 autosomal dominant polycystic kidney disease
autosomal dominant polycystic kidney disease caused by mutation in PKD2
polycystic kidney disease, adult, type II
polycystic kidney disease 2 with or without polycystic liver disease
polycystic kidney disease, adult, type 2
Any nephronophthisis in which the cause of the disease is a mutation in the XPNPEP3 gene.
nephronophthisis (disease) caused by mutation in XPNPEP3
nephronophthisis-like nephropathy type 1
Any Noonan syndrome in which the cause of the disease is a mutation in the NRAS gene.
Noonan syndrome caused by mutation in NRAS
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the INF2 gene.
focal segmental glomerulosclerosis caused by mutation in INF2
focal segmental glomerulosclerosis type 5
Tuberous sclerosis mapped to chromosome 16p13.3 (TSC2 gene).
TSC2 Angiomyolipomas, renal, modifier of
Any Fanconi syndrome in which the cause of the disease is a mutation in the SLC34A1 gene.
Fanconi syndrome caused by mutation in SLC34A1
Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51C gene.
Fanconi Anemia, complementation group type O
Fanconi anemia caused by mutation in RAD51C
Fanconi anemia complementation group type O
Any arthrogryposis-renal dysfunction-cholestasis syndrome in which the cause of the disease is a mutation in the VIPAS39 gene.
VIPAS39 arthrogryposis-renal dysfunction-cholestasis syndrome
arthrogryposis, renal dysfunction, and cholestasis 2
arthrogryposis, renal dysfunction, and cholestasis type 2
arthrogryposis-renal dysfunction-cholestasis syndrome caused by mutation in VIPAS39
Reynolds syndrome (RS) is an autoimmune disorder characterized by the association of primary biliary cirrhosis (PBC) with limited cutaneous systemic sclerosis (lcSSc).
primary biliary cirrhosis and systemic scleroderma
primary biliary cirrhosis, Scleroderma, Raynaud disease, and telangiectasia
Alpha-1-antitrypsin deficiency is a hereditary disease that develops in adulthood and is characterized by chronic liver disorders (cirrhosis), respiratory disorders (emphysema), and rarely panniculitis.
deficiency in Alpa-1-proteinase inhibitor
A nephronophthisis that has material basis in homozygous or compound heterozygous mutation in the TMEM67 gene on chromosome 8q22.1.
Any cranioectodermal dysplasia in which the cause of the disease is a mutation in the WDR35 gene.
cranioectodermal dysplasia caused by mutation in WDR35
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the SDCCAG8 gene.
Senior-Loken syndrome caused by mutation in SDCCAG8
Primary hyperoxaluria type 3 (PH3) is a disorder of glyoxylate metabolism that can be asymptomatic or characterized by oxalate nephrolithiasis.
primary hyperoxaluria caused by mutation in HOGA1
17q11 microdeletion syndrome is a rare severe form of neurofibromatosis type 1 (NF1) characterized by mild facial dysmorphism, developmental delay, intellectual disability, increased risk of malignancies, and a large number of neurofibromas.
neurofibromatosis type 1 microdeletion syndrome
chromosome 17q11.2 deletion syndrome, 1.4-MB
neurofibromatosis 1 microdeletion syndrome
chromosome 17q11.2 deletion syndrome, 1.4Mb
Any Rubinstein-Taybi syndrome in which the cause of the disease is a mutation in the EP300 gene.
Rubinstein-Taybi syndrome caused by mutation in EP300
Rubinstein-Taybi syndrome due to EP300 haploinsufficiency
Any Noonan syndrome in which the cause of the disease is a mutation in the BRAF gene.
Noonan syndrome caused by mutation in BRAF
An asphyxiating thoracic dystrophy has material basis in compound heterozygous mutation in the TTC21B gene on chromosome 2q24.
short-rib thoracic dysplasia 4 with or without polydactyly
Any nephronophthisis in which the cause of the disease is a mutation in the TTC21B gene.
nephronophthisis (disease) caused by mutation in TTC21B
Any nephronophthisis in which the cause of the disease is a mutation in the NEK8 gene.
nephronophthisis (disease) caused by mutation in NEK8
hyperuricemia, pulmonary hypertension, renal failure, and alkalosis syndrome
hyperuricemia-pulmonary hypertension-renal failure-alkalosis syndrome
Any Meckel syndrome in which the cause of the disease is a mutation in the TCTN2 gene.
Meckel syndrome caused by mutation in TCTN2
Any Fanconi anemia in which the cause of the disease is a mutation in the SLX4 gene.
Fanconi Anemia, complementation group type P
Fanconi anemia caused by mutation in SLX4
Fanconi anemia complementation group type P
Hemoglobin H (HbH) disease is a moderate to severe form of alpha-thalassemia characterized by pronounced microcytic hypochromic hemolytic anemia.
Abnormal clinical manifestations of beta thalassemia that are as a result of the underlying genotype.
Fanconi anemia caused by mutations of the FANCG gene.
Fanconi Anemia, complementation group type G
Fanconi anemia complementation group type G
Any Fanconi anemia in which the cause of the disease is a mutation in the FANCL gene.
Fanconi Anemia, complementation group type 50
Fanconi anemia caused by mutation in FANCL
Fanconi anemia complementation group type L
Fanconi Anemia, complementation Group 50
An asphyxiating thoracic dystrophy that has material basis in homozygous or compound heterozygous mutation in the WDR35 gene on chromosome 2p21.1.
short-rib thoracic dysplasia 7 with or without polydactyly
Any cranioectodermal dysplasia in which the cause of the disease is a mutation in the IFT43 gene.
cranioectodermal dysplasia caused by mutation in IFT43
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the MYO1E gene.
MYO1E focal segmental glomerulosclerosis
focal segmental glomerulosclerosis caused by mutation in MYO1E
focal segmental glomerulosclerosis type 6
Any Meckel syndrome in which the cause of the disease is a mutation in the B9D2 gene.
Meckel syndrome caused by mutation in B9D2
Any nephrotic syndrome in which the cause of the disease is a mutation in the PTPRO gene.
nephrotic syndrome caused by mutation in PTPRO
LAMB2-related infantile-onset nephrotic syndrome is a rare primary glomerular disease due to homozygous mutations in LAMB2 gene, characterized by prenatal or early-onset progressive steroid-resistant nephrotic syndrome leading to renal failure, and variable ocular defects including myopia, fundus abnormalities, strabismus or nystagmus, without severe visual impairment or blindness. Patients present in early infancy with massive proteinuria, edema, hypertension, and hyperlipidemia. Psychomotor development is normal.
nephrotic syndrome, type 5, with or without ocular abnormalities
LAMB2-related infantile-onset nephrotic syndrome
Any Meckel syndrome in which the cause of the disease is a mutation in the B9D1 gene.
Meckel syndrome caused by mutation in B9D1
hyperuricemic nephropathy, familial juvenile, 3
hyperuricemic nephropathy, familial juvenile type 3
Any Jeune syndrome in which the cause of the disease is a mutation in the WDR19 gene.
Jeune syndrome caused by mutation in WDR19
short-rib thoracic dysplasia 5 with or without polydactyly
A nephronophthisis that has material basis in homozygous or compound heterozygous mutation in the WDR19 gene on chromosome 4p14.
An instance of systemic lupus erythematosus (disease) that is caused by mutations in DNASE1L3.
Editor note: it is not clear what the ORDO class Orphanet:300345 should be equivalent to, see https://github.com/monarch-initiative/mondo/issues/1164
autosomal systemic lupus erythematosus type 16
Autosomal dominant intermediate Charcot-Marie-Tooth disease type E is characterised by the association of Charcot-Marie-Tooth disease (hereditary peripheral neuropathy) with nephropathy. So far, around 15 cases have been described. All patients had proteinuria (with or without microhematuria) at onset and some patients presented with nephrotic syndrome. In the majority of cases, pathological studies revealed glomerulosclerosis. The mode of transmission is unknown.
Charcot-Marie-Tooth disease dominant intermediate type E
Charcot-Marie-Tooth disease, dominant Intermediate type E
Charcot-Marie-Tooth disease-nephropathy syndrome
Charcot-Marie-Tooth neuropathy with focal segmental glomerulonephritis
autosomal dominant intermediate Charcot-Marie-Tooth disease type E
Charcot-Marie-Tooth disease - nephropathy
Charcot-Marie-Tooth disease, dominant intermediate E
Charcot-Marie-Tooth disease dominant intermediate E
Any pseudohypoaldosteronism type 2 in which the cause of the disease is a mutation in the WNK4 gene.
pseudohypoaldosteronism type 2 caused by mutation in WNK4
Any pseudohypoaldosteronism type 2 in which the cause of the disease is a mutation in the WNK1 gene.
pseudohypoaldosteronism type 2 caused by mutation in WNK1
Any pseudohypoaldosteronism type 2 in which the cause of the disease is a mutation in the KLHL3 gene.
pseudohypoaldosteronism type 2 caused by mutation in KLHL3
Any pseudohypoaldosteronism type 2 in which the cause of the disease is a mutation in the CUL3 gene.
pseudohypoaldosteronism type 2 caused by mutation in CUL3
Any preeclampsia in which the cause of the disease is a mutation in the CORIN gene.
preeclampsia caused by mutation in CORIN
coenzyme Q10 deficiency, primary, type 6
familial steroid-resistant nephrotic syndrome with sensorineural deafness
Idiopathic membranous glomerulonephritis (IMG) is a primary glomerular disease characterized by proteinuria, usually in the nephrotic range, with preserved renal function.
membranous nephropathy, susceptibility to
idiopathic membranous glomerulonephritis
Adenine phosphoribosyltransferase (APRT) deficiency is a rare autosomal recessive (AR) disorder characterized by the formation and hyperexcretion of 2,8-dihydroxyadenine (2,8-DHA) in urine, causing urolithiasis and crystalline nephropathy.
adenine phosphoribosyltransferase deficiency
Congenital nephrotic syndrome-interstitial lung disease-epidermolysis bullosa syndrome is a life-threatening multiorgan disorder which develops in the first months of life, presenting with respiratory distress and proteinuria in the nephrotic range, and leading to severe interstitial lung disease and renal failure. Some patients additionally display cutaneous alterations, ranging from blistering and skin erosions to an epidermolysis bullosa-like phenotype, with toe nail dystrophy and sparse hair.
JEB with respiratory and renal involvement
congenital interstitial lung disease-nephrotic syndrome-epidermolysis bullosa syndrome
congenital nephrotic syndrome-epidermolysis bullosa-pulmonary disease syndrome
interstitial lung disease, nephrotic syndrome, and epidermolysis bullosa, congenital
junctional epidermolysis bullosa with respiratory and renal involvement
congenital nephrotic syndrome - interstitial lung disease - epidermolysis bullosa syndrome
Glomerulonephritis characterized by C3 accumulation with little or absent deposition of immunoglobulin, in the absence of ultrastructural electron-dense transformation seen in dense deposit disease.
complement-mediated membranoproliferative glomerulonephritis
Any interstitial nephritis in which the cause of the disease is a mutation in the FAN1 gene.
interstitial nephritis caused by mutation in FAN1
Any nephronophthisis in which the cause of the disease is a mutation in the ZNF423 gene.
nephronophthisis (disease) caused by mutation in ZNF423
Any nephronophthisis in which the cause of the disease is a mutation in the CEP164 gene.
nephronophthisis (disease) caused by mutation in CEP164
peroxisome biogenesis disorder 3A (Zellweger)
peroxisome biogenesis disorder, complementation group 3
peroxisome biogenesis disorder 4A (Zellweger)
peroxisome biogenesis disorder, complementation group 4
peroxisome biogenesis disorder, complementation group 6
peroxisome biogenesis disorder, complementation group C
peroxisome biogenesis disorder 5A (Zellweger)
peroxisome biogenesis disorder, complementation group 10
peroxisome biogenesis disorder, complementation group 5
peroxisome biogenesis disorder, complementation group F
peroxisome biogenesis disorder 6A (Zellweger)
peroxisome biogenesis disorder, complementation group 7
peroxisome biogenesis disorder, complementation group B
peroxisome biogenesis disorder 7A (Zellweger)
peroxisome biogenesis disorder, complementation group 8
peroxisome biogenesis disorder, complementation group A
peroxisome biogenesis disorder 8A (Zellweger)
peroxisome biogenesis disorder, complementation group 9
peroxisome biogenesis disorder, complementation group D
peroxisome biogenesis disorder, PEX7-related, atypical
peroxisome biogenesis disorder, complementation group 11
peroxisome biogenesis disorder, complementation group R
peroxisome biogenesis disorder 10A (Zellweger)
peroxisome biogenesis disorder, complementation group 12
peroxisome biogenesis disorder, complementation group G
peroxisome biogenesis disorder 11A (Zellweger)
peroxisome biogenesis disorder, complementation group 13
peroxisome biogenesis disorder, complementation group H
peroxisome biogenesis disorder 12A (Zellweger)
peroxisome biogenesis disorder, complementation group 14
peroxisome biogenesis disorder, complementation group J
peroxisome biogenesis disorder 13A (Zellweger)
peroxisome biogenesis disorder, complementation group K
Glomerulonephritis characterized by mesangial proliferation, endocapillary proliferation, and glomerular capillary wall remodeling with immune complex deposits from classical complement pathway activation.
Ig-mediated membranoproliferative glomerulonephritis
Mesangiocapillary glomerulonephritis type 1
immune Complex mediated membranoproliferative glomerulonephritis
membranoproliferative glomerulonephritis type I
hemolytic uremic syndrome, atypical, susceptibility to, 7
nephrotic syndrome, type 7, with membranoproliferative glomerulonephritis
immunoglobulin-mediated membranoproliferative glomerulonephritis
Any Ochoa syndrome in which the cause of the disease is a mutation in the LRIG2 gene.
Ochoa syndrome caused by mutation in LRIG2
Any nephrotic syndrome in which the cause of the disease is a mutation in the ARHGDIA gene.
nephrotic syndrome caused by mutation in ARHGDIA
Any Fanconi anemia in which the cause of the disease is a mutation in the ERCC4 gene.
Fanconi Anemia, complementation group type Q
Fanconi anemia caused by mutation in ERCC4
Fanconi anemia complementation group type Q
Any primary pulmonary hypertension in which the cause of the disease is a mutation in the SMAD9 gene.
primary pulmonary hypertension caused by mutation in SMAD9
Any primary pulmonary hypertension in which the cause of the disease is a mutation in the CAV1 gene.
primary pulmonary hypertension caused by mutation in CAV1
Any primary pulmonary hypertension in which the cause of the disease is a mutation in the KCNK3 gene.
primary pulmonary hypertension caused by mutation in KCNK3
Any Noonan syndrome in which the cause of the disease is a mutation in the RIT1 gene.
Noonan syndrome caused by mutation in RIT1
Any nephronophthisis in which the cause of the disease is a mutation in the ANKS6 gene.
autosomal recessive infantile nephronophthisis
nephronophthisis (disease) caused by mutation in ANKS6
Any Meckel syndrome in which the cause of the disease is a mutation in the TMEM231 gene.
Meckel syndrome caused by mutation in TMEM231
Any paroxysmal nocturnal hemoglobinuria in which the cause of the disease is a mutation in the PIGT gene.
PIGT paroxysmal nocturnal hemoglobinuria
paroxysmal nocturnal hemoglobinuria caused by mutation in PIGT
paroxysmal nocturnal hemoglobinuria type 2
Any renal-hepatic-pancreatic dysplasia in which the cause of the disease is a mutation in the NEK8 gene.
renal-hepatic-pancreatic dysplasia caused by mutation in NEK8
renal-hepatic-pancreatic dysplasia type 2
An asphyxiating thoracic dystrophy that has material basis in compound heterozygous mutation in the WDR60 gene on chromosome 7q36.
short-rib thoracic dysplasia 8 with or without polydactyly
Any Ehlers-Danlos syndrome, musculocontractural type in which the cause of the disease is a mutation in the DSE gene.
DSE Ehlers-Danlos syndrome, musculocontractural type
Ehlers-Danlos syndrome, musculocontractural type 2
Ehlers-Danlos syndrome, musculocontractural type caused by mutation in DSE
Ehlers-Danlos syndrome, musculocontractural type, 2
Any nephrotic syndrome in which the cause of the disease is a mutation in the COQ8B gene.
nephrotic syndrome caused by mutation in COQ8B
Any Fanconi syndrome in which the cause of the disease is a mutation in the EHHADH gene.
Fanconi syndrome caused by mutation in EHHADH
An asphyxiating thoracic dystrophy that has material basis in homozygous or compound heterozygous mutation in the IFT172 gene on chromosome 2p23.
short-rib thoracic dysplasia 10 with or without polydactyly
An asphyxiating thoracic dystrophy that has material basis in homozygous or compound heterozygous mutation in the WDR34 gene on chromosome 9q34.
short-rib thoracic dysplasia 11 with or without polydactyly
Any renal agenesis in which the cause of the disease is a mutation in the FGF20 gene.
renal agenesis (disease) caused by mutation in FGF20
Any nephrotic syndrome in which the cause of the disease is a mutation in the EMP2 gene.
nephrotic syndrome caused by mutation in EMP2
Any nephronophthisis in which the cause of the disease is a mutation in the CEP83 gene.
nephronophthisis (disease) caused by mutation in CEP83
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBS2 gene.
Bardet-Biedl syndrome caused by mutation in BBS2
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBS5 gene.
Bardet-Biedl syndrome caused by mutation in BBS5
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBS7 gene.
Bardet-Biedl syndrome caused by mutation in BBS7
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the TTC8 gene.
Bardet-Biedl syndrome caused by mutation in TTC8
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBS9 gene.
Bardet-Biedl syndrome caused by mutation in BBS9
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBS10 gene.
Bardet-Biedl syndrome caused by mutation in BBS10
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the TRIM32 gene.
Bardet-Biedl syndrome caused by mutation in TRIM32
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBS12 gene.
Bardet-Biedl syndrome caused by mutation in BBS12
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the MKS1 gene.
Bardet-Biedl syndrome caused by mutation in MKS1
A Bardet-Biedl syndrome that has material basis in homozygous mutation in the CEP290 gene on chromosome 12q21.
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the WDPCP gene.
Bardet-Biedl syndrome caused by mutation in WDPCP
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the SDCCAG8 gene.
Bardet-Biedl syndrome caused by mutation in SDCCAG8
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the LZTFL1 gene.
Bardet-Biedl syndrome caused by mutation in LZTFL1
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the BBIP1 gene.
Bardet-Biedl syndrome caused by mutation in BBIP1
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the IFT27 gene.
Bardet-Biedl syndrome caused by mutation in IFT27
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the PAX2 gene.
focal segmental glomerulosclerosis caused by mutation in PAX2
focal segmental glomerulosclerosis type 7
Any Fanconi syndrome in which the cause of the disease is a mutation in the HNF4A gene.
Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young
Fanconi syndrome caused by mutation in HNF4A
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the ANLN gene.
focal segmental glomerulosclerosis caused by mutation in ANLN
focal segmental glomerulosclerosis type 8
Any nephronophthisis in which the cause of the disease is a mutation in the DCDC2 gene.
nephronophthisis (disease) caused by mutation in DCDC2
Any focal segmental glomerulosclerosis in which the cause of the disease is a mutation in the CRB2 gene.
focal segmental glomerulosclerosis caused by mutation in CRB2
focal segmental glomerulosclerosis type 9
Lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome is a rare, genetic developmental defect during embryogenesis malformation syndrome characterized by intrauterine growth restriction, flexion arthrogryposis of all joints, severe microcephaly, renal cystic dysplasia/agenesis/hypoplasia and complex malformations of the brain (cerebral and cerebellar hypoplasia, vermis, corpus callosum and/or occipital lobe agenesis, with or without arhinencephaly), as well as of the genitourinary tract (ureteral agenesis/hypoplasia, uterine hypoplasia and/or vaginal atresia), leading to fetal demise.
lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome
An asphyxiating thoracic dystrophy that has material basis in homozygous mutation in the CEP120 gene on chromosome 5q23.
short-rib thoracic dysplasia 13 with or without polydactyly
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the WDR19 gene.
Senior-Loken syndrome caused by mutation in WDR19
autoimmune interstitial lung, joint, and kidney disease
Editor note: check relationship to RA-ILD
autoimmune interstitial lung disease-arthritis syndrome
hypomagnesemia, seizures, and intellectual disability
hypomagnesemia, seizures, and mental retardation
Any Fanconi anemia in which the cause of the disease is a mutation in the UBE2T gene.
Fanconi Anemia, complementation group type T
Fanconi anemia caused by mutation in UBE2T
Fanconi anemia complementation group type T
An asphyxiating thoracic dystrophy that has material basis in homozygous mutation in the KIAA0586 gene on chromosome 14q23.
short-rib thoracic dysplasia 14 with polydactyly
Any Noonan syndrome in which the cause of the disease is a mutation in the SOS2 gene.
Noonan syndrome caused by mutation in SOS2
Any retinitis pigmentosa in which the cause of the disease is a mutation in the BBS2 gene.
retinitis pigmentosa caused by mutation in BBS2
Any Noonan syndrome in which the cause of the disease is a mutation in the LZTR1 gene.
Noonan syndrome caused by mutation in LZTR1
Any Senior-Loken syndrome in which the cause of the disease is a mutation in the TRAF3IP1 gene.
Senior-Loken syndrome caused by mutation in TRAF3IP1
Any familial nephrotic syndrome in which the cause of the disease is a mutation in the NUP107 gene.
familial nephrotic syndrome caused by mutation in NUP107
Any Wilms tumor in which the cause of the disease is a mutation in the REST gene.
Any familial nephrotic syndrome in which the cause of the disease is a mutation in the NUP93 gene.
familial nephrotic syndrome caused by mutation in NUP93
Any familial nephrotic syndrome in which the cause of the disease is a mutation in the NUP205 gene.
familial nephrotic syndrome caused by mutation in NUP205
Any autosomal recessive infantile hypercalcemia in which the cause of the disease is a mutation in the SLC34A1 gene.
SLC34A1 autosomal recessive infantile hypercalcemia
autosomal recessive infantile hypercalcemia caused by mutation in SLC34A1
Any familial juvenile hyperuricemic nephropathy in which the cause of the disease is a mutation in the SEC61A1 gene.
SEC61A1 familial juvenile hyperuricemic nephropathy
SEC61A1-related autosomal dominant tubulointerstitial kidney disease
familial juvenile hyperuricemic nephropathy caused by mutation in SEC61A1
hyperuricemic nephropathy, familial juvenile, 4
hyperuricemic nephropathy, familial juvenile, type 4
hyperuricemic nephropathy, familial juvenile type 4
short-rib thoracic dysplasia 15 with polydactyly
short-rib thoracic dysplasia 15 with polydactyly; SRTD15
short-rib thoracic dysplasia 16 with or without polydactyly
short-rib thoracic dysplasia 16 with or without polydactyly; SRTD16
tall stature-intellectual disability-renal anomalies syndrome
Any Bardet-Biedl syndrome in which the cause of the disease is a mutation in the IFT74 gene.
Bardet-Biedl syndrome caused by mutation in IFT74
Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.
Fanconi Anemia, complementation group type V
Fanconi anemia caused by mutation in MAD2L2
Fanconi anemia complementation group type V
Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51 gene.
Fanconi Anemia, complementation group type R
Fanconi anemia caused by mutation in RAD51
Fanconi anemia complementation group type R
Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.
Fanconi Anemia, complementation group type U
Fanconi anemia caused by mutation in XRCC2
Fanconi anemia complementation group type U
Any nephronophthisis in which the cause of the disease is a mutation in the MAPKBP1 gene.
nephronophthisis (disease) caused by mutation in MAPKBP1
A benign or malignant neoplasm affecting the thyroid gland.
A carcinoma arising from the thyroid gland. It is usually an adenocarcinoma and includes the following main subtypes: follicular, papillary, medullary, poorly differentiated, and anaplastic.
Editor note: ORDO classifies as inherited but there are non-inherited forms such as Carney triad
Autosomal dominant form of complex hereditary spastic paraplegia.
autosomal dominant complex hereditary spastic paraplegia
autosomal dominant complicated spastic paraplegia
complex hereditary spastic paraplegia, autosomal dominant
autosomal dominant complex spastic paraplegia
Editor note: in ORDO, Orphanet:101957 is classified as genetic, yet has acquired subtypes
Editor note: check how relates to phagocytosis terms
quantitative and/or qualitative congenital phagocyte defect
A rare disorder characterized by recurrent infantile infections and absence of neutrophils in the peripheral blood.
primary immunodeficiency due to a defect in innate immunity
primary immunodeficiency due to a genetic defect in innate immunity
immunodeficiency due to a complement cascade protein anomaly
Editor note: consider merge, see https://docs.google.com/document/d/1wNW8wypaeo7fuBVfeplkD4RQ9-kuEQl0O9U5PdLintE/edit#
immunodeficiency due to a genetic complement cascade protein anomaly
Fevers of unknown etiology recurring over months or years.
An inflammatory disease involving a pathogenic inflammatory response in the brain.
A hereditary spastic paraplegia that is part of a larger syndrome.
complicated hereditary spastic paraplegia
syndrome associated with hereditary spastic paraplegia
multiple congenital anomalies-intellectual disability with or without dysmorphism
multiple congenital anomalies/dysmorphic syndrome-intellectual disability
multiple congenital anomalies-variable intellectual disability with or without dysmorphism syndrome
multiple congenital anomalies/dysmorphic syndrome-variable intellectual disability syndrome
multiple congenital anomalies without intellectual disability with or without dysmorphism
multiple congenital anomalies/dysmorphic syndrome without intellectual disability
Arthrogryposis multiplex congenita (AMC) is a group of disorders characterized by congenital limb contractures. It manifests as limitation of movement of multiple limb joints at birth that is usually non-progressive and may include muscle weakness and fibrosis. AMC is always associated with decreased intrauterine fetal movement which leads secondarily to the contractures.
Editor note: groups different mechanisms:
intestinal disease due to vitamin absorption anomaly
A metabolic disease that involves the intestine.
metabolic disease with intestinal involvement
Hydrops fetalis is a severe and challenging fetal condition usually defined as the excessive accumulation of fetal fluid within the fetal extravascular compartments and body cavities that manifests as edema, pleural and pericardial effusion and ascites. It is the end-stage of a wide variety of disorders. The cause may be immunologic (immune hydrops fetalis, IHF) or non immunologic (non-immune hydrops fetalis, NIHF), depending on the presence or absence of maternal antibodies against fetal red cell antigens (ABO incompatibility or rhesus (Rh) incompatibility).
Atresia of the urethra is a rare congenital bladder outlet obstruction, a fetal lower urinary tract obstruction (fetal LUTO), that is usually fatal. Unless there is some other egress for the urine to escape the bladder, such as patent urachus or anuro-rectal communication, these lesions are not compatible with renal development.
A esophageal malformation that is part of a larger syndrome.
syndrome associated with esophageal malformation
A intestinal malformation that is part of a larger syndrome.
syndrome associated with intestinal malformation
A diaphragmatic or abdominal wall malformation that is not part of a larger syndrome.
isolated diaphragmatic or abdominal wall malformation
nonsyndromic diaphragmatic or abdominal wall malformation
non-syndromic diaphragmatic or abdominal wall malformation
A diaphragmatic or abdominal wall malformation that is part of a larger syndrome.
syndrome associated with diaphragmatic or abdominal wall malformation
syndromic diaphragmatic or abdominal wall malformation
A developmental defect of the eye that is not part of a larger syndrome.
isolated developmental defect of the eye
nonsyndromic developmental defect of the eye
non-syndromic developmental defect of the eye
A developmental defect of the eye that is part of a larger syndrome.
syndrome associated with developmental defect of the eye
syndromic developmental defect of the eye
A central nervous system malformation that is not part of a larger syndrome.
isolated central nervous system malformation
nonsyndromic central nervous system malformation
Editor note: ORDO has various potentially syndromic disease groupings under here, we modify these. See https://github.com/monarch-initiative/mondo-build/issues/58
non-syndromic central nervous system malformation
syndrome with a central nervous system malformation as major feature
syndrome with limb malformations as a major feature
Bardet-Biedl syndrome (BBS) is a ciliopathy with multisystem involvement. It is invariantly characterized by rod-cone dystrophy, and at least three additional non-ocular features such as intellectual disability, obesity, polydactyly, hypogonadism, or renal anomalies as primary manifestations. In the absence of one of these four primary clinical features, the diagnosis of BBS is made when at least two secondary features are observed, including hepatic fibrosis, diabetes mellitus, reproductive and developmental abnormalities, growth retardation, speech delays, or cardiovascular problems
Bartter syndrome is a group of rare renal tubular disease characterized by impaired salt reabsorption in the thick ascending limb of Henle's loop and clinically by the association of hypokalemic alkalosis, hypercalciuria/nephrocalcinosis, increased levels of plasma renin and aldosterone, low blood pressure and vascular resistance to angiotensin II.
aldosteronism with hyperplasia of the adrenal cortex
renal tubular normotensive hypokalemic alkalosis with hypercalciuria
salt-losing tubular disorder, Henle's loop type
salt-wasting tubulopathy, Henle's loop type
hypokalemic alkalosis with hypercalciuria
Autosomal recessive cerebellar ataxias (ARCA) are a heterogeneous group of rare neurological disorders involving both the central and peripheral nervous system (and in some cases other systems and organs), and characterized by degeneration or abnormal development of the cerebellum and spinal cord and, in most cases, early onset occurring before the age of 20 years.
A anorectal malformation that is part of a larger syndrome.
syndrome associated with anorectal malformation
Medullary sponge kidney (MSK) is a birth defect of the tubules - tiny tubes inside the kidneys. In a normal kidney, urine flows through these tubules as it is being formed. In MSK, tiny sacs called cysts form in the medulla (the inner part of the kidney), creating a sponge-like appearance. The cysts keep urine from flowing freely through the tubules. MSK is present at birth but symptoms typically do not occur until adolescence or adulthood. Problems caused by MSK include blood in the urine, kidney stones, and urinary tract infections. MSK rarely leads to more serious problems, such as total kidney failure. There is no cure for this condition, so treatment is aimed at removing kidney stones and treating urinary tract infections with antibiotics.
cystic dilatation of renal collecting tubes
Congenital disorder of glycosylation (CDG) is a fast growing group of inborn errors of metabolism characterized by defective activity of enzymes that participate in glycosylation (modification of proteins and other macromolecules by adding and processing of oligosaccharide side chains). CDG is comprised of phenotypically diverse disorders affecting multiple systems including the central nervous system, muscle function, immunity, endocrine system, and coagulation. The numerous entities in this group are subdivided, based on the synthetic pathway affected, into disorder of protein N-glycosylation, disorder of protein O-glycosylation, disorder of multiple glycosylation, and disorder of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation.
carbohydrate deficient glycoprotein syndrome
carbohydrate-deficient glycoprotein syndrome
carbohydrate-deficient glycoprotein syndromes
Pierre Robin sequence associated with a chromosomal anomaly
Pierre Robin syndrome associated with a chromosomal anomaly
developmental anomaly of metabolic origin
congenital malformation syndrome and short stature
congenital malformation syndrome associated with short stature
malformation syndrome associated with short stature
malformation syndrome with short stature
malformation syndrome with skin/mucosae involvement
rare developmental defect with connective tissue involvement
malformation syndrome with odontal and/or periodontal component
A craniosynostosis that is part of a larger syndrome.
syndrome associated with craniosynostosis
The inherited predisposition toward getting a tumor.
A group of slowly progressive inherited disorders affecting motor and sensory peripheral nerves. Subtypes include HMSNs I-VII. HMSN I and II both refer to CHARCOT-MARIE-Tooth DISEASE. HMSN III refers to hypertrophic neuropathy of infancy. HMSN IV refers to REFSUM DISEASE. HMSN V refers to a condition marked by a hereditary motor and sensory neuropathy associated with spastic paraplegia (see SPASTIC PARAPLEGIA, HEREDITARY). HMSN VI refers to HMSN associated with an inherited optic atrophy (OPTIC ATROPHIES, HEREDITARY), and HMSN VII refers to HMSN associated with retinitis pigmentosa. (From Adams et al., Principles of Neurology, 6th ed, p1343)
Joubert syndrome (JS) and related disorders (JSRD) are a group of developmental delay/multiple congenital anomaly syndromes in which the mandatory feature is the ``molar tooth sign'' (MTS), a complex midbrain-hindbrain malformation recognizable on brain imaging. The MTS is characterized by cerebellar vermis hypodysplasia, thickening and malorientation of the superior cerebellar peduncles and abnormally deep interpeduncular fossa.
Two syndromes of oral, facial, and digital malformations. Type I (Papillon-Leage and Psaume syndrome, Gorlin-Psaume syndrome) is inherited as an X-linked dominant trait and is found only in females and XXY males. Type II (Mohr syndrome) is inherited as an autosomal recessive trait.
A congenital abnormality consisting of an opening or gap in the face, which results from incomplete fusion of one or more of the embryonic facial prominences.
Short rib-polydactyly syndromes are a group of bone malformations characterized by a narrow thorax and polydactyly (usually preaxial).
Craniosynostosis is defined as the premature fusion of one or more cranial sutures leading to secondary distortion of skull shape resulting in skull deformities with a variable presentation. Craniosynostosis may occur in an isolated setting or as part of a syndrome.
Group of systemic vasculitis with a strong association with anca. The disorders are characterized by necrotizing inflammation of small and medium size vessels, with little or no immune-complex deposits in vessel walls.
antineutrophil cytoplasmic antibody-associated vasculitis
Anti-neutrophil cytoplasmic antibody-associated vasculitis
otomandibular dysplasia associated with monogenic syndromes
The presence of an excessively large tongue, which may be congenital or may develop as a result of a tumor or edema due to obstruction of lymphatic vessels, or it may occur in association with hyperpituitarism or acromegaly. It also may be associated with malocclusion because of pressure of the tongue on the teeth. (From Jablonski, Dictionary of Dentistry, 1992)
syndrome or malformation associated with head and neck malformations
rare syndrome with cardiac malformations
An instance of hypertension that is caused by a modification of the individual's genome.
Hemophagocytic syndrome (HPS) is a rare immune disease and a potentially life-threatening disorder characterized by cytokine storm and overwhelming inflammation causing fever, hepatosplenomegaly, cytopenia, hypertriglyceridemia, hyperferritinemia, and hemophagocytosis in bone marrow, liver, spleen or lymph nodes. It can be either primary due to a genetic defect (primary hemophagocytic lymphohistiocytosis), or secondary to malignancies, to infections, most commonly with viruses such as Epstein-Barr virus or cytomegalovirus, human immunodeficiency virus, or to autoimmune disorders such as systemic lupus erythematosus or adult-onset Still disease (secondary hemophagocytic lymphohistiocytosis).
familial erythrophagocytic lymphohistiocytosis
familial hemophagocytic lymphohistiocytosis
Editor note: NCIT treats hemophagocytic syndrome and Hemophagocytic Lymphohistiocytosis as distinct; we merge here but this should be checked. See https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/19
Hb Bart's hydrops fetalis is the most severe form of alpha-thalassemia and is almost always lethal. It is characterized by fetal onset of generalized edema, pleural and pericardial effusions, and severe hypochromic anemia.
The 2p21 microdeletion syndrome consists of cystinuria, neonatal seizures, hypotonia, severe growthand developmental delay, facial dysmorphism, and lactic acidemia.
An instance of aplastic anemia that is acquired during the lifetime of the individual.
Dent disease is a rare genetic renal tubular disease characterized by manifestations of proximal tubule dysfunction.
X-linked recessive hypercalciuric hypophosphatemic rickets
X-linked recessive hypophosphatemic rickets
low-molecular-weight proteinuria with hypercalciuria and nephrocalcinosis
renal Fanconi syndrome with nephrocalcinosis and renal stones
A urogenital tract malformation that is not part of a larger syndrome.
nonsyndromic urogenital tract malformation
non-syndromic urogenital tract malformation
A urogenital tract malformation that is part of a larger syndrome.
syndrome associated with urogenital tract malformation
An inherited degenerative disorder involving the peripheral nerves. It is caused by mutations in the genes that are responsible for the production of proteins necessary for the function and structure of the peripheral nerves. It is characterized by muscle atrophy and weakness in the feet, legs, hands, and arms and loss of sensation in the limbs.
Charcot-Marie-Tooth hereditary neuropathy
Charcot-Marie-Tooth disease/hereditary motor and sensory neuropathy
chromosomal anomaly with epilepsy as a major feature
inflammatory and autoimmune disease with epilepsy
Congenital hypogonadotropic hypogonadism (CHH) is a rare disorder of sexual maturation characterized by gonadotropin (Gn) deficiency with low sex steroid levels associated with low levels of follicle stimulating hormone (FSH) and luteinizing hormone (LH).
congenital hypogonadotropic hypogonadism
Central diabetes insipidus (CDI) is a hypothalamus-pituitary disease characterized by polyuria and polydipsia due to a vasopressin (AVP) deficiency. It can be inherited or acquired (hereditary CDI and acquired CDI).
primary immunodeficiency due to a defect in adaptive immunity
Distal renal tubular acidosis (dRTA) is a disorder of impaired net acid secretion by the distal tubule characterized by hyperchloremic metabolic acidosis. The classic form is often associated with hypokalemia whereas other forms of acquired dRTA may be associated with hypokalemia, hyperkalemia or normokalemia.
A uterovaginal malformation that is not part of a larger syndrome.
incomplete bilateral aplasia of the Mullerian ducts
incomplete bilateral aplasia of the Müllerian ducts
partial bilateral aplasia of the Müllerian ducts
partial bilateral aplasia of the mullerian ducts
A uterovaginal malformation that is part of a larger syndrome.
syndrome associated with uterovaginal malformation
anomaly of puberty or/and menstrual cycle
malformative syndrome with dentinogenesis imperfecta
syndromic diaphragmatic or thoracic malformation
rare insulin-independent diabetes mellitus
rare disorder with secondary hypogonadism
rare disorder with hypogonadotropic hypogonadism
rare disorder with congenital hypogonadotropic hypogonadism
A inherited lipid metabolism disorder that is part of a larger syndrome.
syndrome associated with inherited lipid metabolism disorder
syndromic inherited lipid metabolism disorder
Anemia resulting from bone marrow failure (aplastic or hypoplastic bone marrow). The production of erythroblasts and red cells is markedly decreased, and it may be associated with decreased production of granulocytes (granulocytopenia) and platelets (thrombocytopenia) as well. Aplastic anemia may be idiopathic or secondary due to bone marrow damage by toxins, radiation, or immunologic factors.
MYH9-related disease (MYH9-RD) is an inherited giant platelet disorder with a complex phenotype characterized by congenital thrombocytopenia and possible subsequent manifestations of sensorineural hearing loss, presenile cataracts, elevation of liver enzymes, and/or progressive nephropathy often leading to end-stage renal disease (ESRD). Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly and Sebastian syndrome, previously described as distinct disorders, represent some of the different clinical presentations of MYH9-RD.
rare thrombotic disease of hematologic origin
rare neuroinflammatory or neuroimmunological disease
syndromic neurometabolic disease with non-X-linked intellectual disability
syndromic neurometabolic disease with X-linked intellectual disability
An instance of peripheral neuropathy that is acquired during the lifetime of the individual.
Pulmonary arterial hypertension (PAH) is a group of diseases characterized by elevated pulmonary arterial resistance leading to right heart failure. PAH is progressive and potentially fatal. PAH may be idiopathic and/ or familial, or induced by drug or toxin (drug-or toxin-induced PAH) or associated with other diseases like congenital heart disease, connective tissue disease, HIV, schistosomiasis, portal hypertension (PAH associated with other disease).
A diverse group of lung diseases that affect the lung parenchyma. They are characterized by an initial inflammation of pulmonary alveoli that extends to the interstitium and beyond leading to diffuse pulmonary fibrosis. Interstitial lung diseases are classified by their etiology (known or unknown causes), and radiological-pathological features.
secondary ILD in childhood and adulthood associated with a connective tissue disease
secondary interstitial lung disease in childhood and adulthood associated with a connective tissue disease
A non-syndromic urogenital tract malformation that involves the female organism.
female organism non-syndromic urogenital tract malformation
non-syndromic urogenital tract malformation of female organism
nonsyndromic urogenital tract malformation of female
isolated urogenital tract malformation of female
non-syndromic urogenital tract malformation of female
nonsyndromic urogenital tract malformation of male and female
isolated urogenital tract malformation of male and female
Editor note: consider obsoleting as semantics not clear
non-syndromic urogenital tract malformation of male and female
A systemic disease is one that affects a number of organs and tissues, or affects the body as a whole.
Eosinophilic granulomatosis with polyangiitis (EGPA), previously known as Churg-Strauss syndrome, is a systemic vasculitis of small-to medium vessels, characterized by asthma, transient pulmonary infiltrates, and hypereosinophilia.
Vasculitides, eosinophilic granulomatous
granulomatous Vasculitides, eosinophilic
eosinophilic granulomatosis with polyangiitis
Axial mesodermal dysplasia spectrum is a rare developmental defect during embryogenesis syndrome characterized by congenital manifestations of both oculo-auriculo-vertebral spectrum and caudal regression sequence. Phenotype is highly variable but patients typically present facial dysmorphism (incl. asymmetry, hypertelorism), auricular abnormalities (e.g. preauricular tags, microtia, absence of middle ear ossicles), skeletal malformations (hemivertebrae, hip dislocation, sacral agenesis/dysplasia, talipes equinovarus, flexion deformity of lower limbs), cardiac defects (dextrocardia, septal defects), renal and genitourinary anomalies (such as renal agensis/dysplasia, abnormal external genitalia, cryptorchidia), as well as anal anomalies such as anal atresia and rectovesical fistula.
Polymalformative genetic syndrome with increased risk of developing cancer (PGSIRC) comprises a wide range of syndromes characterized by congenital malformations with a high risk of developing tumors including up to 50 different rare diseases.
polymalformative genetic syndrome with increased risk of developing cancer
An instance of ichthyosis (disease) that is caused by an inherited modification of the individual's genome.
Hereditary photodermatoses are a spectrum of rare photosensitive disorders that are often caused by genetic deficiency or malfunction of various components of the DNA repair pathway. This results clinically in extreme photosensitivity, with many syndromes exhibiting an increased risk of cutaneous malignancies.
genetic central nervous system and retinal vascular disease
rare genetic hypothalamic or pituitary disease
rare genetic parathyroid disease and phosphocalcic metabolism disorder
Bilateral renal agenesis is the most profound form of renal agenesis, characterized by complete absence of kidney development, absent ureters and subsequent absence of fetal renal function resulting in Potter sequence with pulmonary hypoplasia related to oligohydramnios, which is fatal shortly after birth.
Multicystic dysplastic kidney (MCDK) is a congenital anomaly of the kidney and urinary tract (CAKUT) in which one or both kidneys (unilateral or bilateral MCDK respectively) are large, distended by multiple cysts, and non-functional.
Isolated autosomal dominant hypomagnesemia, Glaudemans type (IADHG) is a form of familial primary hypomagnesemia (FPH), characterized by low serum magnesium (Mg) values but normal urinary Mg values. The typical clinical features are recurrent muscle cramps, episodes of tetany, tremor, and muscle weakness, especially in distal limbs. The disease is potentially fatal.
isolated autosomal dominant hypomagnesemia, Glaudemans type
Cleft palate is a fissure type embryopathy that affects the soft and hard palate to varying degrees.
An instance of anomaly of puberty or/and menstrual cycle that is caused by a modification of the individual's genome.
genetic anomaly of puberty or/and menstrual cycle
anomaly of puberty or/and menstrual cycle of genetic origin
Hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency is a hereditary disorder of purine metabolism associated with uric acid overproduction and a continuum spectrum of neurological manifestations depending on the degree of the enzyme deficiency.
hypoxanthine-guanine phosphoribosyltransferase 1 deficiency
An instance of skeletal muscle disease that is acquired during the lifetime of the individual.
rare hereditary disease with peripheral neuropathy
rare hereditary metabolic disease with peripheral neuropathy
Cryopyrin associated periodic syndrome (CAPS) defines a group of autoinflammatory diseases, characterized by recurrent episodes of systemic inflammatory attacks in the absence of infection or autoimmune disease. CAPS comprises 3 disorders on a continuum of severity: severe CINCA syndrome, intermediate Muckle-Wells syndrome (MWS) and milder familial cold urticaria (FCAS).
systemic inflammatory disease associated with an acquired peripheral neuropathy
An instance of vascular anomaly that is caused by a modification of the individual's genome.
Cystinosis is a metabolic disease characterized by an accumulation of cystine inside the lysosomes, causing damage in different organs and tissues, particularly in the kidneys and eyes. Three clinical forms have been described: nephropathic infantile, nephropathic juvenile and ocular.
Atypical hemolytic-uremic syndrome (aHUS) is a thrombotic microangiopathy characterized by mechanical hemolytic anemia, thrombocytopenia, and renal dysfunction.
hemolytic-uremic syndrome without diarrhea
non-diarrhea-associated hemolytic uremic syndrome
D-minus hemolytic uremic syndrome (D-HUS)
A adenocarcinoma that involves the uterine cervix.
lysosomal disease with hypertrophic cardiomyopathy
mitochondrial disease with hypertrophic cardiomyopathy
syndrome associated with hypertrophic cardiomyopathy
familial syndrome associated with hypertrophic cardiomyopathy
An instance of hypertrophic cardiomyopathy that is acquired during the lifetime of the individual.
non-familial hypertrophic cardiomyopathy
A a genetic form of heart disease that occurs when heart (cardiac) muscle becomes thin and weakened in at least one chamber of the heart, causing the open area of the chamber to become enlarged (dilated). As a result, the heart is unable to pump blood as efficiently as usual. To compensate, the heart attempts to increase the amount of blood being pumped through the heart, leading to further thinning and weakening of the cardiac muscle. Over time, this condition results in heart failure.
hypokinetic dilated cardiomyopathy, familial
Editor note: unsure if GARD is familial form
syndrome associated with dilated cardiomyopathy
An instance of restrictive cardiomyopathy that is caused by an inherited modification of the individual's genome.
lysosomal disease with restrictive cardiomyopathy
Hydrocephalus-blue sclera-nephropathy syndrome is a rare, genetic, renal or urinary tract malformation syndrome characterized by nephrotic syndrome with focal segmental sclerosis associated with hydrocephalus, thin skin and blue sclerae. There have been no further descriptions in the literature since 1978.
hydrocephalus-blue sclerae-nephropathy syndrome
Diffuse cutaneous systemic sclerosis (dcSSc) is a subtype of Systemic Sclerosis (SSc) characterized by truncal and acral skin fibrosis with an early and significant incidence of diffuse involvement (interstitial lung disease, oliguric renal failure, diffuse gastrointestinal disease, and myocardial involvement).
progressive cutaneous systemic scleroderma
progressive cutaneous systemic sclerosis
Limited cutaneous systemic sclerosis (lcSSc) is a subtype of systemic sclerosis (SSc) characterized by the association of Raynaud's phenomenon with skin fibrosis limited to the hands, face, feet and forearms.
Limited systemic sclerosis (lSSc) (or SSc sine scleroderma) is a subset of systemic sclerosis (SSc) characterized by organ involvement in the absence of fibrosis of the skin.
systemic sclerosis without skin involvement
progressive systemic sclerosis sine scleroderma
An instance of primary hyperparathyroidism (disease) that is caused by an inherited modification of the individual's genome.
hereditary primary hyperparathyroidism (disease)
Dermatomyositis (DM) is a type of idiopathic inflammatory myopathy characterized by evocative skin lesions and symmetrical proximal muscle weakness.
Nephrogenic diabetes insipidus (NDI) is characterized by polyuria with polydipsia, recurrent bouts of fever, constipation, and acute hypernatremic dehydration after birth that may cause neurological sequelae. Polyuria may exceed 10 litres in children.
vasopressin-resistant diabetes insipidus
mitochondrial oxidative phosphorylation disorder
Neonatal diabetes mellitus presents as hyperglycemia, failure to thrive and, in some cases, dehydration and ketoacidosis which may be severe with coma, in a child within the first months of life.
diabetes mellitus syndrome in newborn infant
metal transport or utilization disorder with epilepsy
energy metabolism disorder with epilepsy
mitochondrial disease with peripheral neuropathy
Oligomeganephronia is a developmental anomaly of the kidneys, and the most severe form of renal hypoplasia, characterized by a reduction of 80% in nephron number and a marked hypertrophy of the glomeruli and tubules.
Beckwith-Wiedemann syndrome due to imprinting defect of type 11p15
Beckwith-Wiedemann syndrome due to imprinting defect of 11p15
Beckwith-Wiedemann syndrome due to CDKN1C mutation
Beckwith-Wiedemann syndrome due to 11p15 microdeletion
Beckwith-Wiedemann syndrome due to 11p15 translocation/inversion
Beta-thalassemia (BT) major is a severe early-onset form of BT characterized by severe anemia requiring regular red blood cell transfusions.
Beta-thalassemia (BT) intermedia is a form of BT characterized by mild to moderate anemia which does not or only occasionally requires transfusion.
rare non surgically correctable form of primary aldosteronism
Familial hyperaldosteronism (FH) is the heritable form of primary aldosteronism (PA) which comprises three identified subtypes to date: FH type I (FH-I) characterized by early-onset hypertension, glucocorticoid remediable adrenocorticotropic hormone (ACTH)-dependent hyperaldosteronism, variable hypokalemia, and overproduction of 18-oxocortisol and 18-hydroxycortisol; FH type II (FH-II) characterized by hypertension of varying severity and hyperaldosteronism not suppressible by dexamethasone; and FH type III (FH-III) characterized by profound hypokalemia, early-onset severe hypertension, non glucocorticoid-remediable hyperaldosteronism, and overproduction of 18-oxocortisol and 18-hydroxycortisol.
Duplication of the urethra is a rare congenital genitourinary anomaly, encompassing a wide spectrum of anatomic variants in which the urethra is partially or totally duplicated, which may be asymptomatic or cause symptoms such as incontinence, recurrent urinary infections and difficulty urinating.
familial amyloid nephropathy due to apolipoprotein A-II variant
familial renal amyloidosis due to apolipoprotein A-II variant
hereditary amyloid nephropathy due to apolipoprotein A-II variant
hereditary renal amyloidosis due to apolipoprotein A-II variant
Atypical hypotonia-cystinuria syndrome is a form of hypotonia-cystinuria type 1 syndrome characterized by mild to moderate intellectual disability in addition to classic hypotonia-cystinuria syndrome phenotype (cystinuria type 1, generalised hypotonia, poor feeding, growth retardation, and minor facial dysmorphism).
Beckwith-Wiedemann syndrome due to NSD1 mutation
Megacystic-megaureter syndrome is an urinary tract malformation characterized by the presence of a massive primary non-obstructive vesicoureteral reflux and a large capacity, smooth, thin walled bladder due to the continual recycling of refluxed urine. Recurrent urinary infections are commonly associated with this condition.
congenital primary megaureter, obstructed form
congenital primary megaureter, refluxing form
congenital primary megaureter, nonrefluxing and unobstructed form
syndrome associated with obesity (disease)
Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous, primarily respiratory disorder characterized by chronic upper and lower respiratory tract disease. Approximately half of PCD patients have an organ laterality defect (situs inversus totalis or situs ambiguus/heterotaxy).
Dextrocardia bronchiectasis and sinusitis
Dextrocardia-bronchiectasis-sinusitis syndrome
Immotile cilia syndrome, Kartagener type
Primary ciliary dyskinesia and situs inversus
Primary ciliary dyskinesia, Kartagener type
bronchiectasis, chronic sinusitis and dextrocardia syndrome
Editor note: we deliberately merge two MESHes here
Mitochondrial oxidative phosphorylation disorder due to nuclear DNA anomalies is a group of clinically heterogeneous diseases, commonly defined by lack of cellular energy due to defects of oxidative phosphorylation (OXPHOS), resulting from pathogenic mutations in the nuclear DNA. Mitochondrial oxidative phosphorylation disorder due to nuclear DNA anomalies includes diseases classified according to defects in: genes encoding structural components of OXPHOS complexes (such as Leigh syndrome, coenzyme Q10 deficiency); genes encoding assembly factors of OXPHOS complexes (such as GRACILE syndrome); genes altering the stability of mitochondrial DNA (such as autosomal dominant progressive external ophthalmoplegia, mitochondrial DNA depletion syndrome); mitochondrial protein synthesis.
OXPHOS disease due to nuclear DNA anomalies
mitochondrial oxidative phosphorylation disorder due to nDNA anomalies
mitochondrial oxidative phosphorylation disorder due to nuclear DNA anomalies
dominant hypophosphatemia with nephrolithiasis or osteoporosis
rare bleeding disorder due to a platelet anomaly
rare bleeding disorder due to a thrombopathy and/or thrombocytopenia
rare coagulopathy due to a platelet anomaly
rare coagulopathy due to a thrombopathy and/or thrombocytopenia
rare hemorrhagic disorder due to a thrombopathy and/or thrombocytopenia
hemorrhagic disorder due to a platelet anomaly
A hemorrhagic disorder due to a platelet anomaly which develops after birth.
rare bleeding disorder due to an acquired platelet anomaly
rare bleeding disorder due to an acquired thrombopathy and/or thrombocytopenia
rare coagulopathy due to an acquired platelet anomaly
rare coagulopathy due to an acquired thrombopathy and/or thrombocytopenia
rare hemorrhagic disorder due to an acquired thrombopathy and/or thrombocytopenia
hemorrhagic disorder due to an acquired platelet anomaly
thrombotic disorder due to a platelet anomaly
inherited nervous system cancer-predisposing syndrome
An osteochondrodysplasia that results in abnormalities of bone growth located in vertebral column, located in epiphysis, located in metaphysis.
spondyloepiphyseal dysplasia and spondyloepimetaphyseal dysplasia
OXPHOS disease due to mitochondrial DNA anomalies
mitochondrial oxidative phosphorylation disorder due to mtDNA anomalies
mitochondrial oxidative phosphorylation disorder due to mitochondrial DNA anomalies
OXPHOS disease due to a point mutation of mitochondrial DNA
OXPHOS disease due to a point mutation of mtDNA
mitochondrial oxidative phosphorylation disorder due to a point mutation of mtDNA
mitochondrial oxidative phosphorylation disorder due to a point mutation of mitochondrial DNA
OXPHOS disease due to a duplication of mitochondrial DNA
OXPHOS disease due to a duplication of mtDNA
mitochondrial oxidative phosphorylation disorder due to a duplication of mtDNA
mitochondrial oxidative phosphorylation disorder due to a duplication of mitochondrial DNA
mtDNA depletion syndrome, hepatocerebral form
Editor note: consider merging with MONDO:0014943
mitochondrial DNA depletion syndrome, hepatocerebral form
Familial visceral myopathy is a rare hereditary myopathic degeneration of both gastrointestinal and urinary tracts that causes chronic intestinal pseudo-obstruction. It usually presents after the first decade of life with megaduodenum, megacystis and symptoms such as abdominal distension and/or pain, vomiting, constipation, diarrhea, dysphagia, and/or urinary tract infections.n.
Alagille-Watson syndrome due to monosomy 20p12
Arteriohepatic dysplasia due to monosomy 20p12
syndromic bile duct paucity due to monosomy 20p12
Alagille syndrome due to 20p12 microdeletion
Alagille-Watson syndrome due to a JAG1 point mutation
arteriohepatic dysplasia due to a JAG1 point mutation
syndromic bile duct paucity due to a JAG1 point mutation
cholestasis with peripheral pulmonary stenosis
hepatic ductular hypoplasia, syndromatic
Alagille syndrome due to a JAG1 point mutation
partial deletion of the short arm of chromosome type 2
partial monosomy of the short arm of chromosome 2
partial deletion of the short arm of chromosome 2
partial deletion of the short arm of chromosome type 10
partial monosomy of the short arm of chromosome 10
partial deletion of the short arm of chromosome 10
partial deletion of the short arm of chromosome type 11
partial monosomy of the short arm of chromosome 11
partial deletion of the short arm of chromosome 11
partial deletion of the short arm of chromosome type 16
partial monosomy of the short arm of chromosome 16
partial deletion of the short arm of chromosome 16
partial deletion of the short arm of chromosome 20
partial monosomy of the short arm of chromosome type 20
partial monosomy of the short arm of chromosome 20
Chromosome 7q deletion is a chromosome abnormality that occurs when there is a missing copy of the genetic material located on the long arm (q) of chromosome 7. The severity of the condition and the signs and symptoms depend on the size and location of the deletion and which genes are involved. Features that often occur in people with chromosome 7q deletion include developmental delay, intellectual disability, behavioral problems, and distinctive facial features. Most cases are not inherited, but people can pass the deletion on to their children. Treatment is based on the signs and symptoms present in each person.
partial deletion of the long arm of chromosome type 7
partial monosomy of the long arm of chromosome 7
partial deletion of the long arm of chromosome 7
Chromosome 8q deletion is a chromosome abnormality that occurs when there is a missing copy of the genetic material located on the long arm (q) of chromosome 8. The severity of the condition and the signs and symptoms depend on the size and location of the deletion and which genes are involved. Features that often occur in people with chromosome 8q deletion include developmental delay, intellectual disability, behavioral problems, and distinctive facial features. Most cases are not inherited, but people can pass the deletion on to their children. Treatment is based on the signs and symptoms present in each person.
partial deletion of the long arm of chromosome type 8
partial monosomy of the long arm of chromosome 8
partial deletion of the long arm of chromosome 8
partial deletion of the long arm of chromosome type 17
partial monosomy of the long arm of chromosome 17
partial deletion of the long arm of chromosome 17
partial deletion of the long arm of chromosome type 22
partial monosomy of the long arm of chromosome 22
partial deletion of the long arm of chromosome 22
partial duplication of chromosome type 11
partial duplication of the short arm of chromosome type 11
partial trisomy of the short arm of chromosome 11
partial duplication of the short arm of chromosome 11
Bartter syndrome with hypocalcemia is a type of Bartter syndrome characterized by hypocalcemia, hypomagnesemia and hypoparathyroidism along with features of Henle's loop dysfunction (polyuria, hypokalemic alkalosis, increased levels of plasma renin and aldosterone, low blood pressure and vascular resistance to angiotensin II). Bartter syndrome with hypocalcemia is a very rare manifestation of autosomal dominant hypocalcemia (ADH)
partial deletion of the long arm of chromosome type X
partial monosomy of the long arm of chromosome X
partial deletion of the long arm of chromosome X
A interstitial lung disease that occurs during childhood.
interstitial lung disease specific to childhood
primary interstitial lung disease specific to childhood
primary ILD specific to childhood due to alveolar structure disorder
primary interstitial lung disease specific to childhood due to alveolar structure disorder
secondary ILD specific to childhood associated with a systemic disease
secondary interstitial lung disease specific to childhood associated with a systemic disease
secondary ILD specific to childhood associated with a connective tissue disease
secondary interstitial lung disease specific to childhood associated with a connective tissue disease
secondary ILD specific to childhood associated with a systemic vasculitis
secondary interstitial lung disease specific to childhood associated with a systemic vasculitis
interstitial lung disease in childhood and adulthood
secondary ILD in childhood and adulthood
secondary interstitial lung disease in childhood and adulthood
secondary ILD in childhood and adulthood associated with a systemic disease
secondary interstitial lung disease in childhood and adulthood associated with a systemic disease
secondary ILD in childhood and adulthood associated with a systemic vasculitis
secondary interstitial lung disease in childhood and adulthood associated with a systemic vasculitis
A low grade childhood congenital malignant neoplasm arising from the kidney. It is characterized by the presence of fibroblastic cells. The majority of cases occur in the first year of life. Complete excision is usually associated with an excellent prognosis.
This syndrome, associating familial adult medullary cystic disease with spastic quadriparesis has been described in two cases so far. Renal transplantation was successful in those two patients.
adult familial nephronophthisis-spastic quadriparesia syndrome
syndrome with a cerebellar malformation as major feature
syndrome with microcephaly as major feature
Editor note: consider deleting all 'other' terms
other syndrome with a central nervous system malformation as major feature
syndrome with a Dandy-Walker malformation as major feature
Arthrogryposis-Renal dysfunction-Cholestasis (ARC) syndrome is a multisystem disorder, characterized by neurogenic arthrogryposis multiplex congenita, renal tubular dysfunction and neonatal cholestasis with low serum gamma-glutamyl transferase activity.
arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome
arthrogryposis, renal dysfunction, and cholestasis
arthrogryposis-renal dysfunction-cholestasis
arthrogryposis - renal dysfunction - cholestasis
arthrogryposis multiplex congenita, renal dysfunction, and cholestasis
arthrogryposis renal dysfunction cholestasis syndrome
arthrogryposis-renal dysfunction-cholestasis syndrome
An instance of mesenchymal cell neoplasm that is caused by an inherited modification of the individual's genome.
An instance of systemic or rheumatic disease that is caused by a modification of the individual's genome.
hereditary systemic or rheumatic disease
genetic systemic or rheumatologic disease
rare bleeding disorder due to a constitutional thrombocytopenia
rare bleeding disorder due to a quantitative platelet defect
rare coagulopathy due to a constitutional thrombocytopenia
rare coagulopathy due to a quantitative platelet defect
rare hemorrhagic disorder due to a constitutional thrombocytopenia
rare hemorrhagic disorder due to a quantitative platelet defect
hemorrhagic disorder due to a constitutional thrombocytopenia
sickle cell disease and related diseases
Heritable pulmonary arterial hypertension (HPAH) is a form of pulmonary arterial hypertension (PAH), occurring due to mutations in PAH predisposing genes or in a familial context. HPAH is characterized by elevated pulmonary arterial resistance leading to right heart failure. HPAH is progressive and potentially fatal.
familial pulmonary arterial hypertension
hereditary pulmonary arterial hypertension
heritable pulmonary arterial hypertension
syndrome with pulmonary hypertension as a major feature
Osteopetrosis, also known as marble bone disease, is a descriptive term that refers to a group of rare, heritable disorders of the skeleton characterized by increased bone density on radiographs.
Vitamin B12-responsive methylmalonic acidemia (MA) is an inborn error of vitamin B12 (cobalamin) metabolism characterized by recurrent ketoacidotic comas or transient vomiting, dehydration, hypotonia and intellectual deficit, which responds to vitamin B12. There are three types: cblA, cblB and cblD-variant 2 (cblDv2).
vitamin B12-responsive methylmalonic aciduria
vitamin B12-responsive methylmalonic acidemia
Inflammation of the glomeruli that is characterized by a rapid loss in renal function with glomerular crescent formation observed on biopsy; it is often seen in patients with concomitant autoimmune disease, like Goodpasture's syndrome or systemic lupus erythematosus.
A disorder characterized by inflammation of the entire uvea which includes the iris, ciliary body, and choroid. Causes include systemic infections, sarcoidosis, and cancers.
systemic diseases with posterior uveitis
A inherited ichthyosis that is not part of a larger syndrome.
A inherited ichthyosis that is part of a larger syndrome.
syndrome associated with inherited ichthyosis
Autosomal recessive form of inherited ichthyosis.
autosomal recessive inherited ichthyosis
ichthyosis, congenital, autosomal recessive
inherited ichthyosis, autosomal recessive
Editor note: ORDO classifies as non-syndromic but syndromic forms exist
autosomal recessive congenital ichthyosis
autosomal ichthyosis syndrome with prominent neurologic signs
autosomal ichthyosis syndrome with prominent neurologics signs
autosomal ichthyosis syndrome with fatal disease course
autosomal ichthyosis syndrome with other associated signs
renal caliceal diverticuli-deafness syndrome
A recently described mass-forming lesion that occurs in the pancreas, submandibular glands, lacrimal glands, lymph nodes, and hepatobiliary tract. It is characterized by the presence of marked tissue sclerosis and infiltration by numerous plasma cells. The plasma cells show immunohistochemical staining for IgG4 and the serum IgG4 levels are often increased.
Immunoglobulin G4-related sclerosing disease
IgG4-positive multiorgan lymphoproliferative syndrome
IgG4-related systemic sclerosing disease
systemic IgG4-related plasmacytic syndrome
systemic IgG4-related sclerosing syndrome
Epstein-Barr virus-associated mesenchymal tumor
Vitamin B12-unresponsive methylmalonic acidemia type mut0 is an inborn error of metabolism characterized by recurrent ketoacidotic comas or transient vomiting, dehydration, hypotonia and intellectual deficit, which does not respond to administration of vitamin B12.
complete deficiency of methylmalonyl-CoA mutase
vitamin B12-unresponsive methylmalonic aciduria type mut0
vitamin B12-unresponsive methylmalonic acidemia type mut0
autoinflammatory syndrome with immune deficiency
autoinflammatory syndrome with skin involvement
Methylmalonic acidemia is an inborn error of vitamin B12 metabolism characterized by gastrointestinal and neurometabolic manifestations resulting from decreased function of the mitochondrial enzyme methylmalonyl-CoA mutase.
methylmalonic aciduria without homocystinuria
methylmalonic acidemia without homocystinuria
Renal-hepatic-pancreatic dysplasia is a rare, genetic, developmental defect during embryogenesis syndrome characterized by the triad of pancreatic fibrosis (and cysts, with a reduction of parenchymal tissue), renal dysplasia (with peripheral cortical cysts, primitive collecting ducts, glomerular cysts and metaplastic cartilage) and hepatic dysgenesis (enlarged portal areas containing numerous elongated binary profiles with a tendancy to perilobular fibrosis). Situs abnormalities, skeletal anomalies and anencephaly have also been associated. Patients that survive the neonatal period present renal insufficiency, chronic jaundice and insulin-dependant diabetes.
syndrome with limb duplication, polydactyly, syndactyly, and/or hyperphalangy
Caudal regression sequence is a rare congenital malformation of the lower spinal segments associated with aplasia or hypoplasia of the sacrum and lumbar spine.
Renal tubular dysgenesis is a rare disorder of the fetus characterized by absent or poorly developed proximal tubules of the kidneys, persistent oligohydramnios, leading to Potter sequence (facial dysmorphism with large and flat low-set ears, lung hypoplasia arthrogryposis and limb positioning defects), and skull ossification defects. It can be acquired during fetal development due to drugs taken by the mother or certain disorders (twin-twin transfusion syndrome, TTTS) or inherited in an autosomal recessive manner.
Junctional epidermolysis bullosa (JEB) is a form of inherited epidermolysis bullosa characterized by involvement of the skin and mucous membranes, and is defined by the formation of blistering lesions between the epidermis and the dermis at the lamina lucida level of the cutaneous basement membrane zone and by healing of lesions with atrophy and/or exuberant granulation tissue formation.
congenital junctional epidermolysis bullosa
epidermolysis bullosa hereditaria letalis
Familial primary hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is a form of familial primary hypomagnesemia (FPH), characterized by renal magnesium (Mg) and calcium (Ca) wasting, nephrocalcinosis, kidney failure and, in some cases, severe ocular impairment. Two subtypes of FHHNC are described: FHHNC with severe ocular involvement (FHHNCOI) and without severe ocular involvement (FHHN).
familial primary hypomagnesemia with hypercalciuria and nephrocalcinosis
familial primary hypomagnesemia with hypocalcuria
Familial primary hypomagnesemia with normocalcuria (FPHN) is a form of familial primary hypomagnesemia (FPH) which is characterized by low magnesium values but normal calcium values in the serum. The disorder consists of three distinct forms which are: autosomal recessive primary hypomagnesemia with normocalcuria and hypocalcemia (ARPHN), familial primary hypomagnesemia with normocalcuria and normocalcemia (FPHNN) and isolated autosomal dominant hypomagnesemia, Glaudemans type.
familial primary hypomagnesemia with normocalcuria
vitamin B12-responsive methylmalonic aciduria, type cblDv2
vitamin B12-responsive methylmalonic acidemia, type cblDv2
An acquired metabolic disease that is has its basis in the disruption of neutral amino acid transport.
inborn error of neutral amino acid transport
inborn neutral amino acid transport disorder
rare inborn error of neutral amino acid transport
disorder of neutral amino acid transport
erythrocyte UDP-galactose-4-epimerase deficiency
erythrocyte epimerase deficiency galactosemia
erythrocyte uridine diphosphate galactose-4-epimerase deficiency
erythrocyte galactose epimerase deficiency
generalized UDP-galactose-4-epimerase deficiency
generalized epimerase deficiency galactosemia
generalized uridine diphosphate galactose-4-epimerase deficiency
generalized galactose epimerase deficiency
disorder of carbohydrate absorption and transport
Sialidosis is a lysosomal storage disease, belonging to the group of oligosaccharidoses or glycoproteinoses, with a wide clinical spectrum that is divided into two main clinical subtypes: sialidosis type I, the milder, non dysmorphic form of the disease characterized by gait abnormalities, progressive visual loss, bilateral macular cherry red spots and myoclonus, that presents in adolescence or adulthood (second or third decade of life); and sialidosis type II the more severe, early onset form, characterized by a progressive and severe mucopolysaccharidosis-like phenotype with coarse facies, visceromegaly, dysostosis multiplex, and developmental delay. Bilateral macular cherry red spots are also present. Sialidosis type II has been further divided into congenital (with hydrops fetalis), infantile and juvenile presentations.
A disease that has its basis in the disruption of protein N-linked glycosylation.
disorder of protein N-linked glycosylation
A disease that has its basis in the disruption of protein O-linked glycosylation.
disorder of protein O-linked glycosylation
disorder of glycosphingolipid and GPI-anchored proteins glycosylation
disorder of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation
inborn disorder of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation
disorder of peroxisomal alpha-, beta- and omega-oxidation
An acquired metabolic disease that is has its basis in the disruption of porphyrin-containing compound metabolic process.
disorder of porphyrin and haem metabolism
inborn disorder of porphyrin and haem metabolism
inborn error of porphyrin-containing compound metabolic process
inborn porphyrin-containing compound metabolic process disorder
inherited disorder of porphyrin metabolism
rare inborn error of porphyrin-containing compound metabolic process
Editor note: we follow ORDO and treat this as inborn. However, some form of porphyria (e.g PCT) may be acquired.
An instance of bilirubin metabolism disease that is caused by an inherited modification of the individual's genome.
disorder of bilirubin metabolism and excretion
inborn disorder of bilirubin metabolism and excretion
disorder of metabolite absorption and transport
disorder of vitamin and non-protein cofactor absorption and transport
disorder of mineral absorption and transport
An acquired metabolic disease that is has its basis in the disruption of cellular copper ion homeostasis.
inborn cellular copper ion homeostasis disorder
inborn error of cellular copper ion homeostasis
rare inborn error of cellular copper ion homeostasis
disorder of zinc metabolism and transport
An acquired metabolic disease that is has its basis in the disruption of magnesium ion transport.
rare inborn error of magnesium ion transport
Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome describes a spectrum of Mullerian duct anomalies characterized by congenital aplasia of the uterus and upper 2/3 of the vagina in otherwise phenotypically normal females. It can be classified as either MRKH syndrome type 1 (corresponding to isolated utero-vaginal aplasia) or MRKH syndrome type 2 (utero-vaginal aplasia associated with other malformations).
A metabolic disorder characterized by deficiency of high density (alpha) lipoprotein in the blood.
Primary systemic amyloidosis (PSA) is a form of AL amyloidosis caused by the aggregation and deposition of insoluble amyloid fibrils derived from misfolded monoclonal immunoglobulin light chains usually produced by a plasma cell tumor and characterized by multiple organ involvement.
systemic Immunoglobulin Light chain amyloidosis
Primary localized amyloidosis is a form of AL amyloidosis caused by the aggregation of insoluble amyloid fibrils derived from misfolded monoclonal immunoglobulin light chains usually produced by a plasma cell tumor and characterized by localized amyloid deposition with clinical manifestations restricted to the organ involved, most frequently urinary tract (bladder), eye, respiratory tract (larynx, lungs), and skin.
Autosomal dominant proximal renal tubular acidosis (AD pRTA) is a form of proximal renal tubular acidosis (pRTA) characterized by an isolated defect in the proximal tubule leading to the decreased reabsorption of bicarbonate and consequently causing urinary bicarbonate wastage. Mild growth retardation and reduced bone density are extra-renal complications.
proximal renal tubular acidosis, autosomal dominant
autosomal dominant proximal renal tubular acidosis
A hypersensitivity reaction type II disease that involves the skin of body.
autoimmune disease of skin and connective tissue
integument hypersensitivity reaction type II disease
skin of body hypersensitivity reaction type II disease
autoimmune disease with skin involvement
Senior-Loken syndrome (SLSN) is a very rare autosomal recessive oculo-renal disease characterized by the association of nephronophthisis (NPHP), a chronic kidney disease, with retinal dystrophy.
renal dysplasia-retinal aplasia syndrome
Papillary renal cell carcinoma is a rare subtype of renal cell carcinoma, arising from the renal tubular epithelium and showing a papillary growth pattern, which typically manifests with hematuria, flank pain, palpable abdominal mass or nonspecific symptoms, such as fatigue, weight loss or fever. Symptoms related to metastatic spread, such as bone pain or persistent cough, are frequently associated since early diagnosis is not common. It is typically multifocal, bilateral, and in most cases sporadic, although different hereditary syndromes, such as Hereditary leiomyoma renal cell carcinoma, Birt-Hogg-DubC) syndrome and Tuberous sclerosis, may predispose to the development of papillary renal cell carcinoma.
papillary (chromophil) renal cell carcinoma
papillary renal carcinoma, malignant - (subtype)
papillary renal cell carcinoma, bilateral - (subtype)
papillary renal cell carcinoma, familial - (subtype)
papillary renal cell carcinoma, multiple - (subtype)
papillary renal cell carcinoma, sporadic - (subtype)
Chromophobe renal cell carcinoma is a rare subtype of renal cell carcinoma, originating from the intercalating cells of the collecting ducts and macroscopically manifesting as a well-circumscribed, highly lobulated, solid tumor that is usually diagnosed at an early stage. It is frequently asymptomatic, or may present with nonspecific symptoms, such as weight loss, fever or fatigue. The classic presentation observed in renal tumors (hematuria, flank pain and palpable mass) is occasionally observed and usually indicates an advanced stage of the disease. It is most frequently sporadic however, several familial cases, associated with Birt-Hogg DubC) syndrome, have been described.
chromophobe cell carcinoma of the kidney
MiT family translocation renal cell carcinoma (t-RCC) is a rare subtype of renal cell carcinoma with recurrent genetic abnormalities, harboring rearrangements of the TFE3 (Xp11 t-RCC) or TFEB [t(6;11) t-RCC] genes. The t(6;11) t-RCC has distinctive histologic features of biphasic appearance with larger epitheloid and smaller eosinophilic cells. The symptoms are usually non-specific and include hematuria, flank pain, palpable abdominal mass and/or systemic symptoms of anemia, fatigue and fever.
carcinoma associated with MITF/TFE translocation
MIT family translocation renal cell carcinoma
Renal cell carcinoma that develops in patients who are long-term survivors of childhood neuroblastoma.
renal cell cancer associated with neuroblastoma
renal cell carcinoma after neuroblastoma
renal cell carcinoma associated with neuroblastoma
Tubulocystic renal cell carcinoma is an extremely rare subtype of renal cell carcinoma most frequently characterized by a small, solitary, well-circumscribed, unencapsulated renal tumor composed of multiple small to medium-sized cysts with a white or gray, spongy ("bubble wrap-like") cut surface. Patients are usually asymptomatic or could manifest with abdominal pain, abdominal distension and/or hematuria. Progression, recurrence and metastasis rarely occur although lymph node, bone, pleura and liver mestatsis have been reported.
inherited renal cancer-predisposing syndrome
Familial nonmedullary thyroid carcinoma (fNMTC) is a rare non-syndromic form of thyroid cancer characterized by occurrence of thyroid carcinoma (TC) as the primary feature in a familial setting.
Note the OMIM phenotypic series lacks a member classified by ORDO
Exstrophy-Epispadias Complex (EEC) represents a spectrum of genitourinary malformations ranging in severity from epispadias (E) and classical bladder exstrophy (CEB) to exstrophy of the cloaca (EC) as the most severe form. Depending on severity, the EEC may involve the urinary system, the musculoskeletal system, the pelvis, the pelvic floor, the abdominal wall, the genitalia and sometimes the spine and the anus.
bladder exstrophy-epispadias-cloacal extrophy complex
bladder exstrophy-epispadias-cloacal exstrophy complex
This syndrome is characterised by progressive calcification of the brain and spinal cord, growth retardation, psychomotor anomalies, deafness and anaemia. Renal tubular acidosis was found in one patient. To date, this syndrome has been described in only two patients from one family.
central nervous system calcification-deafness-tubular acidosis-anemia syndrome
Hypertrophic cardiomyopathy and renal tubular disease due to mitochondrial DNA mutation is a mitochondrial oxidative phosphorylation disorder characterized by hypertrophic and dilated cardiomyopathy, failure to thrive, myopathy with generalized hypotonia and increased creatine kinase, developmental delay and/or regression with cerebral atrophy on brain MRI, renal manifestations including chronic renal failure, renal tubular acidosis and lactic acidosis. Additional clinical features include seizures and respiratory failure.
hypertrophic cardiomyopathy and renal tubular disease due to mtDNA mutation
hypertrophic cardiomyopathy and renal tubular disease due to mitochondrial DNA mutation
non-familial rare disease with dilated cardiomyopathy
An instance of periodic fever syndrome that is caused by an inherited modification of the individual's genome.
46,XY disorder of sex development of endocrine origin
46,XY DSD due to impaired androgen production
46,XY disorder of sex development due to impaired androgen production
46,XY DSD due to a cholesterol synthesis defect
46,XY disorder of sex development due to a cholesterol synthesis defect
Congenital conditions of atypical sexual development associated with abnormal sex chromosome constitutions including monosomy; trisomy; and mosaicism.
sex chromosome disorder of sex development
Takayasu arteritis (TAK) is a rare inflammatory large-vessel vasculitis primarily affecting the aorta and its major branches, but also other large vessels, causing stenosis, occlusion, or aneurysm.
pharyngeal arch artery syndromic disease
juvenile idiopathic inflammatory myopathy
non-Ig-mediated membranoproliferative glomerulonephritis
non-immunoglobulin-mediated membranoproliferative glomerulonephritis
immunodeficiency due to absence of thymus
Thomas syndrome is characterised by renal anomalies, cardiac malformations and cleft lip or palate. It has been described in six patients. Transmission was suggested to be autosomal recessive.
Potter sequence-cleft lip/palate-cardiopathy syndrome
Trisomy 13 is a chromosomal anomaly caused by the presence of an extra chromosome 13 and is characterized by brain malformations (holoprosencephaly), facial dysmorphism, ocular anomalies, postaxial polydactyly, visceral malformations (cardiopathy) and severe psychomotor retardation.
Trisomy 18 is a chromosomal abnormality associated with the presence of an extra chromosome 18 and characterized by growth delay, dolichocephaly, a characteristic facies, limb anomalies and visceral malformations.
A congenital defect characterized by failure of the neural tube to close completely; this results in the presence of openings in the brain or spinal cord. Examples of neural tube defects include encephalocele and spina bifida.
A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use.
A malignant neoplasm arising from muscle tissue, adipose tissue, blood vessels, fibrous tissue, or other supportive tissues excluding the bones.
non-rhabdomyosarcoma soft tissue sarcoma, NOS
Familial Mediterranean fever (FMF) is an autoinflammatory disorder characterized by recurrent short episodes of fever and serositis resulting in pain in the abdomen, chest, joints and muscles.
A hereditary disorder that leads to a selective defect in renal or intestinal magnesium absorption, resulting in a low serum magnesium concentration.
Familial primary hypomagnesemia with normocalciuria and normocalcemia (FPHNN) is a form of familial primary hypomagnesemia (FPH), characterized by low serum magnesium (Mg) values but inappropriate normal urinary Mg values (i.e. renal hypomagnesemia). The typical symptoms are weakness of the limbs, vertigo, headaches, seizures, brisk tendon reflexes and mild to moderate psychomotor delay.
familial primary hypomagnesemia with normocalciuria and normocalcemia
Hereditary xanthinuria is a purine metabolism disorder due to inherited deficiency of the xanthine dehydrogenase/oxidase enzyme and is characterized by very low (or undetectable) concentrations of uric acid in blood and urine and very high concentration of xanthine in urine, leading to urolithiasis.
Galactosemia is a group of rare genetic metabolic disorders characterized by impaired galactose metabolism resulting in a range of variable manifestations encompassing a severe, life-threatening disease (classic galactosemia), a rare mild form (galactokinase deficiency) causing cataract, and a very rare form with variable severity (galactose epimerase deficiency) resembling classic galactosemia in the severe form.
disorder of phospholipids, sphingolipids and fatty acids biosynthesis
An acquired metabolic disease that is has its basis in the disruption of mitochondrial genome maintenance.
inborn error of mitochondrial genome maintenance
inborn mitochondrial genome maintenance disorder
rare inborn error of mitochondrial genome maintenance
A genetically heterogeneous condition, typically inherited in an autosomal recessive fashion, characterized by coenzyme Q10 deficiency.
combined oxidative phosphorylation defect
mitochondrial disorder due to a defect in mitochondrial protein synthesis
The mitochondrial DNA (mtDNA) depletion syndrome (MDS) is a clinically heterogeneous group of mitochondrial disorders characterized by a reduction of the mtDNA copy number in affected tissues without mutations or rearrangements in the mtDNA. MDS is phenotypically heterogeneous, and can affect a specific organ or a combination of organs, with the main presentations described being either hepatocerebral (i.e. hepatic dysfunction, psychomotor delay), myopathic (i.e. hypotonia, muscle weakness, bulbar weakness), encephalomyopathic (i.e. hypotonia, muscle weakness, psychomotor delay) or neurogastrointestinal (i.e gastrointestinal dysmotility, peripheral neuropathy). Additional phenotypes include fatal infantile lactic acidosis with methylmalonic aciduria, spastic ataxia (early-onset spastic ataxia-neuropathy syndrome), and Alpers syndrome.
hemolytic-uremic syndrome without diarrhea with DGKE deficiency
atypical hemolytic-uremic syndrome with DGKE deficiency
Nephrotic syndrome for which no cause has been identified.
Hereditary glaucoma is a clinically diverse group of rare eye disorders with genetic predisposition characterized by elevated intraocular pressure (IOP) and glaucomatous changes of the optic nerve head, leading to field defects, visual loss and blindness. Hereditary glaucoma can be sub-classified as primary (congenital glaucoma, juvenile glaucoma) or secondary according to the presence or absence of systemic or other ocular anomalies (iridogoniodysgenesis, Stickler syndrome, Coats syndrome). The clinical presentation is variable and is based on age, severity of glaucoma, presence of ocular abnormalities and development of secondary IOP related abnormalities.
mtDNA depletion syndrome, hepatocerebrorenal form
mitochondrial DNA depletion syndrome, hepatocerebrorenal form
Von Recklinghausen disease due to NF1 mutation or intragenic deletion
neurofibromatosis type 1 due to NF1 mutation or intragenic deletion
Hypocomplementemic urticarial vasculitis (HUV) is an immune complex-mediated small vessel vasculitis characterized by urticaria and hypocomplementemia (low C1q with or without low C3 and C4), and usually associated with circulating anti-C1q autoantibodies. Arthritis, pulmonary disease, ocular inflammation, and glomerulonephritis are common systemic manifestations.
Mac Duffie hypocomplementemic urticarial vasculitis
McDuffie hypocomplementemic urticarial vasculitis
hypocomplementemic urticarial vasculitis
Editor note: ORDO has these as genetic, but some forms may not be genetic - check this
A disorder of the development of bone in which ossification is affected.
dysostosis with limb anomaly as a major feature
dysostosis with limb and face anomalies as a major feature
rare disorder with dystonia and other neurologic or systemic manifestation
congenital disorder of glycosylation with neurological involvement
non-X-linked CDG with intellectual disability as a major feature
non-X-linked congenital disorder of glycosylation with intellectual disability as a major feature
congenital disorder of glycosylation with epilepsy as a major feature
congenital disorder of glycosylation with hepatic involvement
CDG with cardiac malformation as a major feature
congenital disorder of glycosylation with cardiac malformation as a major feature
congenital disorder of glycosylation with intestinal involvement
congenital disorder of glycosylation with skin involvement
congenital disorder of glycosylation with nephropathy as a major feature
congenital disorder of glycosylation with developmental anomaly
Joubert syndrome with Jeune asphyxiating thoracic dystrophy (JATD) is an extremely rare genetic bone disorder characterized by the classic features of Joubert syndrome (i.e. malformation of the brainstem causing ataxia, hypotonia,cognitive impairment, and abnormal eyemovements), associated with the skeletal anomalies found in JATD including short-rib dysplasia and narrow thorax causing respiratory failure, short limbs, and metaphyseal changes.
Joubert syndrome with Jeune asphyxiating thoracic dystrophy
Transplacentally acquired neonatal autoimmune disease
A self-limited skin rash that appears in the neonatal period and usually resolves in four to six months after birth. It is caused by placental transfer of maternal autoantibodies, usually anti-Ro antibody. In a minority of cases, it is associated with congenital heart block, hepatitis, or thrombocytopenia. The mothers of the affected babies may be asymptomatic or suffer from systemic lupus erythematosus, Sjogren's syndrome, or rheumatoid arthritis.
Necrotic changes in the bone tissue due to interruption of blood supply. Most often affecting the epiphysis of the long bones, the necrotic changes result in the collapse and the destruction of the bone structure.
rare hereditary disease with avascular necrosis
An instance of osteonecrosis that is caused by a modification of the individual's genome.
An instance of avascular necrosis that is caused by a modification of the individual's genome.
rare male infertility due to gonadotropic axis disorder
rare male infertility due to hypothalamic-pituitary-testicular axis disorder
rare male infertility due to hypothalamic-pituitary-gonadal axis disorder
rare male infertility due to adrenal disorder
Male infertility due to testicular dysgenesis or sperm disorder
male infertility due to gonadal dysgenesis or sperm disorder
Male infertility due to asthenozoospermia
male infertility due to sperm motility disorder
rare disorder due to impaired sperm transport
rare disorder with obstructive azoospermia
rare male fertility disorder with obstructive azoospermia
rare female infertility due to gonadotropic axis disorder
rare female infertility due to hypothalamic-pituitary-ovarian axis disorder
female infertility due to hypothalamic-pituitary-gonadal axis disorder
rare disorder with female infertility due to a congenital hypogonadotropic hypogonadism
female infertility due to a congenital hypogonadotropic hypogonadism
rare female infertility due to an adrenal disorder
female infertility due to an anomaly of ovarian function
female infertility due to ovarian dysgenesis
rare female infertility due to ovarian dysgenesis
rare female infertility due to gonadal dysgenesis
female infertility due to gonadal dysgenesis
rare female infertility due to an implantation defect
female infertility due to an implantation defect
An instance of rare male infertility due to hypothalamic-pituitary-gonadal axis disorder that is caused by a modification of the individual's genome.
genetic rare male infertility due to hypothalamic-pituitary-gonadal axis disorder
rare male infertility due to gonadotropic axis disorder of genetic origin
rare male infertility due to hypothalamic-pituitary-testicular axis disorder of genetic origin
rare male infertility due to hypothalamic-pituitary-gonadal axis disorder of genetic origin
Male infertility due to impaired sperm transport of genetic origin
male infertility due to obstructive azoospermia of genetic origin
rare genetic disorder due to impaired sperm transport
Editor note: unclear how this is distinguished from parent; sib is Congenital bilateral absence of vas deferens
rare genetic disorder with obstructive azoospermia
An instance of rare female infertility due to hypothalamic-pituitary-gonadal axis disorder that is caused by a modification of the individual's genome.
genetic rare female infertility due to hypothalamic-pituitary-gonadal axis disorder
rare female infertility due to gonadotropic axis disorder of genetic origin
rare female infertility due to hypothalamic-pituitary-testicular axis disorder of genetic origin
rare female infertility due to hypothalamic-pituitary-gonadal axis disorder of genetic origin
female infertility due to an anomaly of ovarian function of genetic origin
female infertility due to an implantation defect of genetic origin
Autosomal recessive distal renal tubular acidosis (AR dRTA) is an inherited form of distal renal tubular acidosis (dRTA) characterized by hypokalemic hyperchloremic metabolic acidosis. Deafness often occurs either early or later on in life but may be absent or never be diagnosed.
autosomal recessive distal renal tubular acidosis (disease)
distal renal tubular acidosis (disease), autosomal recessive
autosomal recessive distal renal tubular acidosis
global developmental delay - lung cysts - overgrowth - Wilms tumor syndrome
Clear cell papillary renal cell carcinoma is a rare, indolent subtype of clear cell renal carcinoma, arising from epithelial cells in the renal cortex. It most frequently manifests with a well-circumscribed, well-encapsulated, unicentric, unilateral, small tumor that typically does not metastasize. Clinically it can present with flank or abdominal pain or hematuria, although most patients are usually asymptomatic at the time of diagnosis. Bilateral and/or multifocal presentation should raise the suspicion of von Hippel-Lindau syndrome.
clear cell papillary renal cell carcinoma
Acquired cystic disease-associated renal cell carcinoma is a rare subtype of renal cell carcinoma, ocurring in the context of end-stage kidney disease and acquired cystic kidney disease, characterized by a usually well circumscribed, solid, multifocal, bilateral tumor with inter- or intracellular microlumen formation (leading to cribiform architecture). Tumors are often diagnosed incidentally in early stages, although complications caused by renal cysts (dull flank or abdominal pain, fever) or renal parenchymal bleeding may mask the underlying neoplastic process. Most have an indolent behavior.
acquired cystic disease-associated renal cell carcinoma
An instance of dysostosis that is caused by a modification of the individual's genome.
dysostosis of genetic origin with limb anomaly as a major feature
rare genetic skeletal development disorder
Mild phosphoribosylpyrophosphate (PRPP) synthetase superactivity is the mild and late-onset form of PRPP synthetase superactivity, an X-linked disorder of purine metabolism associated with hyperuricemia and hyperuricosuria, leading to urolithiasis and gout. This form is not associated with any neuropathy or central nervous system (CNS) disorders.
mild phosphoribosylpyrophosphate synthetase superactivity
Severe phosphoribosylpyrophosphate (PRPP) synthetase superactivity is the severe and early-onset form of PRPP synthetase superactivity, an X-linked disorder of purine metabolism associated with hyperuricemia and hyperuricosuria, that is characterized by urolithiasis, gout and neurodevelopmental anomalies.
severe phosphoribosylpyrophosphate synthetase superactivity
Nephropathic infantile cystinosis is the most common and severe form of cystinosis, a metabolic disease characterized by an accumulation of cystine inside the lysosomes that causes damage in different organs and tissues, particularly in the kidneys and eyes.
lysosomal cystine transport protein, defect of
Renal agenesis (RA) is a form of renal tract malformation characterized by the complete absence of development of one or both kidneys (unilateral RA or bilateral RA respectively), accompanied by absent ureter(s).
May be obsoleted. The semantics of the ORDO class are not clear
rare genetic odontal or periodontal disorder
A manifestation of von Hippel-Lindau disease or other familial renal cell cancer syndromes that present as a malignant epithelial neoplasm of the kidney. It is characterized by the presence of lipid-containing clear cells within a vascular network. The tumor usually is bilateral and polycentric, and metastasizes to unusual sites. Late metastasis is common.
hereditary clear cell renal cell adenocarcinoma
hereditary clear cell renal cell carcinoma
hereditary conventional (clear cell) renal cell carcinoma
hereditary conventional renal cell carcinoma
Patent urachus is a type of congenital urachal anomaly characterized by a persistent communication between the bladder and the umbilicus, secondary to non occlusion of the urachal lumen, manifesting as clear drainage from the umbilicus.
Urachal sinus is a type of congenital urachal anomaly resulting from the failure of the umbilical end of the urachus to close, without continuity to the bladder, and that is usually asymptomatic but can present with continuous cloudy umbilical discharge, tender midline infraumbilical mass and fever when infected.
Urachal diverticulum is the rarest type of congenital urachal anomaly resulting from the failure of the distal urachus to close at its point of connectivity to the bladder that is usually asymptomatic but can be associated with recurrent urinary tract infections and other complications.
Pulmonary veno-occlusive disease and/or pulmonary capillary hemangiomatosis (PVOD and/or PCH) constitutes a rare subgroup of pulmonary arterial hypertension (PAH) characterized by obliterative fibrosis of the small pulmonary veins and venules and/or capillary infiltration of the pulmonary interstitium leading to increased pulmonary vascular resistance and right ventricular dysfunction.
pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis
Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.
Normosmic idiopathic hypogonadotropic hypogonadism
hypogonadotropic hypogonadism with or without anosmia
normosmic congenital hypogonadotropic hypogonadism
congenital idiopathic hypogonadotropic hypogonadism
isolated congenital gonadotropin deficiency
Editor note: consider obsoleting as represents a finding
genetic otorhinolaryngological malformation
Congenital urachal anomaly (CUA) describes a group of urachal remnants, found more frequently in males than females, that result from incomplete closure of the urachus (an embryological remnant of the allantois) during prenatal development, and that are usually asymptomatic (and found as an incidental finding on a radiological study) but can also present with umbilical discharge (in patent urachus or urachal sinus), infraumblical mass and pain, or with complications such as obstruction and infection. CUAs include patent urachus, urachal sinus, urachal cyst and urachal diverticulum.
ACTH-independent Cushing syndrome due to rare cortisol-producing adrenal tumor
Hereditary amyloidosis refers to a group of inherited conditions that make up one of the subtypes of amyloidosis. Hereditary amyloidosisis characterized by the deposit of an abnormal protein called amyloid in multiple organs of the body where it should not be, which causes disruption of organ tissue structure and function. In hereditary amyloidosis, amyloid deposits most often occur in tissues of the heart, kidneys, and nervous system. While symptoms of hereditary amyloidosis may appear in childhood, most individuals do not experience symptoms until adulthood. There are many types of hereditary amyloidosis associated with different gene mutations and abnormal proteins. The most common type of hereditary amyloidosis is transthyretin amyloidosis (ATTR),a condition in which the amyloid deposits are most often made up of the transthyretin protein which is made in the liver. Other examplesof hereditary amyloidosis include, but are not limited to, apolipoprotein AI amyloidosis (A ApoAI), gelsolin amyloidosis (A Gel), lysozyme amyloidosis (A Lys), cystatin C amyloidosis (A Cys), fibrinogen Aα-chain amyloidosis (A Fib), and apolipoprotein AII amyloidosis (A ApoAII). Most types of hereditary amyloidosis are inherited in an autosomal dominant manner. Treatment is focused on addressing symptoms of organ damage and slowing down the production of amyloid when possible through methods such as liver transplants.
An inherited or acquired disorder of electrolyte metabolism, characterized by the inability of the renal tubules to respond to aldosterone. It is manifested by hyperkalemic metabolic acidosis, urinary salt wasting, normal or increased aldosterone secretion and normal glomerular filtration rate.
A rare, genetic disorder in which symptoms are generally secondary to the abnormal location of the organs within the thoracic, abdominal, or peritoneal cavities. Anatomic and functional problems can include cardiac defects, intestinal malrotation leading to volvulus, biliary atresia, and various defects of the central nervous system, urinary tract, and skeleton.
rare vascular malformation of major vessels
immunodeficiency due to a complement regulatory deficiency
An instance of rare vascular tumor that is caused by a modification of the individual's genome.
lethal multiple congenital anomalies/dysmorphic syndrome
A benign neoplasm that involves the metanephros.
An instance of otorhinolaryngologic disease that is caused by a modification of the individual's genome.
Congenital hypopituitarism is characterized by multiple pituitary hormone deficiency, including somatotroph, thyrotroph, lactotroph, corticotroph or gonadotroph deficiencies, due to mutations of pituitary transcription factors involved in pituitary ontogenesis.
congenital combined pituitary hormone deficiency
non-acquired combined pituitary hormone deficiency
Jeune syndrome, also called asphyxiating thoracic dystrophy, is a short-rib dysplasia characterized by a narrow thorax, short limbs and radiological skeletal abnormalities including "trident" aspect of the acetabula and metaphyseal changes.
asphyxiating thoracic dystrophy of the newborn
short-rib thoracic dysplasia with or without polydactyly
Chondroectodermal dysplasia-like syndrome
Joubert syndrome (JS) is characterized by congenital malformation of the brainstem and agenesis or hypoplasia of the cerebellar vermis leading to an abnormal respiratory pattern, nystagmus, hypotonia, ataxia, and delay in achieving motor milestones.
Charcot-Marie-Tooth disease intermediate type
Intermediate hereditary motor and sensory neuropathy
Charcot-Marie-Tooth disease dominant intermediate
Charcot-Marie-Tooth disease recessive intermediate
intermediate Charcot-Marie-Tooth disease
COL4A1 or COL4A2-related cerebral angiopathy
COL4A1 or COL4A2-related cerebral small vessel disease
COL4A1 or COL4A2-related cerebral angiopathy with hemorrhagic tendancy
COL4A1 or COL4A2-related cerebral small vessel disease with hemorrhagic tendancy
syndromic constitutional thrombocytopenia
Urachal cyst is a congenital urachal anomaly characterized by a failure of complete closure of the urachus, in which both ends are closed but the central lumen remains patent. It is typically asymptomatic but may become clinically significant when infected, presenting as a mass in the umbilical region accompanied by abdominal pain and fever.
Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. BehC'et disease) to relatively minor skin disease.
Thrombotic thrombocytopenic purpura (TTP) is an aggressive and life-threatening form of thrombotic microangiopathy (TMA) characterized by profound peripheral thrombocytopenia, microangiopathic hemolytic anemia (MAHA) and organ failure of variable severity and is comprised of congenital TTP and acquired TTP.
Membranoproliferative glomerulonephritis (MPGN) is a chronic progressive kidney disorder characterized by glomerular capillary wall structural changes and mesangial cell proliferation leading to nephrotic syndrome, hypocomplementemia, hypertension, proteinuria and end-stage kidney disease. MPGN can be due to either idiopathic (type 1, 2 and 3 MPGN) or secondary (associated with infectious and immune complex diseases) causes.
primary membranoproliferative glomerulonephritis
MODY (maturity-onset diabetes of the young) is a rare, familial, clinically and genetically heterogeneous form of diabetes characterized by young age of onset (generally 10-45 years of age) with maintenance of endogenous insulin production, lack of pancreatic beta-cell autoimmunity, absence of obesity and insulin resistance and extra-pancreatic manifestations in some subtypes.
maturity-onset diabetes of the young (disease)
Cushing's syndrome (CS) encompasses a group of hormonal disorders caused by prolonged and high exposure levels to glucocorticoids that can be of either endogenous (adrenal cortex production) or exogenous (iatrogenic) origin.
adrenal hyperfunction resulting from pituitary ACTH excess
ectopic adrenocorticotropic hormone syndrome
nodular primary adrenocortical dysplasia
Editor mote: DOID merged this into primary hyperaldosteronism but we believe this to be wrong. Update: fixed https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/525; consider adding subclass for inherited form
Meckel syndrome (MKS) is a rare, lethal, genetic, multiple congenital anomaly disorder characterized by the triad of brain malformation mainly occipital encephalocele, large polycystic kidneys, and polydactyly as well as associated abnormalities that may include cleft lip/palate, cardiac and genital anomalies, central nervous system (CNS) malformations, liver fibrosis, and bone dysplasia.
22q11.2 deletion syndrome (DS) is a chromosomal anomaly which causes a congenital malformation disorder whose common features include cardiac defects, palatal anomalies, facial dysmorphism, developmental delay and immune deficiency.
Congenital primary megaureter (PM) is an idiopathic condition in which the bladder and bladder outlet are normal but the ureter is dilated to some extent. It may be obstructed, refluxing or unobstructed and not refluxing.
Homocystinuria without methylmalonic aciduria is an inborn error of vitamin B12 (cobalamin) metabolism characterized by megaloblastic anemia, encephalopathy and, sometimes, developmental delay, and associated with homocystinuria and hyperhomocysteinemia. There are three types of homocystinuria without methylmalonic aciduria; cblE, cblG and cblD-variant 1 (cblDv1).
functional methionine synthase deficiency
homocystinuria without methylmalonic aciduria
A genetic syndrome usually inherited as an X-link trait. It is caused by abnormalities in the COL4A5 gene. It affects males more often than females and is characterized by hematuria, progressive renal insufficiency, hearing loss, and ocular abnormalities.
Neurofibromatosis type 1 (NF1) is a clinically heterogeneous, neurocutaneous genetic disorder characterized by cafe-au-lait spots, iris Lisch nodules, axillary and inguinal freckling, and multiple neurofibromas.
Noonan Syndrome (NS) is characterised by short stature, typical facial dysmorphism and congenital heart defects.
LCAT (lecithin-cholesterol acyltransferase) deficiency is a rare lipoprotein metabolism disorder characterized clinically by corneal opacities, and sometimes renal failure and hemolytic anemia, and biochemically by severely reduced HDL cholesterol.
lecithin-cholesterol acyltransferase deficiency
An embryonal pediatric tumor of the kidney which may also be seen rarely in adults. The peak incidence of Wilms tumor is between the second and fifth year of life. Microscopically, it is composed of a mixture of cellular elements (blastemal, stromal, and epithelial). The most common sites of metastasis include the regional lymph nodes, lungs, and liver.
Progressive tubulointerstitial injury, inherited in an autosomal recessive pattern, caused by mutations in genes involved in ciliary function, which may result in an end stage renal failure.
Familial idiopathic steroid-resistant nephrotic syndrome is characterized by a nephrotic syndrome with often early onset.
familial idiopathic steroid-resistant nephrotic syndrome
An autosomal recessive form of osteopetrosis caused by mutation(s) in at least 8 genes related to osteoclast function. This condition is characterized by the failure of osteoclasts to resorb bone, resulting in impaired bone modeling/remodeling, and skeletal fragility despite increased bone mass; it is also associated with hematopoietic insufficiency, hypocalcemia, disturbed tooth eruption, nerve entrapment syndromes, and growth impairment. Some cases are also associated with progressive neurological deterioration.
autosomal recessive malignant osteopetrosis
autosomal recessive osteopetrosis (disease)
osteopetrosis (disease), autosomal recessive
Clinical conditions caused by an abnormal chromosome constitution in which there is extra or missing chromosome material (either a whole chromosome or a chromosome segment). (from Thompson et al., Genetics in Medicine, 5th ed, p429)
multiple congenital anomalies/dysmorphic syndrome
tumor of hematopoietic and lymphoid tissues
Leukodystrophies are a group of rare, progressive, metabolic, genetic diseases that affect the brain, spinal cord and often the peripheral nerves. Each type of leukodystrophy is caused by a specific gene abnormality that leads to abnormal development or destruction of the white matter (myelin sheath) of the brain. The myelin sheath is the protective covering of the nerve and nerves can't function normally without it. Each type of leukodystrophy affects a different part of the myelin sheath, leading to a range of neurological problems.
Editor note: At this time DO has two classes 'hypomyelinating leukodystrophy' and one 'leukodystrophy'
An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule.
Rare inherited disorders resulting from an enzyme defect in biochemical and metabolic pathways affecting proteins, fats, carbohydrates metabolism or organelle function.
A group of congenital disorders of lipid metabolism, caused by loss of the normal peroxisomes. Signs and symptoms include developmental delays, mental retardation, facial abnormalities, hepatomegaly, and hypotonia.
Any disease that impairs the functioning of the muscles, either directly, being pathologies of the voluntary muscle, or indirectly, being pathologies of nerves or neuromuscular junctions
A benign, intermediate, or malignant neoplasm involving the bone or articular cartilage.
rare parathyroid disease and phosphocalcic metabolism anomaly
Editor note: the original ORDO class name is 'vascular anomaly or angioma' but it is implicitly congenital due to its superclasses. TODO revise after https://github.com/Orphanet/ORDO/issues/2
Hereditary spastic paraplegias (HSP) comprise a genetically and clinically heterogeneous group of neurodegenerative disorders characterized by progressive spasticity and hyperreflexia of the lower limbs.
A disorder characterized by the localized or diffuse accumulation of amyloid protein in various anatomic sites. It may be primary, due to clonal plasma cell proliferations; secondary, due to long standing infections, chronic inflammatory disorders, or malignancies; or familial. It may affect the nerves, skin, tongue, joints, heart, liver, spleen, kidneys and adrenal glands.
Editor note: in DO this is classified as acquired metabolic, but contains familial subtypes
Brachydactyly ('short digits') is a general term that refers to disproportionately short fingers and toes, and forms part of the group of limb malformations characterized by bone dysostosis.
Steroid-sensitive nephrotic syndrome (SSNS) is a kidney disease defined by selective proteinuria, hypoalbuminaemia and, on renal biopsy, minimal changes without immunoglobulin deposits.
idiopathic steroid-sensitive nephrotic syndrome
Congenital membranous nephropathy due to maternal anti-neutral endopeptidase (NEP) alloimmunization (CMNEPA) is a glomerular disease characterized by severe renal failure and nephrotic syndrome at birth, which rapidly improve in the first weeks of life.
fetomaternal alloimmunization with antenatal glomerulopathies
neonatal glomerulopathy due to Neprilysin alloimmunization
neonatal membranous glomerulopathy with maternal NEP deficiency
neonatal membranous glomerulopathy with maternal neutral endopeptidase deficiency
congenital membranous nephropathy due to maternal anti-neutral endopeptidase alloimmunization
hypotrichosis-lymphedema-telangiectasia-membranoproliferative glomerulonephritis syndrome
hypotrichosis-lymphedema-telangiectasia-renal defect syndrome
glomerulonephritis with sparse hair and telangiectases
telangiectatic membranoproliferative glomerulonephritis
A hemorrhagic disorder due to a platelet anomaly which occurs from birth.
rare bleeding disorder due to a constitutional platelet anomaly
rare bleeding disorder due to a constitutional thrombopathy and/or thrombocytopenia
rare coagulopathy due to a constitutional platelet anomaly
rare coagulopathy due to a constitutional thrombopathy and/or thrombocytopenia
rare hemorrhagic disorder due to a constitutional platelet anomaly
rare hemorrhagic disorder due to a constitutional thrombopathy and/or thrombocytopenia
hemorrhagic disorder due to a constitutional platelet anomaly
1 mmHg). The thin septae between the veins and the collecting system in the renal fornices rupture, with resultant left sided haematuria.
An instance of nervous system disease that is caused by a modification of the individual's genome.
An instance of retinal degeneration that is caused by an inherited modification of the individual's genome.
Editor note: This class deliberately merges distinct concepts of RD and inherited RD in other ontologies, as we believe these the same
Microscopic polyangiitis (MPA) is an inflammatory, necrotizing, systemic vasculitis that affects predominantly small vessels (i.e. small arteries, arterioles, capillaries, venules) in multiple organs.
Relapsing polychondritis (RP) is a rare, clinically heterogeneous, multisystemic inflammatory disease characterized by inflammation of the cartilage and proteoglycan rich structures leading to cartilage damage with joint, ocular and cardiovascular involvement.
Polymyositis (PM) is a rare idiopathic inflammatory myopathy characterized by symmetric proximal muscle weakness and elevated muscle enzymes.
Pseudohypoaldosteronism type 1 (PHA1) is a primary form of mineralocorticoid resistance presenting in the newborn with renal salt wasting, failure to thrive and dehydration.
pseudohypoaldosteronism type I autosomal recessive
Pseudohypoaldosteronism type 2 (PHA2) is a rare inherited form of hypertension characterized by hyperkalemia, hyperchloremic metabolic acidosis, normal or elevated aldosterone, low renin, and normal renal function.
hyperkalemia-hypertension syndrome, Gordon type
mineralocorticoid resistant hyperkalemia
hyperpotassemia and hypertension familial
SchC6nlein-Henoch purpura (SHP) is a systemic IgA vasculitis that affects small vessels. It is characterized by skin purpura, arthritis, and abdominal and/or renal involvement.
Aniridia is a congenital ocular malformation characterized by the complete or partial absence of the iris. It can be isolated or part of a syndrome (isolated and syndromic aniridia).
A congenital condition that results in swelling in the arms or legs, and can occur during adolescence or adulthood. Loss of motion and pain may also accompany the swelling. Protein-rich lymphatic fluid accumulates in tissues, engorging and enlarging vessels and often causing visible swelling, tenderness, and pain. Left untreated, the affected tissues may continue to swell, and can become hardened or fibrotic and susceptible to infection.
We place OMIM:601665 here, although this includes
Rubinstein-Taybi syndrome is a rare malformation syndrome characterized by congenital anomalies (microcephaly, specific facial characteristics, broad thumbs and halluces and postnatal growth retardation), short stature, intellectual disability and behavioural characteristics.
proximal chromosome 16p13.3 deletion syndrome
disorder of amino acid and organic acid metabolism
disorder of amino acid and other organic acid metabolism
inborn disorder of amino acid and other organic acid metabolism
Retinitis pigmentosa (RP) is an inherited retinal dystrophy leading to progressive loss of the photoreceptors and retinal pigment epithelium and resulting in blindness usually after several decades.
A inherited organic acidemia that involves the brain.
An acquired metabolic disease that is has its basis in the disruption of carbohydrate metabolic process.
disorder of carbohydrate transport and metabolism
inborn carbohydrate metabolic process disorder
inborn error of carbohydrate metabolic process
inborn errors of carbohydrate metabolism
rare inborn error of carbohydrate metabolic process
disorder of amino acid absorption and transport
Editor note: consider changing to transport
inborn disorder of amino acid absorption and transport
disorder of cobalamin metabolism and transport
inborn disorder of cobalamin metabolism and transport
An acquired metabolic disease that is has its basis in the disruption of sulfur amino acid metabolic process.
cytosolic methyl group transfer or sulfur amino acid metabolism disorder
inborn error of sulfur amino acid metabolic process
inborn sulfur amino acid metabolic process disorder
rare inborn error of sulfur amino acid metabolic process
disorder of methionine cycle and sulfur amino acid metabolism
inborn disorder of methionine cycle and sulfur amino acid metabolism
An acquired metabolic disease that is has its basis in the disruption of glucose transport.
Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment, and is comprised of the phenotypic variants Zellweger syndrome (ZS), neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD).
peroxisome biogenesis disorders, Zellweger syndrome spectrum
peroxisomal biogenesis disorders, Zellweger syndrome spectrum
peroxisome biogenesis disorder-Zellweger syndrome spectrum
disorder of phenylalanin or tyrosine metabolism
inborn disorder of phenylalanin or tyrosine metabolism
An acquired metabolic disease that is has its basis in the disruption of purine nucleobase metabolic process.
inborn error of purine nucleobase metabolic process
inborn purine nucleobase metabolic process disorder
rare inborn error of purine nucleobase metabolic process
An acquired metabolic disease that is has its basis in the disruption of sterol biosynthetic process.
inborn error of sterol biosynthetic process
inborn sterol biosynthetic process disorder
rare inborn error of sterol biosynthetic process
An acquired metabolic disease that is has its basis in the disruption of generation of precursor metabolites and energy.
inborn error of generation of precursor metabolites and energy
inborn generation of precursor metabolites and energy disorder
rare inborn error of generation of precursor metabolites and energy
An inherited metabolic disorder in which harmful amounts of lipids accumulate in cells and tissues. Because of a functionally impaired hydrolase or auxiliary protein, their lipid substrates cannot be degraded, accumulate in the lysosome, and slowly spread to other intracellular membranes.
disorder of lysosomal amino acid transport
inborn disorder of lysosomal amino acid transport
inborn errors of purine-pyrimidine metabolism
inborn purine-pyrimidine metabolic disorder
disorder of purine or pyrimidine metabolism
inborn disorder of purine or pyrimidine metabolism
An inherited metabolic disorder that affects the lysosomal degradation of the spinhgolipids. Representative examples include Gaucher disease, Tay-Sachs disease, and Niemann-Pick disease.
An acquired metabolic disease that is has its basis in the disruption of sterol metabolic process.
inborn error of sterol metabolic process
inborn sterol metabolic process disorder
rare inborn error of sterol metabolic process
Vitamin B12-unresponsive methylmalonic acidemia type mut- is an inborn error of metabolism characterized by recurrent ketoacidotic comas or transient vomiting, dehydration, hypotonia and intellectual deficit, which does not respond to administration of vitamin B12.
partial deficiency of methylmalonyl-CoA mutase
vitamin B12-unresponsive methylmalonic aciduria type mut-
vitamin B12-unresponsive methylmalonic acidemia type mut-
A skin disease that involves the epidermis.
Disorders of cornification that are characterized by visible scaling and/or hyperkeratosis of most or all of the skin. Inherited ichthyoses, defined as the generalized form of Mendelian disorders of cornification, affect most or all of the skin. This etiologically and phenotypically heterogenous group of conditions is caused by mutations in various different genes important for keratinocyte differentiation and epidermal barrier function. Acquired forms of ichthyosis can be observed with certain autoimmune, inflammatory, metabolic, endocrine, or infectious diseases or with malignancies.
Epidermal keratinocytes undergo a unique form of terminal differentiation and programmed cell death known as cornification. Cornification leads to the formation of the outermost skin barrier, i.e. the cornified layer, as well as to the formation of hair and nails.
Inherited epidermolysis bullosa (EB) encompasses a number of disorders characterized by recurrent blister formation as the result of structural fragility within the skin and selected other tissues.
A epidermal appendage anomaly that involves the nail.
A nail anomaly that is part of a larger syndrome.
A epidermal appendage anomaly that involves the sebaceous gland.
epidermal appendage anomaly of sebaceous gland
sebaceous gland epidermal appendage anomaly
The term ''ectodermal dysplasia'' defines a heterogeneous group of heritable disorders of the skin and its appendages characterized by the defective development of two or more ectodermal derivatives, including hair, teeth, nails, sweat glands and their modified structures (i.e. ceruminous, mammary and ciliary glands). The spectrum of clinical manifestations is wide and may include additional manifestations from other ectodermal, mesodermal and endodermal structures.
A pigmentation disease that involves the zone of skin.
A disease that involves the superficial vasculature.
disorder of blood vessels affecting skin
Excess fluid collection in tissues, causing swelling. It is the result of obstruction of lymphatic vessels or lymph nodes.
lymphatic edema (morphologic abnormality)
Changes in the organism associated with senescence, occurring at an accelerated rate.
Milroy disease is a frequent form of primary lymphedema characterized generally by painless, chronic lower-limb lymphedema found at birth or developing in the early neonatal period.
Scleroderma is a rare autoimmune connective tissue disorder characterized by abnormal hardening of the skin and, sometimes, other organs. It is classified into two main forms: localized scleroderma and systemic sclerosis (SSc), the latter comprising three subsets; diffuse cutaneous SSc (dcSSc), limited cutaneous SSc (lcSSc) and limited SSc (lSSc).
Tuberous sclerosis complex (TSC) is a neurocutaneous disorder characterized by multisystem hamartomas and associated with neuropsychiatric features.
Adult-onset Still disease (AOSD) is a rare inflammatory multisystem disorder characterized clinically by fever of unknown origin, arthralgia or arthritis, hyperleucocytosis, and typical skin rash.
Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.
Boichis syndrome consists of the association of congenital nephronophthisis leading to renal failure, and hepatic fibrosis. It has been described in five members of one family, two of whom died from renal failure. The association of Boichis syndrome with tapetoretinal degeneration and intellectual deficit has also been reported in one family: the so-called Senior-Boichis syndrome could be in fact the same entity, and was later reported in a 12 year-old child.
nephronophthisis-hepatic fibrosis syndrome
Collagen type III glomerulopathy is a rare glomerular disease characterized by abnormal accumulation of type III collagen within the mesangium and subendothelial space of the glomerulus. Clinically it usually manifests with proteinuria (often in the nephrotic range), microscopic hematuria, peripheral edema and/or hypertension. In some cases progression to end-stage renal failure is observed.
Steroid-resistant, sporadic idiopathic nephrotic syndrome, is a heterogeneous entity. Nephrotic syndrome is characterised by marked proteinuria, with reduced plasmatic levels of albumin, and potentially with oedema.
sporadic idiopathic steroid-resistant nephrotic syndrome
Beta-thalassemia (BT) is characterized by deficiency (Beta+) or absence (Beta0) of synthesis of the beta globin chains of hemoglobin (Hb).
AL Amyloidosis is a plasma cell disorder characterized by the aggregation and deposition of insoluble amyloid fibrils derived from misfolding of monoclonal immunoglobulin light chains usually produced by a plasma cell tumor. It usually presents as primary systemic amyloidosis (PSA) with multiple organ involvement and less frequently as primary localized amyloidosis (PLA) restricted to a single organ.
Secondary amyloidosis is a form of amyloidosis, that complicates chronic inflammatory disorders (mainly rheumatoid arthritis) and is characterized by the aggregation and deposition of amyloid fibrils composed of serum amyloid A protein, an acute phase reactant. Although spleen, suprarenal gland, liver and gut are frequent sites of amyloid deposition, the clinical picture is dominated by renal involvement.
non-amyloid monoclonal immunoglobulin deposition disease
Endocrine tumours, also referred to as neuroendocrine tumours (NETs), are defined by a common phenotype which is characterized by the expression of general markers (neuron specific enolase, chromogranin, synaptophysin) and hormone secretion products. These tumours may be localized in any part of the body and are generally discovered in non-specific situations, i.e. not immediately suggestive of NETs (tests for inherited predisposition to tumours or for a clinical syndrome caused by abnormal hormone secretion).
Editor note: TODO design pattern, often NCIT uses 'neuroendocrine tumor' for particular grading with 'neuroendocrine neoplasm' as the superclass
Turner syndrome is a chromosomal disorder associated with the complete or partial absence of an X chromosome.
Editor note: consider splitting BU syndrome
A spectrum of developmental anomalies that affect the development of the anterior segment of the eyeball resulting from abnormalities of neural crest migration and differentiation during embryologic development (Axenfeld-Rieger syndrome, Peters anomaly, posterior keratoconus, and iridoschisis).
familial ocular anterior segment mesenchymal dysgenesis
Amelogenesis imperfecta (AI) represents a group of developmental conditions affecting the structure and clinical appearance of the enamel of all or nearly all the teeth in a more or less equal manner, and which may be associated with morphologic or biochemical changes elsewhere in the body.
An inherited disorder that causes a gradual loss of kidney function that eventually leads to the need for kidney transplantation or dialysis between the ages of 30 and 70, which is caused by a mutation in the UMOD gene, which leads to the build-up of the altered uromodulin protein in the tubules of the kidney, leading to slow loss of kidney function. Patients with ADTKD-UMOD have high blood levels of uric acid before kidney failure develops, and some affected individuals may develop gout.
autosomal dominant medullary cystic kidney disease type 2
UMOD-related autosomal dominant tubulointerstitial kidney disease
autosomal dominant medullary cystic kidney disease with hyperuricemia
A disease that has its basis in the disruption of heart development.
congenital non-syndromic heart malformation
rare congenital non-syndromic heart malformation
A lymphedema that is part of a larger syndrome.
Infantile Bartter syndrome with deafness, a phenotypic variant of Bartter syndrome is characterized by maternal polyhydramnios, premature delivery, polyuria and sensorineural deafness and is associated with hypokalemic alkalosis, increased levels of plasma renin and aldosterone, low blood pressure, and vascular resistance to angiotensin II.
Bartter syndrome with sensorineural deafness
infantile Bartter syndrome with sensorineural deafness
Typical hemolytic-uremic syndrome (typical HUS) is a thrombotic microangiopathy characterized by mechanical hemolytic anemia, thrombocytopenia, and renal dysfunction that is usually associated with prodromal enteritis caused by Shigella dysentriae type 1 or E. Coli.
D-plus hemolytic uremic syndrome (D+HUS)
Autosomal dominant form of intermediate Charcot-Marie-Tooth disease.
autosomal dominant intermediate Charcot-Marie-Tooth disease
intermediate Charcot-Marie-Tooth disease, autosomal dominant
autosomal dominant intermediate Charcot-Marie-Tooth
CREST syndrome is a subtype of limited cutaneous systemic sclerosis (lcSSc) whose name is an acronym for the cardinal clinical features of the syndrome: calcinosis, Raynaud's phenomenon, esophageal dysmotility, sclerodactyly and telangiectasia.
calcinosis-Raynaud phenomenon-esophageal involvement-sclerodactyly-telangiectasia syndrome
calcinosis - Raynaud phenomenon - esophageal involvement - sclerodactyly - telangiectasia
calcinosis Raynaud phenomenon sclerodactyly telangiectasia
calcinosis, Raynaud's phenomenon, esophageal dismobility, sclerodactyly, telangiectasia syndrome
calcinosis-Raynaud phenomenon-sclerodactyly-telangiectasia
phenomenon-sclerodactyly-telangiectasia, calcinosis-Raynaud
46,XY DSD due to a testosterone synthesis defect
46,XY disorder of sex development due to a testosterone synthesis defect
Fanconi syndrome (FS) is a generalized disorder of renal proximal tubule function. In adults over 50 years of age, FS is frequently related to the urinary secretion of a monoclonal immunoglobulin (Ig) light chain (LC), almost always of the kappa isotype.
acquired Fanconi syndrome secondary to monoclonal gammopathy
acquired monoclonal immunoglobulin light chain-associated Fanconi syndrome
acquired monoclonal Ig light chain-associated Fanconi syndrome
Immunotactoid or fibrillary glomerulopathy is a group of very rare glomerular diseases, composed of immunotactoid glomerulopathy (ITG) and non-amyloid fibrillary glomerulopathy (non-amyloid FGP), that are characterized by mesangial deposition of monoclonal microtubular or polyclonal fibrillar deposits. Both present clinically with nephrotic range proteinuria, hematuria and renal insufficiency leading to renal failure in many cases. ITG is more likely to manifest with underlying lymphoproliferative disease, hypocomplementemia, dysproteinemia, monoclonal gammopathy or occult cryoglobulinemia. Non-amyloid FGP is 10 times more frequent than ITG.
Immunotactoid or fibrillary glomerulonephritis
fibrillary glomerulonephritis and immunotactoid glomerulopathy
immunotactoid or fibrillary glomerulopathy
Zellweger syndrome (ZS) is the most severe variant seen in the peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS), characterized by neuronal migration defects in the brain, dysmorphic craniofacial features, profound hypotonia, neonatal seizures, and liver dysfunction.
Curator note: this refers to the severe form of Zellweger spectrum, see https://github.com/monarch-initiative/mondo-build/issues/61
Unilateral renal agenesis (URA) is a form of renal agenesis characterized by the complete absence of development of one kidney accompanied by an absent ureter.
Renal hypoplasia is a developmental anomaly in which one or both kidneys (unilateral or bilateral renal hypoplasia, respectively) have a deficit in the number of nephrons and may be small. Oligomeganephronia represents a severe variant of hypoplasia in which nephron number is reduced by 80% and nephrons are markedly hypertrophied.
Renal dysplasia is a form of renal malformation in which the kidney(s) are present but their development is abnormal and incomplete. Renal dysplasia can be unilateral or bilateral, segmental, and of variable severity, with renal aplasia corresponding to extreme dysplasia.
Congenital megacalycosis is a rare renal malformation, characterized by non-obstructive dilation of the renal calyces as well as an increased calyceal number (12-20), with a normal renal pelvis, ureter, and bladder. It may be unilateral or bilateral and is usually asymptomatic unless complicated by nephrolithiasis and urinary tract infection.
Posterior urethral valve (PUV) is the most common anomaly of fetal lower urinary tract obstruction (LUTO)and is characterized by an abnormal congenital obstructing membrane that is located within the posterior urethra associated with significant obstruction of the male bladder restricting normal bladder emptying.
Pauci-immune glomerulonephritis (GN) is one of the most frequent causes of rapidly progressive GN (RPGN). It is characterized clinically by renal manifestations of RPGN (hematuria, hypertension) leading to renal failure within days or weeks, and may be associated with manifestations of systemic vasculitis (arthralgia, fever, seizures, mono neuritis and lung involvement). Pauci-immune GN is histologically characterized by focal necrotizing and crescentic GN, with mild or absent glomerular staining for immunoglobulin and complement by fluorescence microscopy, which may manifest either as part of a systemic small vessel vasculitis (including microscopic polyangiitis, granulomatosis with polyangiitis and eosinophilic granulomatosis with polyangiitis), or rarely as part of renal-limited vasculitis (RLV, idiopathic crescentic GN). Immunologic classification is based on the presence or absence of circulating anti-neutrophil cytoplasmic antibodies (ANCAs), namely pauci-immune-GN with ANCA and pauci-immune GN without ANCA.
Transient pseudohypoaldosteronism is a renal tubulopathy characterized by renal tubular resistance to aldosterone, characterized by hyponatremia, metabolic acidosis and hyperkalemia and manifesting as dehydration, secondary to urinary tract malformation and infections in infants.
Unilateral renal dysplasia is a form of renal dysplasia (RD), a renal tract malformation in which the development of one kidney is abnormal and incomplete. Unilateral RD can be segmental, and of variable severity, with renal aplasia corresponding to extreme RD.
Bilateral renal dysplasia is a form of renal dysplasia (RD), a renal tract malformation in which the development of both kidneys is abnormal and incomplete. Bilateral RD can be segmental, and of variable severity, with renal aplasia corresponding to extreme RD.
idiopathic steroid-sensitive nephrotic syndrome with focal segmental glomerulosclerosis
idiopathic steroid-sensitive nephrotic syndrome with focal segmental hyalinosis
idiopathic steroid-sensitive nephrotic syndrome with minimal change
idiopathic steroid-sensitive nephrotic syndrome with diffuse mesangial proliferation
familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial proliferation
familial idiopathic steroid-resistant nephrotic syndrome with minimal changes
familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial sclerosis
sporadic idiopathic steroid-resistant nephrotic syndrome with focal segmental glomerulosclerosis
sporadic idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis
sporadic idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial sclerosis
polydactyly with neonatal chondrodystrophy type 2
short rib-polydactyly syndrome Majewski type
short rib-polydactyly syndrome, Majewski type
Short rib-polydactyly syndrome, Verma-Naumoff type is a short rib-polydactyly syndrome, characterized by short limb dwarfism, short ribs with thoracic dysplasia, postaxial polydactyly and protuberant abdomen. Associated multiple malformations include cardiovascular defects, renal agenesis /hypoplasia, anormal clocal development (ambiguous genitalia, anal atresia) and cerebellar hypoplasia. Short rib-polydactyly syndrome, Verma-Naumoff type follows an autosomal recessive mode of transmission. The disease is usually fatal in the perinatal period.
polydactyly with neonatal chondrodystrophy type III
short rib polydactyly syndrome Verma Naumoff type
short rib-polydactyly syndrome, Verma-Naumoff type
short-rib dysplasia (with or without polydactyly)
ciliopathies with major skeletal involvement
primary osteodysplasia with increased bone density
primary skeletal dysplasia with increased bone density
primary bone dysplasia with increased bone density
primary osteodysplasia with defective bone mineralization
primary skeletal dysplasia with defective bone mineralization
primary bone dysplasia with defective bone mineralization
lysosomal storage disease with skeletal involvement
A group of syndromes caused by genetic birth defects that may lead to the development of malignancies. It is characterized by a large body size or large body parts at birth, or excessive body growth early in childhood. Representative examples include neurofibromatosis, Beckwith-Wiedemann syndrome, and Sturge-Weber syndrome.
A urinary system disease characterized by structural malformations in the kidney and/or urinary tract containing vesicoureteral reflux.
congenital anomalies of kidney and urinary tract
congenital anomalies of the kidney and urinary tract
congenital anomaly of kidney and urinary tract
A renal or urinary tract malformation that is not part of a larger syndrome.
isolated congenital anomaly of kidney and urinary tract
nonsyndromic congenital anomaly of kidney and urinary tract
nonsyndromic renal or urinary tract malformation
isolated renal or urinary tract malformation
non-syndromic renal or urinary tract malformation
A renal or urinary tract malformation that is part of a larger syndrome.
syndrome associated with congenital anomaly of kidney and urinary tract
syndromic congenital anomaly of kidney and urinary tract
syndromic renal or urinary tract malformation
A disease involving the renal glomerulus.
Secondary glomerular diseases are conditions with glomerular pathology in which an underlying cause can be established
Type II mixed cryoglobulinemia, a relatively rare clinico-serological subtype of mixed cryoglobulinemia (MC), is an immune complex disorder characterized by purpura, weakness and arthralgia and defined immunochemically by cryoglobulins composed of polyclonal IgGs (autoantigens) and monoclonal IgM (autoantibody).
Type III mixed cryoglobulinemia, a relatively rare clinico-serological subtype of mixed cryoglobulinemia (MC), is an immune complex disorder characterized by purpura, weakness and arthralgia and defined immunochemically by cryoglobulins containing both polyclonal IgGs and polyclonal IgMs.
light and heavy chain deposition disease
Light chain deposition disease (LCDD) is a rare condition characterized by the deposition of specific proteins (monoclonal light chains) in the kidneys and other organs. Light chains are used to make antibodies that the body needs to fight infection. People with LCDD make too many light chains, which get deposited in many body tissues. While LCDD can occur in any organ, the kidneys are always involved. Signs and symptoms of LCDD may include protein in the urine ; decreased kidney function; and/or nephrotic syndrome. Rarely, a person with LCDD may have symptoms from cardiac (heart) or liver involvement. The underlying cause of LCDD is unknown. It is often associated with multiple myeloma. LCDD may progress to multiple myeloma, or it may be present with multiple myeloma when it is first diagnosed. The goal of treating LCDD is to slow the production of light chains and their damage to organs. Treatment may include chemotherapy with a drug called Bortezomib ; autologous stem cell transplantation ; immunomodulatory drugs; and/or kidney transplant. If untreated, end-stage renal disease occurs in 70% of cases.
familial amyloid nephropathy due to apolipoprotein A-I variant
familial renal amyloidosis due to apolipoprotein A-I variant
hereditary amyloid nephropathy due to apolipoprotein A-I variant
hereditary renal amyloidosis due to apolipoprotein A-I variant
familial amyloid nephropathy due to lysozyme variant
familial renal amyloidosis due to lysozyme variant
hereditary amyloid nephropathy due to lysozyme variant
hereditary renal amyloidosis due to lysozyme variant
familial amyloid nephropathy due to fibrinogen A alpha-chain variant
hereditary amyloid nephropathy due to fibrinogen A alpha-chain variant
hereditary renal amyloidosis due to fibrinogen A alpha-chain variant
An idiopathic inflammatory myopathy of childhood resulting in muscle weakness.
Dense deposit disease, a histological subtype of MPGN is an idiopathic chronic progressive kidney disorder distinguished by the presence of intra-membranous dense deposits in addition to immune complex subendothelial deposits in the glomerular capillary walls. This form often has a higher recurrence rate after a kidney transplant and is associated with extra-renal manifestations such as familial drusen.
Mesangiocapillary glomerulonephritis type 2
membranoproliferative glomerulonephritis type 2
glomerulonephritis membranoproliferative type 2
The syndromes of microangiopathic hemolytic anemia, thrombocytopenia, and variable signs of organ impairment, due to platelet aggregation in the microcirculation.
hemolytic-uremic syndrome without diarrhea with H factor anomaly
atypical hemolytic-uremic syndrome with H factor anomaly
atypical HUS with anti-factor H antibodies
hemolytic-uremic syndrome without diarrhea with anti-factor H antibodies
atypical hemolytic-uremic syndrome with anti-factor H antibodies
Acquired thrombotic thrombocytopenic purpura is the non-hereditary form of thrombotic thrombocytopenic purpura (TTP), characterized by profound peripheral thrombocytopenia, microangiopathic hemolytic anemia (MAHA) and single or multiple organ failure of variable severity.
acquired thrombotic thrombocytopenic purpura
autoimmune thrombotic thrombocytopenic purpura
idiopathic thrombotic thrombocytopenic purpura
An instance of cystic kidney disease that is caused by an inherited modification of the individual's genome.
nephropathy secondary to a storage or other metabolic disease
Any disease in which the causes of the disease is a perturbation of the renal tubule leading to its dysfunction.
hematological disorder with renal involvement
A group of disorders of the innate immune system characterized by attacks of seemingly unprovoked inflammation without significant levels of either autoantibodies or autoreactive T cells more characteristic of autoimmune disease.
Editor note: todo - investigate diseases that have autoinflammatory and autommune components, e.g. IBD, Ankylosing Spondylitis, Axial Spondyloarthropathy, perhaps adult Onset Still's Disease. Consider disjointness axiom
A disease that has its basis in the disruption of embryonic morphogenesis.
developmental defect during embryogenesis
rare developmental defect during embryogenesis
Epispadias is a congenital genitourinary malformation belonging to the spectrum of the exstrophy-epispadias complex (EEC) and is characterized in males by an ectopic meatus or a mucosal strip in place of the urethra on the penile dorsum and in females by bifid clitoris and a variable cleft of the urethra.
Editor note: consider merging with familial hypopituitarism
non-acquired pituitary hormone deficiency
secondary non-acquired combined pituitary hormone deficiency
disease associated with non-acquired combined pituitary hormone deficiency
An instance of hypopituitarism that is acquired during the lifetime of the individual.
Acro-pectoro-renal field defect is a very rare association of a Poland anomaly, that is characterized by unilateral absence or hypoplasia of the pectoralis major muscle (most frequently involving the sternocostal head) and a variable degree of ipsilateral hand anomalies (including symbrachydactyly, brachydactyly, absent thumb and hypoplastic fingers), combined with a genito-urinary anomaly. Associated genito-urinary anomalies reported include renal hypoplasia or agenesis, duplex collecting system, ureteropelvic junction obstruction, hypospadias and undescended testicles.
brachydactyly, absent pectoral muscles and agenesis/hypoplasia of kidneys
Editor note: see https://github.com/monarch-initiative/mondo-build/pull/120
pituitary hormone deficiency secondary to storage disease
An instance of primary ovarian failure that is caused by an inherited modification of the individual's genome.
Beckwith-Wiedemann syndrome due to 11p15 microduplication
Beckwith-Wiedemann syndrome due to paternal uniparental disomy of chromosome type 11
Mosaic paternal uniparental disomy of chromosome 11
Beckwith-Wiedemann syndrome due to paternal uniparental disomy of chromosome 11
rare otorhinolaryngological malformation
A muscle tissue disease characterized by congenital joint contractures of hand and feet.
arthrogryposis multiplex congenita distal
An acute inflammatory process affecting the brain parenchyma. Causes include viral infections and less frequently bacterial infections, toxins, and immune-mediated processes.
Editor note: consider merging with brain inflammation
Unilateral renal hypoplasia is a form of renal hypoplasia, a renal developmental anomaly in which one kidney is small and has a deficit in the number of nephrons present.
Bilateral renal hypoplasia is a form of renal hypoplasia, a renal developmental anomaly in which both kidneys are small and have a deficit in the number of nephrons present.
Unilateral multicystic dysplastic kidney is the form of multicystic dysplastic kidney (MCDK), a congenital anomaly of the kidney and urinary tract (CAKUT), in which one kidney is large, distended by multiple cysts, and non-functional.
unilateral multicystic dysplastic kidney
Bilateral multicystic dysplastic kidney (MCDK) is a lethal form of multicystic dysplastic kidney (MCDK), a congenital anomaly of the kidney and urinary tract (CAKUT), in which both kidneys are large, distended by non-communicating multiple cysts and non-functional.
'Renal tubular dysgenesis due to twin-twin transfusion syndrome (TTTS) is an acquired form of renal tubular dysgenesis that develops in donor fetuses due to the uneven shunting of growth factor and nutrients to the kidney of the recipient and is characterized by absent or poorly developed proximal tubules, persistent oligohydramnios and consequently the Potter sequence (facial dysmorphism with large and flat low-set ears, lung hypoplasia, arthrogryposis and limb positioning defects).'
renal tubular dysgenesis due to twin-twin transfusion
sporadic idiopathic steroid-resistant nephrotic syndrome with collapsing glomerulopathy
Pauci-immune glomerulonephritis (GN) with antineutrophil cytoplasmic antibodies (ANCA) is a form of rapidly progressive GN comprising about 90% of pauci-immune glomerulonephritis, and associated with the presence of circulating ANCA (mostly directed against proteinase-3 (PR3) and myeloperoxidase (MPO)). Patients usually present with hematuria and rapidly declining renal function, often leading to dialysis within weeks without treatment. Cutaneous, pulmonary, musculoskeletal and nervous involvement may be observed in case of systemic disease, and the correlation between ANCA titer and disease activity has been demonstrated.
pauci-immune glomerulonephritis with antineutrophil cytoplasmic antibody
pauci-immune glomerulonephritis with ANCA
Pauci-immune glomerulonephritis (GN) without antineutrophilic cytoplasmic antibodies (ANCA) is a form of rapidly progressive glomerulonephritis comprising 10-43% of pauci-immune glomerulonephritis and characterized by the absence of ANCA. In comparison with pauci-immune GN with ANCA, patients lacking ANCA may be younger at onset of the disease and have a shorter interval from onset of the disease to diagnosis. They have fewer extra renal manifestations (e.g. involvement of lung, eye, ear, nose and throat), fewer constitutional symptoms (e.g. fever, weight loss, muscle pain and arthralgia) and a high prevalence of nephrotic syndrome and chronic renal lesions. Their prognosis is generally poorer.
antineutrophil cytoplasmic antibody-negative pauci-immune glomerulonephritis
pauci-immune glomerulonephritis without antineutrophil cytoplasmic antibody
pauci-immune glomerulonephritis without ANCA
Non-amyloid fibrillary glomerulopathy (non-amyloid FGP) is a rare cause of glomerulonephritis (GN) characterized by glomerular accumulation of non-amyloid fibrils in the mesangium and the glomerular (and rarely tubular) basement membrane, that mainly presents with renal insufficiency, micro-hematuria and nephrotic range proteinuria. Non-amyloid FGP and immunotactoid glomerulopathy (ITG) are often grouped together as pathogenetically related diseases.
Congo red-negative amyloidosis-like glomerulopathy
non-amyloid fibrillary glomerulonephritis
Immunotactoid glomerulopathy (ITG) is a very rare condition characterized by glomerular accumulation of microtubules in the mesangium and the glomerular basement membrane, that mainly presents with proteinuria, micro-hematuria, nephrotic syndrome, renal insufficiency and hematologic malignancy. ITG and non-amyloid fibrillary glomerulopathy (non-amyloid FGP) are often grouped together as pathogenetically related diseases.
Pseudohypoparathyroidism (PHP) is a heterogeneous group of endocrine disorders characterized by normal renal function and resistance to the action of parathyroid hormone (PTH), manifesting with hypocalcemia, hyperphosphatemia and elevated PTH levels and that includes the subtypes PHP type 1a (PHP-1a), PHP type 1b (PHP-1b), PHP type 1c (PHP-1c), PHP type 2 (PHP-2) and pseudopseudohypoparathyroidism (PPHP).
A narrowing of renal arteries that is present since birth.
Editor note: todo. ORDO includes vasculitis here but this is not normally included in the SARDs
rare disease with odontological manifestation
rare neurologic disease with psychiatric involvement
visceral malformation of the liver, biliary tract, pancreas or spleen
diaphragmatic or abdominal wall malformation
Differences of sex development in individuals with 46,XY karyotype.
syndrome with 46,XY disorder of sex development
autosomal recessive congenital cerebellar ataxia
autosomal recessive metabolic cerebellar ataxia
A chromosomal anomaly that involves an autosome.
A chromosomal abnormality consisting of the presence of one chromosome in addition to the normal diploid number.
Dysmorphologic diseases with phakomatosis
The Ehlers–Danlos syndromes (EDS) are a clinically and genetically heterogeneous group of heritable connective tissue disorders (HCTDs) characterized by joint hypermobility, skin hyperextensibility, and tissue fragility.
A epilepsy syndrome that occurs during childhood.
This type of grouping class represents an older way of classifying diseases, and represented here https://www.epilepsydiagnosis.org/index.html.
A rare group of disorders characterized by the development of myoclonic and tonic-clonic epileptic seizures associated with progressive degeneration of the nervous system.
progressive myoclonic epilepsy (disorder) [ambiguous]
Male infertility due to impaired sperm transport
male infertility due to obstructive azoospermia
A group of inherited hemolytic anemias caused by erythrocyte membrane defects. This includes hereditary pyropoikilocytosis, hereditary spherocytosis and hereditary elliptocytosis.
hemolytic anemia due to erythrocyte membrane defect
rare constitutional hemolytic anemia due to a red cell membrane anomaly
constitutional hemolytic anemia due to membrane defect
constitutional megaloblastic anemia due to vitamin B12 metabolism disorder
vitamin B12- and folate-independent constitutional megaloblastic anemia
A syndromic intellectual disability with an X-linked mode of inheritance.
intellectual disability, X-linked syndromic
syndromic X-linked intellectual disability
syndromic intellectual disability, X-linked
X-linked syndromic intellectual disability
A disease involving the skeletal muscle tissue.
disease or disorder of skeletal muscle tissue
skeletal muscle tissue disease or disorder
An umbrella term for diseases which have chronic muscle inflammation and weakness of unknown etiology. The types of idiopathic inflammatory myopathy are further defined by either clinicopathologic criteria or by the presence of certain autoantibodies.
idiopathic inflammatory myopathy, familial
A aniridia that is part of a larger syndrome.
rare eye disease due to a differentiation anomaly
A congenital abnormality characterized by the presence of a continuous layer of skin extending over the eyeballs and the absence of eyelids and the palpebral fissure.
anomaly of the secretory and excretory apparatus of the lacrimal system
A hereditary disease that is associated with congenital ocular anomalies such as conditions associated with mesodermal dysgenesis of the neural crest, phakomatoses characterized by hamartomas, metabolic disorders, mitotic disorders, and other congenital disorders and associated with acquired conditions such as tumors, uveitis, and trauma.
glaucoma associated with neural crest cell migration anomaly
secondary dysgenetic glaucoma associated with neural crest cell migration anomaly
rare disease with glaucoma as a major feature
A cataract (disease) that is part of a larger syndrome.
syndrome associated with cataract (disease)
cataract associated with a metabolic disease
A retinitis pigmentosa that is part of a larger syndrome.
syndrome associated with retinitis pigmentosa
Macular dystrophy that is related to a change in a gene.
unclassified primitive or secondary maculopathy
rare strabismus and restriction syndrome
Oculomotor palsy that arises from lesions in the supranuclear pathways controlling extraocular movement.
Editor note: TODO review literature. Consider relationship to ocular nerve, supranuclear pathway includes other nerves
oculomotor apraxia or related oculomotor disease
connective tissue disease with eye involvement
onycho-patellar syndrome with eye involvement
metabolic disease associated with ocular features
metabolic disease with pigmentary retinitis
An inflammatory process affecting a part of or the entire uvea. Causes include inflammatory agents (e.g., herpes simplex, herpes zoster, leptospirosis) and systemic diseases (e.g., inflammatory bowel disease, multiple sclerosis, systemic lupus erythematosus, ankylosing spondylitis). Patients present with pain and redness in the eye, light sensitivity, and blurred and decreased vision.
transposition of the great arteries and conotruncal cardiac anomaly
congenital aorta, aortic arch or pulmonary arteries anomaly
congenital anomaly of the great arteries
Noonan syndrome and Noonan-related syndrome
Editor note: add qualifier for mosaicism
Turner syndrome due to structural X chromosome anomalies
rare familial disorder with hypertrophic obstructive cardiomyopathy
rare familial disorder with hypertrophic subaortic stenosis
rare familial disorder with hypertrophic cardiomyopathy
Adrenocorticotropic hormone (ACTH) independent Cushing syndrome is a form of endogenous Cushing syndrome (CS) that may result from excess secretion of cortisol by either a unilateral and benign (adrenocortical adenoma: 55-60%) or malignant (adrenocortical carcinoma: 35-40 %) adrenocortical tumor or by bilateral adrenal secretion by macronodular adrenal hyperplasia (AIMAH), as an isolated disease or as part of McCune-Albright syndrome (MAS), or by primary pigmented nodular adrenocortical disease (PPNAD), as an isolated disease or as part of Carney complex (CNC).
adrenocorticotropic hormone-independent Cushing syndrome
corticotropin-independent Cushing syndrome
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
A tumor with perivascular epithelioid cell differentiation characterized by the absence of pleomorphism and scarcity or absence of mitotic figures.
benign neoplasm with perivascular epithelioid cell differentiation
neoplasm with perivascular epithelioid cell differentiation, benign
Infection due to organisms from the genus Mycobacteria.
A disease or disorder that involves the retroperitoneal space.
disease or disorder of retroperitoneal space
retroperitoneal space disease or disorder
A syndrome resulting from the inadequate absorption of nutrients in the small intestine. Symptoms include abdominal pain, bloating, and diarrhea.
Any Simpson-Golabi-Behmel syndrome in which the cause of the disease is a mutation in the GPC3 gene.
Simpson-Golabi-Behmel syndrome caused by mutation in GPC3
Any Liddle syndrome in which the cause of the disease is a mutation in the SCNN1B gene.
Liddle syndrome caused by mutation in SCNN1B
A chromosomal abnormality consisting of the absence of one chromosome from the normal diploid number.
A benign or malignant, primary or metastatic neoplasm involving the respiratory tract.
A usually autosomal dominant and less frequently autosomal recessive genetic disorder characterized by the presence of numerous cysts in the kidneys leading to end-stage renal failure. The autosomal dominant trait is associated with abnormalities on the short arm of chromosome 16. Symptoms in patients with the autosomal dominant trait usually appear at middle age and include abdominal pain, hematuria, and high blood pressure. Patients may develop brain aneurysms and liver cysts. Patients with the autosomal recessive trait present with progressive renal failure early in life and symptoms resulting from hepatic fibrosis. The autosomal recessive trait is associated with abnormalities of chromosome 6. Polycystic kidney disease may also result as a side effect in patients on renal dialysis.
A transitional cell carcinoma that arises from the renal pelvis and ureter.
renal pelvis and ureter transitional cell cancer
renal pelvis and ureter transitional cell carcinoma
renal pelvis and ureter urothelial carcinoma
transitional cell cancer of renal pelvis and ureter
transitional cell cancer of the renal pelvis and ureter
transitional cell carcinoma of renal pelvis and ureter
urothelial carcinoma of the renal pelvis and ureter
renal pelvis/ureter urothelial carcinoma
central nervous system or retinal vascular disease
Editor note: even though retinal diseases may be located outside the CNS, they are often indicators of CNS disease
disease of central nervous system or retinal vasculature
Disease having a short and relatively severe course.
A disease characterized by low serum levels of vitamin B12, either inherited or acquired.
pulmonary venoocclusive disease 1, autosomal dominant
An inherited disorder that causes a gradual loss of kidney function, caused by a mutation in the MUC1 gene that leads to production of an abnormal mucin 1 protein, which deposits in the kidney and leads to slow loss of kidney function.
MUC1-related autosomal dominant medullary cystic kidney disease
autosomal dominant medullary cystic kidney disease without hyperuricemia
autosomal dominant tubulointerstitial kidney disease due to mutations in MUC1
medullary cystic kidney disease, autosomal dominant
MUC1-related autosomal dominant tubulointerstitial kidney disease
autosomal recessive infantile hypercalcemia 1
Note that this encompasses both syndromic and non-syndromic types.
HYPOMAGNESEMIA, SEIZURES, AND MENTAL RETARDATION 1
hypomagnesemia, seizures, and intellectual disability 1
HYPOMAGNESEMIA, SEIZURES, AND MENTAL RETARDATION 2
hypomagnesemia, seizures, and intellectual disability 2
vertebral, cardiac, renal, and limb defects syndrome
congenital vertebral-cardiac-renal anomalies syndrome
Any Liddle syndrome in which the cause of the disease is a mutation in the SCNN1G gene.
Liddle syndrome caused by mutation in SCNN1G
A disease characterized by the presence of brachydactyly, including syndromic and non-syndromic forms.
A disease caused by disturbed function of ion channel subunits or the proteins that regulate them.
An instance of epidermal appendage anomaly that is caused by a modification of the individual's genome.
An instance of nail anomaly that is caused by a modification of the individual's genome.
An instance of sebaceous gland anomaly that is caused by a modification of the individual's genome.
A neoplasm composed of at least two distinct cellular populations.
A benign, borderline, or malignant neoplasm characterized by the presence of an epithelial and a fibrous component. Representative examples are fibroadenoma and phyllodes tumor.
A sarcoma that arises from the bone. Representative examples are osteosarcoma and chondrosarcoma.
A broad classification for disorders in which the development of neoplasms typically occur in association with a characteristic set of signs or symptoms. These disorders may be inherited or acquired.
Any disease or disorder affecting the head and/or neck region.
craniocervical region disease or disorder
disease or disorder of craniocervical region
The RASopathies are developmental syndromes caused by germline mutations (or in rare cases by somatic mosaicism) in genes that alter the Ras subfamily and mitogen-activated protein kinases that control signal transduction.
disorder of Ras protein signal transduction
A hereditary neoplastic syndrome in which tumors grow in the nervous system. There are typically 3 main types recognized, but other forms with uncertain etiology exist.
A benign or malignant, primary or metastatic neoplasm involving the urinary system. --2003
Editor note: note the ONCOTREE class is more general than just bladder
A malignant neoplasm affecting the endocrine glands. Representative examples include thyroid gland carcinoma, parathyroid gland carcinoma, pituitary gland carcinoma, and adrenal cortex carcinoma.
malignant neoplasm of the endocrine gland
A pathological process with signs indicating it may become cancerous. Representative examples include leukoplakia, dysplastic nevus, actinic keratosis, xeroderma pigmentosum, and intraepithelial neoplasia.
Editor note: check classification. Also consider changing def, NCIT defines as disease. Also consider a grouping for this and paraneoplastic syndrome
A benign or malignant neoplasm arising during childhood.
A neoplasm arising from arteries or veins.
Any cranioectodermal dysplasia in which the cause of the disease is a mutation in the IFT122 gene.
cranioectodermal dysplasia caused by mutation in IFT122
Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.
An endophytic lesion in the urinary tract which shares several morphologic features with urothelial papilloma. This lesion may recur after complete excision. Transitional cell carcinomas may arise within inverted urothelial papillomas.
A benign or malignant, primary or metastatic neoplasm involving the lungs. Representative examples of benign neoplasms include adenoma, papilloma, chondroma, and endobronchial lipoma. Representative examples of malignant neoplasms include carcinoma, carcinoid tumor, sarcoma, and lymphoma.
Diminished or absent ability of a female to achieve conception.
female reproductive system infertility disorder
infertility disorder of female reproductive system
An characteristic of a disease that varies depending on whether the disease appears as an isolated feature or whether the disease is a syndrome consisting of multiple features.
An characteristic of a disease in which the disease is not manifested as an isolated feature but has multiple distinct features.
An characteristic of a disease in which the disease is manifested as an isolated feature.
A disease or disorder is defined as rare in Europe when it affects fewer than 1 in 2000. A disease or disorder is defined as rare in the USA when it affects fewer than 200,000 persons at any given time. Here we take the European definition to be consistent with Orphanet.
A characteristic of a disease in which the disease is present at birth, regardless of cause.
A disease that involves the genitourinary system.
disease or disorder of genitourinary system
genitourinary system disease or disorder
Any disease or disorder that disrupts the process development of an anatomical structure. Can be due to genetic or environmental causes. Typically happens during embryogenesis, but also includes post-embryonic development.
disorder of development or morphogenesis
A benign, precancerous, or malignant neoplasm that affects the female reproductive system. Representative examples include uterine corpus leiomyoma, endocervical polyp, ovarian carcinoma, cervical carcinoma, and endometrial carcinoma.
female reproductive organ neoplasm (disease)
female reproductive system neoplasm (disease)
neoplasm of the female reproductive system
A characteristic of a disease in which the cause of the disease is a genetic problem inherited from either or both parents.
A benign or malignant neoplasm affecting the kidney. Representative examples of benign renal neoplasms include fibroma, lipoma, oncocytoma, and juxtaglomerular cell tumor. Representative examples of malignant renal neoplasms include renal cell carcinoma, renal pelvis carcinoma, Wilms tumor, rhabdoid tumor, sarcoma, and lymphoma.
A disease involving a pathogenic inflammatory response in the anatomical structure.
An inflammatory disease involving a pathogenic inflammatory response in the muscle tissue.
inflammatory disorder of muscle (disorder)
Disorders caused by imbalances in the protein homeostasis network - synthesis, folding, and transport of proteins; post-translational modifications; and degradation or clearance of misfolded proteins.
A disease that has its basis in the disruption of intestinal motility.
A disease that has its basis in the disruption of DNA repair.
A grouping of diseases based on molecular activity, cellular process or subcellular component.
A disease that disrupts the functioning of an organ system.
A neoplasm (disease) that involves the adrenal gland.
A neoplasm (disease) that involves the uterine cervix.
A neoplasm (disease) that involves the urethra.
A neoplasm (disease) that involves the nervous system.
A in situ carcinoma that involves the renal pelvis.
stage 0is carcinoma of the kidney pelvis
stage 0is kidney renal pelvis urothelial cancer
stage 0is renal pelvis urothelial carcinoma
stage 0is renal pelvis urothelial carcinoma aJCC v7
A cancer that involves the adrenal cortex.
malignant neoplasm of the adrenal cortex
A neoplasm (disease) that involves the thoracic segment of trunk.
thoracic segment of trunk neoplasm (disease)
A neoplasm (disease) that involves the uterus.
A neoplasm (disease) that involves the adipose tissue.
A neoplasm (disease) that involves the parathyroid gland.
A benign neoplasm that involves the zone of skin.
A benign neoplasm that involves the renal pelvis.
A benign neoplasm that involves the adrenal gland.
A hamartoma (disease) that involves the lung.
A benign or malignant mesenchymal neoplasm arising from smooth, skeletal, or cardiac muscle.
A disease that involves the renal tubule.
Neoplasms composed of connective tissue, including elastic, mucous, reticular, osseous, and cartilaginous tissue. The concept does not refer to neoplasms located in connective tissue.
That disease that arises from defects in the development of tissues containing cells commonly derived from the embryonic neural crest cell lineage.
disorder of neural crest cell development
Virus diseases caused by the bunyaviridae.
A Disease due to or propagated by sexual contact.
Viral diseases which are potentially transmitted or propagated by sexual conduct.
Pus within the collecting system of the kidney.
An autosomal recessive, oculo-reno-skeletal syndrome characterized by bilateral atypical macular coloboma, familial juvenile nephronophthisis and mesomelic skeletal dysplasia of upper limbs with bilateral radiohumeral fusion.
atypical macular coloboInOwlma, familial juvenile nephronophthisis and skeletal abnormality
corneal crystals myopathy and nephropathy
corneal crystals myopathy and neuropathy
A disorder characterized by the partial or complete loss of the ability to detect sounds due to damage to the ear structures or inability of the brain to properly interpret or process the auditory signals it receives from the anatomic structures of the ear.
This modifier may be obsoleted in favor of MAO
Editor note: see https://github.com/monarch-initiative/mondo-build/issues/75
kidney disease caused by BK polyomavirus
Degeneration of the cerebellum. It may be an inherited condition, a paraneoplastic syndrome, or secondary to autoimmune disorders.
Fanconi syndrome, ichthyosis, dysmorphism, jaundice and diarrhoea
Diabetes insipidus caused by excessive intake of water due to psychological factors or damage to the thirst-regulating mechanism.
A form of diabetes insipidus that manifests during pregnancy (or in some cases, after pregnancy). It is characterized by theappearance of a polyuric-polydipsic syndrome that resultsin fluid intake ranging from 3 to 20 L/day. It is also charac-terized by excretion of abnormally high volumes of dilutedurine. This polyuria is insipid, i.e., the urine concentrationof dissolved substances is very low.
Any glycogen storage disease due to glucose-6-phosphatase deficiency in which the cause of the disease is a mutation in the SLC37A4 gene.
glucose-6-phosphate translocase deficiency
glycogen storage disease I caused by mutation in SLC37A4
This class may be deprecated in future. There are two types of GSDI: glycogen storage disease type Ia (GSDIa) and glycogen storage disease type Ib (GSDIb). Two other forms of GSDI have been described, and they were originally named types Ic and Id. However, these types are now known to be variations of GSDIb; for this reason, GSDIb is sometimes called GSD type I non-a. https://ghr.nlm.nih.gov/condition/glycogen-storage-disease-type-i
glycogen storage disease type 1 due to SLC37A4 mutation
Cystic hamartoma of lung and kidney is a rare developmental malformation reported in 3 patients characterized by the presence of benign hamartomatous cysts in kidney and lung, clinically presenting as abdominal mass. Others associated features include hyperplastic nephromegaly, medullary dysplasia and mesoblastic nephroma. There have been no further descriptions in the literature since 1987.
A disease that involves the facial skeleton.
Either an isolated neoplasm or a syndrome with neoplasm as a major feature.
Editor note: TODO https://www.ncbi.nlm.nih.gov/pubmed/2325105
C1q nephropathy is a kidney disease in which a large amount of protein is lost in the urine. It is one of the many diseases that can cause the nephrotic syndrome.
An inherited genetic disorder that affects the connective tissues. Representative examples include Ehlers-Danlos syndrome and Marfan syndrome.
An inherited disorder characterized by progressive degeneration and atrophy of the nervous system.
A disease that has its basis in the disruption of cardiovascular system development.
cardiovascular system development disease
congenital Abnormality of the circulatory system
congenital anomaly of cardiovascular system
disorder of cardiovascular system development
An instance of skin disease that is caused by a modification of the individual's genome.
A benign, intermediate, or malignant neoplasm arising from vascular tissue including arteries, veins, venous sinuses, lymphatic vessels, arterioles and capillaries. It may occur in essentially any body location and is characterized by the presence of vascular channel formation and endothelial cells.
Editor note: consider expanding to include endocrine
A disorder that is caused by the deficiency of a vitamin. The deficiency may result from either suboptimal vitamin intake or conditions that prevent the vitamin's use or absorption in the body. Representative examples include beriberi caused by thiamine deficiency, scurvy caused by vitamin C deficiency, and rickets caused by vitamin D deficiency.
An inherited disorder that causes calcium and other minerals to accumulate in the elastic fibers of the skin, eyes, and blood vessels, and less frequently in other areas such as the digestive tract.
pseudoxanthoma elasticum (inherited or acquired)
A disease that has its basis in the disruption of GPI anchor biosynthetic process.
disorder of GPI anchor biosynthetic process
glycosylphosphatidylinositol biosynthesis defect
A disease that has its basis in the disruption of glycosylation.
Impairment of the renal function due to chronic kidney damage.
transitional cell neoplasm of the urinary tract
Cognitive disorders characterized by an impaired ability to perceive the nature of objects or concepts through use of the sense organs. These include spatial neglect syndromes, where an individual does not attend to visual, auditory, or sensory stimuli presented from one side of the body.
A disease that involves the visual system.
A disease that involves the cutaneous appendage.
disease or disorder of cutaneous appendage
A modifier that can be applied to a tumor class describing abnormal tumor histology or morphology. It is an indicator of how quickly a tumor is likely to grow and spread
A term that refers to the cellular differentiation of a malignant cellular infiltrate. A cancer is defined through grades I-IV (or 1-4), or as well, moderately, poorly differentiated or undifferentiated.
A morphologic qualifier indicating that a cancerous lesion is well differentiated.
A morphologic qualifier indicating that a cancerous lesion is moderately differentiated.
A morphologic qualifier indicating that a cancerous lesion is poorly differentiated.
A morphologic qualifier indicating that a cancerous lesion is undifferentiated.
tumor grade 1 or 2, general grading system
A morphologic qualifier indicating that a neoplastic lesion is moderately to poorly differentiated.
tumor grade 2 or 3, general grading system
Used to describe tumor samples that exhibit poorly differentiated or undifferentiated cells. They are generally expected to be fast growing and aggressive.
tumor grade 3 or 4, general grading system
A broad grouping of diseases based on major body subdivisions.
renal dysplasia, megalocystis, and sirenomelia
Any primary pulmonary hypertension in which the cause of the disease is a mutation in the BMPR2 gene.
primary pulmonary hypertension caused by mutation in BMPR2
pulmonary hypertension, primary, 1, with hereditary hemorrhagic telangiectasia
pulmonary hypertension, primary, Dexfenfluramine-associated
pulmonary hypertension, primary, Fenfluramine-associated
A non-neoplastic or neoplastic disorder arising as a result of the immunologic defects caused by Autoimmune deficiency Syndrome.
AIDS/HIV - relatedDisease associated with AIDS
A non-neoplastic or neoplastic disorder that develops in a patient with immunodeficiency. Representative examples include AIDS-related disorders and disorders that develop following organ transplantation.
Hypertrophic cardiomyopathy caused by mutations in the genes encoding components of the sarcomere, in the absence of predisposing conditions.
A disorder that is related to pregnancy. Representative examples include ectopic pregnancy, toxemia of pregnancy, and gestational trophoblastic tumor.
disorder of pregnancy, childbirth, or puerperium
Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases.
Kidney damage that results from chronically elevated blood pressure; complications include glomerular damage resulting in proteinuria and hematuria.
A malignant neoplasm arising exclusively from the soft tissues.
A benign or malignant neoplasm that affects the retroperitoneum.
A non-neoplastic or neoplastic disorder that affects structures of the skull.
A hypertensive disorder that develops during pregnancy.
hypertension associated disorders of pregnancy
hypertension-associated pregnancy disorder
Wilms tumor of the kidney which occurs in adults.
A Wilms tumor of the kidney which occurs in children.
A mixed epithelial stromal tumor of the kidney with malignant stromal features.
malignant mixed epithelial stromal tumor of the kidney
mixed epithelial stromal tumor of the kidney, malignant
A benign or malignant neoplasm that affects the heart and/or vessels. Representative examples of benign neoplasms include atrial myxoma, hemangioma, and lymphangioma. Representative examples of malignant neoplasms include pericardial malignant mesothelioma and angiosarcoma.
An epithelial neoplasm of the female reproductive system arising from mesonephric remnants.
A benign epithelial neoplasm of the female reproductive system arising from mesonephric remnants.
Mesonephroma, benign (morphologic abnormality)
Tumors or cancer of the urogenital system in either the male or the female.
An instance of neuroendocrine neoplasm that is caused by an inherited modification of the individual's genome.
Any congenital anomaly of kidney and urinary tract in which the cause of the disease is a mutation in the TBX18 gene.
TBX18 congenital anomaly of kidney and urinary tract
congenital anomalies of kidney and urinary tract type 2
congenital anomaly of kidney and urinary tract caused by mutation in TBX18
congenital anomalies of kidney and urinary tract 2
Disorders caused by the intentional or unintentional ingestion or exposure to chemical substances such as pharmaceutical preparations; noxae; and pesticides.
Fanconi Renotubular Syndrome, Acadian Variant
VERTEBRAL, CARDIAC, RENAL, AND LIMB DEFECTS SYNDROME 3
A variant of Wilms tumor of the kidney characterized by the presence of cystic spaces separated by septa. The septa contain immature epithelial cells, immature stromal cells, and blastema cells. Surgical resection is usually curative.
cystic partially differentiated nephroblastoma
An autoimmune form of glomerulonephritis (disease).
CONGENITAL ANOMALIES OF KIDNEY AND URINARY TRACT 3
A autosomal dominant polycystic kidney disease that has material basis in mutation in the PKD4 gene.
polycystic kidney disease 4 with or without hepatic disease
polycystic kidney disease 4 with or without polycystic liver disease
polycystic kidney disease, infantile, type 1
primary adrenal insufficiency-steroid-resistant nephrotic syndrome due to SGPL1 deficiency
familial steroid-resistant nephrotic syndrome with adrenal insufficiency
Any polycystic kidney disease in which the cause of the disease is a mutation in the DZIP1L gene.
polycystic kidney disease caused by mutation in DZIP1L
short-rib thoracic dysplasia 19 with or without polydactyly
infection-related hemolytic uremic syndrome
atypical Fanconi syndrome-neonatal hyperinsulinism syndrome
short-rib thoracic dysplasia 18 with polydactyly
A malignant neoplasm that affects the kidney and occurs in childhood.
A benign or malignant (primary or metastatic) neoplasm affecting the adrenal cortex. (NCI05)
A neoplasm arising from the epithelial cells. It is characterized by the absence of morphologic features associated with malignancy (severe cytologic atypia, tumor cell necrosis, and high mitotic rate). Benign epithelial neoplasms remain confined to the original site of growth and only rarely metastasize to other anatomic sites.
A disease that has its basis in the disruption of carbohydrate metabolic process.
disorder of carbohydrate metabolic process
A disease that has its basis in the disruption of porphyrin-containing compound metabolic process.
disorder of porphyrin-containing compound metabolic process
porphyrin-containing compound metabolic process disease
disorder of porphyrin and heme metabolism
A disease that has its basis in the disruption of purine nucleobase metabolic process.
disorder of purine nucleobase metabolic process
purine nucleobase metabolic process disease
A disease that has its basis in the disruption of cellular amino acid metabolic process.
cellular amino acid metabolic process disease
disorder of cellular amino acid metabolic process
An instance of auditory system disease that is caused by an inherited modification of the individual's genome.
A carcinoma that is not confined to the epithelium, and has spread to the surrounding stroma.
A invasive carcinoma that involves the urothelium.
infiltrating transitional cell carcinoma of the urinary tract
A malignant neoplasm derived from the transitional epithelium of the urinary tract (urinary bladder, ureter, urethra, or renal pelvis). It is frequently papillary.
transitional cell carcinoma of the urinary tract
transitional cell carcinoma of the urothelial tract
A form of polydipsia characterised by excessive fluid intake in the absence of physiological stimuli to drink.
Acute form of kidney papillary necrosis.
A constitution or condition of the body which makes the tissues react in special ways to certain extrinsic stimuli and thus tends to make the individual more than usually susceptible to certain diseases.
An instance of osteosclerosis that is caused by an inherited modification of the individual's genome.
A condition due to deficiency in any member of the vitamin B complex. These B vitamins are water-soluble and must be obtained from the diet because they are easily lost in the urine. Unlike the lipid-soluble vitamins, they cannot be stored in the body fat.
A group of disorders characterized by ectodermal-based malformations and neoplastic growths in the skin, nervous system, and other organs.
A number of genetic and acquired diseases come in this category and may affect one or more of these tissues. However, in some conditions, such as von Hippel-Lindau disease, ectodermal presentation is minimal. Editor note: Phakomatoses are inconsistently defined, and there is a lack of consensus about what conditions are included in this category
An instance of multiple congenital anomalies/dysmorphic syndrome that is caused by an inherited modification of the individual's genome.
hereditary multiple congenital anomalies/dysmorphic syndrome
genetic multiple congenital anomalies/dysmorphic syndrome
An instance of multiple congenital anomalies/dysmorphic syndrome-variable intellectual disability syndrome that is caused by an inherited modification of the individual's genome.
genetic multiple congenital anomalies-variable intellectual disability with or without dysmorphism syndrome
hereditary multiple congenital anomalies/dysmorphic syndrome-variable intellectual disability syndrome
genetic multiple congenital anomalies/dysmorphic syndrome-variable intellectual disability syndrome
An instance of multiple congenital anomalies/dysmorphic syndrome without intellectual disability that is caused by an inherited modification of the individual's genome.
genetic multiple congenital anomalies without intellectual disability (with or without dysmorphism)
hereditary multiple congenital anomalies/dysmorphic syndrome without intellectual disability
genetic multiple congenital anomalies/dysmorphic syndrome without intellectual disability
An instance of lethal multiple congenital anomalies/dysmorphic syndrome that is caused by an inherited modification of the individual's genome.
hereditary lethal multiple congenital anomalies/dysmorphic syndrome
genetic lethal multiple congenital anomalies/dysmorphic syndrome
CNS disorder characterized by severe behavioral retardation, hypotonia, inability to talk, marked tremors, gait disturbances and inability to concentr
neuroaxonal dystrophy renal tubular acidosis
hereditary renal disease and preauricular pits
familial infantile nephrotic syndrome with ocular abnormalities
renal dysplasia or hydronephrosis, oligohydramnios and subsequent lung hypoplasia due to urethral obstruction
A disorder of the nervous system related to a vascular etiology.
Amyopathic dermatomyositis is a form of dermatomyositis characterized by the presence of typicalskin findingswithout muscle weakness.Some of the skinchanges that suggest dermatomyositis include a pink rash on the face, neck, forearms and upper chest; Gottron's papules and heliotrope eyelids. Pruritis and photosensitivity are common, as is scalp inflammation and thinning of the hair.While patients with amyopathic dermatomyositis should not have clinically evident muscle weakness, minor muscle abnormalities may be included.Fatigue is reported in at least 50% of patients. Some cases have beenassociated with internal malignancy and/or interstitial lung disease. Treatment may include sun avoidance, ample use of sunscreen, topical corticosteroids, antimalarial agents, methotrexate, mycophenolate mofetil, or intravenous (IV) immunoglobulin.
A viral, bacterial, fungal, or parasitic infectious process that affects the digestive system.
A non-neoplastic or neoplastic disorder which results from exposure to radiation. Examples of non-neoplastic disorders include dermatitis, enteritis, stomatitis, pneumonitis, and cerebritis. Examples of neoplastic disorders include myelodysplastic syndromes, leukemias, and sarcomas.
An infectious process caused by adenovirus. The virus may cause respiratory illness, conjunctivitis, gastroenteritis, and cystitis.
Editor note: check adenovirus vs adenoviridae
An inflammatory process affecting an artery.
A medical condition characterized by major shock and renal failure after a crushing injury to skeletal muscle.
acute renal failure due to rhabdomyolysis
Purpura associated with a reduction in circulating blood platelets which can result from a variety of factors.
Inflammation that includes the brain, spinal cord and surrounding tissues secondary to systemic lupus erythematosus (SLE); it is associated with neurological and/or psychiatric features.
central nervous system systemic lupus Erythematosis
neuropsychiatric systemic lupus erythematosus
systemic lupus Erythematosis, central nervous system
A manifestation of systemic lupus erythematosus with a widespread vesiculobullous eruption.
Any disease affecting the vitreous body of the eye.
The inheritance of only one mutated beta-globin allele (beta+ or beta0).
BBS21 is an autosomal recessive ciliopathy characterized by obesity, postaxial polydactyly, retinal degeneration, and mild cognitive impairment ({1:Heon et al., 2016}; {2:Khan et al., 2016}).nnFor a general phenotypic description and a discussion of genetic heterogeneity of Bardet-Biedl syndrome, see BBS1 (OMIM:209900).
Short-rib thoracic dysplasia (SRTD) with or without polydactyly refers to a group of autosomal recessive skeletal ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. SRTD encompasses Ellis-van Creveld syndrome (EVC) and the disorders previously designated as Jeune syndrome or asphyxiating thoracic dystrophy (ATD), short rib-polydactyly syndrome (SRPS), and Mainzer-Saldino syndrome (MZSDS). Polydactyly is variably present, and there is phenotypic overlap in the various forms of SRTDs, which differ by visceral malformation and metaphyseal appearance. Nonskeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of SRTD are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life (summary by {1:Huber and Cormier-Daire, 2012} and {2:Schmidts et al., 2013}).nnThere is phenotypic overlap with the cranioectodermal dysplasias (Sensenbrenner syndrome; see CED1, OMIM:218330).
short-rib thoracic dysplasia 20 with polydactyly
A benign, intermediate, or malignant neoplasm that affects the connective and soft tissue.
musculoskeletal and soft tissue neoplasm
Editor note: we follow NCIT in making this a grouping of all soft tissue and connective tissue neoplasms, including bone
A non-metastasizing neoplasm that arises from the soft tissue.
A disease or disorder that involves the erythrocyte.
psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome
Nephrotic syndrome, occurring in the pediatric population, in which proteinuria does not normalize with administration of steroids; this condition is unresponsive to a minimum of four weeks administration of oral corticosteroids.
nephrotic syndrome of childhood - steroid resistant
SRNS - steroid-resistant nephrotic syndrome
Nephrotic syndrome, occurring in the pediatric population, characterized by the normalization of proteinuria with the administration of corticosteroids.
nephrotic syndrome of childhood - steroid sensitive
An instance of dystonic disorder that is caused by an inherited modification of the individual's genome.
A neoplasm arising from hematopoietic cells found in the bone marrow, peripheral blood, lymph nodes and spleen (organs of the hematopoietic system). Hematopoietic cell neoplasms can also involve other anatomic sites (e.g. central nervous system, gastrointestinal tract), either by metastasis, direct tumor infiltration, or neoplastic transformation of extranodal lymphoid tissues. The commonest forms are the various types of leukemia, Hodgkin and non-Hodgkin lymphomas, myeloproliferative neoplasms, and myelodysplastic syndromes.
hematopoietic and lymphoid cell neoplasm
hematopoietic neoplasms including Lymphomas
A primary or metastatic malignant neoplasm that affects the renal pelvis.
A disease or disorder that involves the abdominal segment of trunk.
abdominal segment of trunk disease or disorder
disease or disorder of abdominal segment of trunk
A disease or disorder that involves the limb.
A benign mesenchymal neoplasm composed of adipose (fatty) tissue. The most common representative of this category is the lipoma.
adipose tissue benign connective and soft tissue neoplasm
benign connective and soft tissue neoplasm of adipose tissue
A disease or disorder that involves the lymphoid system.
A disease or disorder that involves the face.
A disease or disorder that involves the upper digestive tract.
disease or disorder of upper digestive tract
disorder of upper gastrointestinal tract
upper digestive tract disease or disorder
A disease or disorder that involves the cardiac ventricle.
disease or disorder of cardiac ventricle
A disease that has its basis in the disruption of cholesterol metabolic process.
disorder of cholesterol metabolic process
Examples: disorder of cholesterol catabolism (disorder), disorder of cholesterol synthesis (disorder)
A disease that has its basis in the disruption of glycoprotein metabolic process.
disorder of glycoprotein metabolic process
Examples: alpha-n-acetylgalactosaminidase deficiency (disorder), carbohydrate-deficient glycoprotein syndrome (disorder), alpha-1-antitrypsin deficiency (disorder), alpha-2-antitrypsin deficiency (disorder), sialidosis (disorder), aspartylglucosaminuria (disorder), fucosidosis (disorder), mannosidosis (disorder), i-cell disease (disorder), glycoprotein storage disorder (disorder)
A disease that has its basis in the disruption of steroid metabolic process.
A disease that has its basis in the disruption of carbohydrate transport.
A disease that has its basis in the disruption of cholesterol biosynthetic process.
disorder of cholesterol biosynthetic process
cholesterol biosynthetic process disease
A disease that has its basis in the disruption of organic acid metabolic process.
disorder of organic acid metabolic process
Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions.
A disease or disorder that is induced by either chemical or radiation exposure.
radiation or chemically induced disorder
A characteristic of an infectious disease in which the disease affects an immunologically normal host.
A pregnancy induced hypertensive state that occurs after 20 weeks of gestation characterized by an increase in blood pressure, along with body swelling and proteinuria.
A disorder either associated with an increased risk for malignant transformation (e.g., intraepithelial neoplasia, leukoplakia, dysplastic nevus, myelodysplastic syndrome) or that develops as a result of the presence of an existing malignant neoplasm (e.g., paraneoplastic syndrome).
short-rib thoracic dysplasia 17 with or without POLYDACTYLY
Any polycystic kidney disease in which the cause of the disease is a mutation in the DNAJB11 gene.
polycystic kidney disease caused by mutation in DNAJB11
polycystic kidney disease 6 with or without polycystic liver disease
Renal damage and impaired renal function secondary to urinary tract obstruction.
A disease that has its basis in the disruption of sulfur compound metabolic process.
disorder of sulfur compound metabolic process
sulfur compound metabolic process disease
vertebral, cardiac, renal, and limb defects syndrome 1
vertebral, cardiac, renal, and limb defects syndrome 2
hypohidrosis-electrolyte imbalance-lacrimal gland dysfunction-ichthyosis-xerostomia syndrome
hypohidrosis, electrolyte imbalance, lacrimal gland dysfunction, ichthyosis, and xerostomia
Probably related to a recessive gene, this is Fanconi Syndrome, characterised by adult onset.
Fanconi Syndrome caused by exposure to noxious agents.
Fanconi syndrome caused by degraded tetracycline
An autoimmune disease characterized by sudden onset of photopsias and scotomata in patients with no family history of retinitis pigmentosa, followed by visual field and central vision loss.
Metabolic epilepsies are conceptualized as having a distinct metabolic abnormality that has been demonstrated to be associated with a substantially increased risk of developing epilepsy in appropriately designed studies. Metabolic disorders have genetic origin; however, the metabolic abnormalities are a separate disorder interposed between the genetic defect and the epilepsy.
An epilepsy syndrome that has an onset during variable ages and stages of life.
variable age at onset electroclinical syndrome
A disease or disorder that affects the neuroendocrine gland, any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli.
An inheritable form of pseudoxanthoma elasticum (PXE), that causes calcium and other minerals to accumulate in the elastic fibers of the skin, eyes, and blood vessels, and less frequently in other areas such as the digestive tract. PXE may cause the following symptoms: growth of yellowish bumps on the skin of the neck, under the arms, or in the groin area; reduced vision; periodic weakness in the legs (claudication); or bleeding in the gastrointestinal tract, particularly the stomach. A clinical diagnosis of PXE can be made when an individual is found to have both the characteristic eye findings and yellow bumps on the skin. ABCC6 is the only gene known to be associated with this condition. Currently, there is no treatment for this condition, but affected individuals may benefit from routine visits to an eye doctor who specializes in retinal disorders, and by having regular physical examinationswith their primary physician.
Pathophysiology: In PXE, there is mineralization (accumulation of calcium and other minerals) and fragmentation of the elastin-containing fibers in connective tissue, but primarily in the midlaminar layer of the dermis, Bruch's membrane and the midsized arteries.[12] Recent studies hypothesize that PXE is a metabolic disease, and that its features arise because metabolites of vitamin K cannot reach peripheral tissues
An infectious disease where a pathogen is carried and transmitted by another organism that acts as disease vector.
Accelerated aging syndromes often caused by inheritable gene mutations resulting in decreased telomere lengths.
An autosomal recessive condition caused by mutation(s) in the CTNS gene, encoding cystinosin. It is a sub-type of cystinosis, in which accumulation of cystine in the kidney results in renal dysfunction.
An autosomal recessive disorder characterized by onset of megaloblastic anemia associated with decreased serum vitamin B12 (cobalamin, Cbl) in infancy or early childhood. Low molecular weight (LMW) proteinuria is frequently present, but sometimes occurs later and is usually mild or subclinical. Patients often present with vague symptoms, including failure to thrive, loss of appetite, fatigue, lethargy, and/or recurrent infections. Some patients may present later in childhood with neurologic abnormalities related to B12 deficiency, such as sensorimotor neuropathy and/or cognitive disturbances.
enterocyte intrinsic factor receptor, defect of
pernicious anemia, juvenile, due to selective intestinal malabsorption of vitamin b12, with proteinuria
An autosomal recessive disorder characterized by onset of megaloblastic anemia associated with decreased serum vitamin B12 (cobalamin, Cbl) in infancy or early childhood. Low molecular weight (LMW) proteinuria is frequently present, but usually occurs later and is usually mild or subclinical. Patients often present with vague symptoms, including failure to thrive, loss of appetite, fatigue, lethargy, and/or recurrent infections. Treatment with vitamin B12 results in sustained clinical improvement of the anemia. The proteinuria is nonprogressive, and affected individuals do not have deterioration of kidney function; correct diagnosis is important to prevent unnecessary treatment. The disorder results from a combination of vitamin B12 deficiency due to selective malabsorption of the vitamin, and impaired reabsorption of LMW proteins in the proximal renal tubule. These defects are caused by disruption of the AMN/CUBN complex that forms the 'cubam' receptor responsible for intestinal uptake of B12/GIF (CBLIF).
Renal tubular acidosis (RTA) that is caused by a generalized transport abnormality of the distal tubule. The transport of electrolytes such as sodium, chloride, and potassium that normally occurs in the distal tubule is impaired. This form is distinguished from classical distal RTA and proximal RTA because it results in high levels of potassium in the blood instead of low levels.
autosomal dominant intellectual disability
intellectual disability, autosomal dominant
An instance of cutis laxa that is inherited.
An instance of thrombocytopenia that is inherited.
An instance of paroxysmal nocturnal hemoglobinuria that is inherited.
hereditary paroxysmal nocturnal hemoglobinuria
inherited paroxysmal nocturnal hemoglobinuria
An instance of paroxysmal nocturnal hemoglobinuria that is inherited or acquired.
Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal hematopoietic stem cell disorder characterized by corpuscular hemolytic anemia, bone marrow failure and frequent thrombotic events.
acquired paroxysmal nocturnal hemoglobinuria
An X-linked intellectual deficiency in which not enough information is known, reported or published to indicate whether a gene causes non-syndromic or syndromic presentations.
The sum of morphological and functional disturbances induced by cell and tissue damage, either from intrinsic gene dysfunction or as a result of external factors.
Phenotypic observation of the presence or absence of a pathological entity.
A pathological process of loss or degradation of function, or structural integrity, of a tissue, organ or cell.
The process, normal or abnormal, of damage repair or wound closure.
Replacement of connective tissue by fibro-fatty deposits and scar tissue.
Any pathological thickening or hardening of a tissue.
Inappropriate or aberrant activation or suppression of the immune or inflammatory response.
Tissue response to inappropriate immune/inflammatory process.
Renal disease characterised by diffuse inflammatory changes in glomeruli not in response to an infectious agent or treatment.
A tissue reaction to an internal or external injury.
Degenerative process characteristic of a particular tissue.
Characterised by irregular lipid deposits in the wall of arteries, causing narrowing of their lumens and proceeding eventually to fibrosis and calcification.
Note that in mouse and rats the initial lesions are mostly in the medial layer while in human they occur in the intima.
Accumulation of substances within, on the surface of or between cells.
intracellular and extracellular accumulation
Extracellular deposition of amyloid protein.
Any group of chemically diverse proteins that appears microscopically homogeneous, but is composed of linear non-branching aggregated fibrils aranged in sheets when see under the electron microscope.
Intra or extracellular deposition of calcium usually as calcium phosphate.
Developmental and structural abnormalities occurring during embryonic development or during adult life.
developmental and structural abnormality
Deposition of any homogeneous inorganic material.
Structural, physical or other general defect of prenatal development of the embryo and the placenta, or such as are acquired in the adult.
developmental or adult structural defect
Persistence of metanephrogenic blastema or its presence in the wrong place or at the wrong time. Associated with hyperplastic nephrogenic rests.
The organic response of tissues to external insult, injury or underlying genetic or epigenetic lesion.
Processes occurring during cell and tissue damage of either intrinsic or extrinsic etiology.
Anatomically located instance of pathological response or entity.
Physical entity or structure associated with normal or abnormal tissue healing or repair following extrinsic or intrinsic damage.
A circumscribed collection of purulent exudate frequently associated with swelling and other signs of inflammation.
Generally occur following damage or infection with subsequent inflammatory response. Result of the body`s defensive reaction to foreign material.
Formation of an epithelium bounded cavity not associated with neoplasia.
Abnormal retention of lipids within a cell. Physically apparent as lipid within liposomes of parenchymal cells.
Most commonly associated with degenerative change in the liver.
Abnormal development (of organs or tissues) or an abnormal structure resulting from such growth.
The word dysplasia as commonly used refers to a precursor state to neoplasia. This is not the context used for this MPATH term.
A focal malformation resembling a neoplasm which results from faulty development of an organ; composed of an abnormal mixture of tissue elements, or an abnormal proportion of a single element. Growth and location are usually normal for that tissue cf. Heterotopia/Choristoma MPATH:76/MPATH:477.
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type 1 HIV1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type I HIV-1
human immunodeficiency virus type-1 HIV-1
human immunodeficiency virus type 1 HIV-1
human immunodeficiency virus type 2 HIV-2
human immunodeficiency virus type 2, HIV-2
purple photosynthetic bacteria and relatives
Mycobacterium tuberculosis typus humanus
Mycobacterium tuberculosis variant tuberculosis
Saccharomyces cerevisiae 'var. diastaticus'
Homo sapiens
An individual's total number of brothers and sisters.
The age of the subject at the time of the vaccination.
A group of people characterized by the practice of a common religion.
A member of the Jewish faith whose ancestors lived in North Africa, the Middle East, Portugal or Spain.
Individuals who do not necessarily identify with any particular race or others who do not wish to self select into a racial category(ies).
The age at which permanent cessation of menses occurs.
The age at which permanent cessation of menses occurred. (NCI)
A person having origins in the original peoples of Asia, but not China, India, Korea, the Philippine Islands or Vietnam.
A person having origins in the original peoples of the Pacific Islands, but not Guam, Hawaii, the Mariana Islands or Samoa.
A person of Mexican or Mexican American culture or origin, regardless of race.
A person of Cuban culture or origin, regardless of race.
A person of Spanish culture or origin, but not Cuban, Mexican, Puerto Rican, South or Central American, regardless of race.
The time elapsed between the day of conception and the day of delivery.
Chronological age reduced by the number of weeks born before 40 weeks of gestation; most appropriately used to describe children up to 3 years of age who were born preterm.
Best estimate of the first day of last menstrual period to birth plus time elapsed from day of birth.
A person's optimum weight as calculated by a standard methodology.
The money received by retired workers who have paid in to the Social Security system during their working years.
A fixed sum paid regularly to a person by their former employer.
The pressure within the left ventricle following the completion of diastolic filling, just prior to systole.
The pressure within the left ventricle of the heart at the end of the period when the chambers of the heart refill with blood and just before the contraction begins.
The pressure in the left ventricle at any point prior to the ejection of its contents into the aorta (systole).
The pressure within the left ventricle of the heart during the contraction of the left ventricle of the heart.
An approximate calculation of the gestational age of the fetus.
The number of education years that a subject has competed.
The number of years of education that a person has completed.
The age at which the first episode occurred.
The age at which the first hospitalization event occurred.
The age at which the first treatment event occurred.
The age at which the first treatment for the condition occurred.
The maternal body weight adjusted for the weight of the gravid uterus. This is derived by subtracting the gravid uterus weight from the total maternal body weight.
Gravid Uterus Adjusted Maternal Body Weight
An estimate or direct measurement of the heaviness of a fetus.
A measurement of the average weight of all live fetuses.
A measurement of the average weight of all live female fetuses.
A measurement of the average weight of all live male fetuses.
A measurement of the total weight of all live fetuses.
The age at which a minor assumes legal control over their person, actions, and decisions.
Denotes a person whose ancestry is in any of the countries of the central part of the African continent: Burundi, the Central African Republic, Chad, the Democratic Republic of the Congo, and Rwanda.
Denotes a person whose ancestry is in any of the countries of the northern part of the African continent: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia, and Western Sahara.
Denotes a person whose ancestry is in the country of South Africa.
Denotes a person whose ancestry is in any of the countries of the Americas or the Caribbean where Spanish or Portuguese is spoken.
Denotes a person whose ancestry is in any of the countries of South America.
Denotes a person whose ancestry is in any of the Asian countries south of China, east of India, west of New Guinea and north of Australia.
Denotes a person whose ancestry is in any of the Asian countries between the Caspian Sea in the west, China in the east, Afghanistan in the south, and Russia in the north.
Denotes a person whose ancestry is in the country or continent of Australia.
Denotes a person whose ancestry is in the country of New Zealand.
Denotes a person whose ancestry is in the country of Iceland.
Denotes a person whose ancestry is in the countries of Scandinavia: Denmark, Norway and Sweden. Finland and Iceland are generally included as part of the Scandinavian region.
A collection of ethnic geographical categories including African American, North American, Latin American, Caribbean, and South American.
A collection of ethnic geographical categories including Australian and New Zealander.
A collection of ethnic geographical categories including Middle Eastern and Hispanic.
Denotes a person of African ancestral origins whose family settled in America.
A person having origins in the original peoples of sub-Saharan Africa and the United States.
A person having origins in the original peoples of sub-Saharan Africa or the Caribbean.
Denotes a person of African ancestral origins whose family settled in Central America.
A person having origins in the original peoples of sub-Saharan Africa and Central America.
Denotes a person of African ancestral origins whose family settled in South America.
A person having origins in the original peoples of sub-Saharan Africa and South America.
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa and Central America.
A person having origins in the original peoples of Europe, the Middle East, or North Africa, and Central America.
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa and South America.
A person having origins in the original peoples of Europe, the Middle East, or North Africa, and South America.
The maximum pressure exerted into the systemic arterial circulation during the contraction of the right ventricle of the heart.
Blood pressure within the left atrium. It is commonly measured indirectly by a pulmonary capillary wedge pressure.
The estimated arithmetic average of atrial pressure.
An approximate determination of the weight of a body.
An approximate determination of the weight of the subject.
The result of a body mass index measurement.
Indicates a body mass index measurement less than 19.
Indicates a body mass index measurement greater than or equal to 19 but below 21.
Indicates a body mass index measurement greater than or equal to 21 but below 23.
Indicates a body mass index measurement greater than or equal to 23.
Body Mass Index Greater Than or Equal to 23
An indication that an individual's age is or was greater than 85 years.
An indication that an individual's age is or was between 80 and 85 years.
An indication that an individual's age is or less than 80 years.
A quantitative estimate of the pressure in a given cardiovascular structure during ventricular systole.
The age at which the full-time use of an entity occurred.
The age at which the full-time use of a pre-specified object first occurred.
Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, and who was either born in the United States or who was naturalized as a citizen of the United States.
A person having origins in the original peoples of Asia and the United States.
A person having origins in any of the Black racial groups of Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American". (OMB)
A person having origins in any of the black racial groups of Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American." (FDA)
A general indicator of the body fat an individual is carrying based upon the ratio of weight to height.
A general indicator of the body fat an individual is carrying based upon the ratio of weight to height. (NCI)
A measure that relates body weight to height. BMI is sometimes used to measure total body fat and whether a person is a healthy weight. Excess body fat is linked to an increased risk of some diseases including heart disease and some cancers.
A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease.
Denotes social groups with a shared history, sense of identity, geography, and cultural roots.
A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender)
Any finite or infinite collection of subjects from which a sample is drawn for a study to obtain estimates for values that would be obtained if the entire population were sampled. [AMA style Manual]
A subjective and comparative term describing a lack of sufficient wealth (usually understood as capital, money, material goods, or resources especially natural resources) to live what is understood in a society as a "normal" life: for instance, to be capable of raising a healthy family, and especially educating children and participating in society. A person living in this condition of poverty is said to be poor. The meaning of "sufficient" varies widely across the different political and economic areas of the world.
An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.
A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. The term, "Spanish origin," can be used in addition to "Hispanic or Latino." (OMB)
A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. (NCI)
Characteristics of a person such as education and occupation, used to describe the person's position in stratification systems, access to services, etc.
Ashkenazi Jews, also called Ashkenazim, are Jews who are descendants of Jews from Germany, Poland, Austria and Eastern Europe.
One of two major ancestral groups of Jewish individuals, comprised of those whose ancestors lived in Eastern Europe (Germany, Poland, Russia). The other group is designated Sephardic Jews and includes those whose ancestors lived in North Africa, the Middle East, and Spain. Most Jews living in the United States are Ashkenazi Jews.
Denotes a person having origins in any indigenous people of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment. The concept refers to population subgroups such as Eskimos, Aleuts, Inupiat, Yupik, Alutiiq, Egegik,and Pribilovian, Alaskan Athabascan, Tlingit, and Haida. The concept refers also to individuals who classify themselves as such.
A demographic parameter indicating the average amount of earnings made by a family in a particular population or/and during a particular period of time.
a demographics parameter useful for identifying socio-economic groups.
The distinguishing qualities or prominent aspects of an individual person.
Age of first menstruation. A risk factor for breast cancer
The age at which the first menstruation event occurred. (NCI)
The age at which a woman gave birth to her first live child.
An indication of a person's current tobacco and nicotine consumption as well as some indication of smoking history.
Current Tobacco and Nicotine Consumption Status
How long something has existed; elapsed time since birth.
How long something has existed; elapsed time since birth. (NCI)
The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart.
The maximum blood pressure in the systemic arterial circulation during the cardiac cycle.
The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling.
The minimum blood pressure in the systemic arterial circulation during the cardiac cycle.
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. (NCI)
A system, commonly called the INR, established by the World Health Organization (WHO) and the International Committee on Thrombosis and Hemostasis for reporting the results of blood coagulation (clotting) tests. All results are standardized using the international sensitivity index (ISI) for the particular thromboplastin reagent and instrument combination utilized to perform the test; the ratio of a patient's clotting time to the lab's mean reference value is normalized against the ISI. (from medterms.com and medicine.ucsf.edu)
A birth weight that is less than 2500 grams.
The length of a person's life, stated in months since birth.
The length of a person's life, stated in years since birth.
A gain or recurrent benefit during a period of time, usually measured in money that derives from capital or labor.
Income is one of the major demographic parameters used in population-based biomedical research.
A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. (OMB)
Native Hawaiian or Other Pacific Islander
Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuu. (FDA)
A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification. (NCI)
Denotes a person of African ancestral origins whose family settled in the Caribbean region.
A person having origins in the original peoples of sub-Saharan Africa and the Caribbean.
A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB)
A person having origins in any of the original peoples of North and South America (including Central America), and who maintains tribal affiliation or community attachment. (FDA)
A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB)
A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent including, for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (FDA)
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa. (OMB)
Denotes a person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. (FDA)
A person having origins in the original peoples of the Indian sub-continent.
A person having origins in any of the original peoples of the Indian subcontinent.
The concept is close to the term South Asian but several major South Asian populations such as Pakistani and Bangladeshi may not identify with it.
Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka.
Denotes a person with African ancestral origins who self identifies, or is identified, as African. The concept does not refer to those of other ancestry, for example, European and South Asian. In practice, the term mainly refers to people originated from forty-eight sub-Saharan Africa nations; and excludes individuals from North Africa countries, e.g. such as Algeria, Morocco, Egypt, Tunisia with Arab and Berber ethnicity.
A person having origins in any of the original peoples of sub-Saharan Africa.
Aleutian - a person having origins from the Aleut indigenous group of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment.
The native people inhabiting the Arctic of northern Canada, Greenland, Alaska, or eastern Siberia. The two main groups referred to as Eskimo are the Yupik and Inuit. A third group, the Aleut, is related. In Canada and Greenland, the term Eskimo has fallen out of favor, as it is considered pejorative by the natives and has been replaced by the term Inuit.
A person having origins in any of the original peoples of China.
A person having origins in any of the original peoples of Japan..
A person having origins in any of the original peoples of the Philippine Islands.
A person having origins in any of the original peoples of the Philippines.
A person having origins in any of the original peoples of Hawaii.
A person having origins in any of the original peoples of Korea.
A person having origins in any of the original peoples of North and South Korea.
A person having origins in any of the original peoples of Viet Nam.
Denotes the inhabitants of Laos, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Laos.
Denotes a person having origins in any of the original Hmong people originating in China around the Yellow River or Hoang Ho.
The native people originating in China around the Yellow River or Hoang Ho.
Early in the 19th century, the Hmong migrated to French Indochina, which comprised Vietnam, Cambodia and Laos. In 1947, Hmong officially became citizens of Loas. Later a number of Hmong emigrated to Thailand and the United States.
Denotes the inhabitants of Cambodia (formerly Kampuchea), a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Cambodia (formerly Kampuchea).
Denotes the inhabitants of Thailand, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Thailand.
Denotes a person from any of the islands in the western pacific encompassing the area from the Philippines in the west, Indonesia to the south west, Papua New Guinea and Melanesia to the south, and Polynesia to the south-east and east.
A person having origins in any of the original peoples of Micronesia.
Denotes any of the indigenous Chamorro people of Guam and the Mariana Islands or persons of that ancestry.
Denotes the inhabitants of Guam, a person from there, or their descendants elsewhere.
Denotes a person from any of the over 1,000 islands in the central and southern Pacific Ocean bounded by a triangle with its three corners at Hawaii, New Zealand, and Easter Island or a person of that ancestry.
A person having origins in any of the original peoples of Polynesia.
Denotes the inhabitants of Tahiti, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Samoa.
Denotes the inhabitants of Tonga, a person from there, or their descendants elsewhere.
Denotes a person from any of the islands in the region extending from the west Pacific to the Arafura Sea, north and north-east of Australia. or of that ancestry.
A person having origins in any of the original peoples of Melanesia.
Denotes the inhabitants of Fiji, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Papua New Guinea, a person from there, or their descendants elsewhere.
Primarily refers to a person having origins in the original peoples of the Indian sub-continent, a subset of which formed Pakistan. The term also refers to a person from Pakistan, whether or not ancestors were from India.
A person having origins in any of the original peoples of Pakistan.
Denotes the inhabitants of Bangladesh, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Bangladesh.
Denotes the inhabitants of Sri Lanka, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Sri Lanka.
Denotes the inhabitants of Bhutan, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Bhutan.
Denotes the inhabitants of Myanmar (formerly Burma), a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Myanmar (formerly Burma).
Denotes the inhabitants of Taiwan, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Taiwan.
Denotes the inhabitants of Indonesia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Indonesia.
Denotes the inhabitants of Malaysia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Malaysia.
Denotes the inhabitants of the japanese island of Okinawa, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Okinawa.
Denotes the inhabitants of Iwo Jima, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Iwo Jima.
Denotes the inhabitants of the Maldives, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the Maldives.
Denotes the inhabitants of Nepal, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Nepal.
Denotes the inhabitants of Singapore, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Singapore.
Denotes the inhabitants of Madagascar, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Madagascar.
Denotes the inhabitants of Barbados, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Barbados.
Denotes the inhabitants of Dominica, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Dominica.
Denotes the inhabitants of Haiti, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Haiti.
Denotes the inhabitants of Jamaica, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Jamaica.
Denotes the inhabitants of Tobago, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Tobago.
Denotes the inhabitants of Trinidad, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Trinidad.
Denotes the inhabitants of the West Indies, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the West Indies.
Denotes the inhabitants of Botswana, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Botswana.
Denotes the inhabitants of Ethiopia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Ethiopia.
Denotes the inhabitants of Liberia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Liberia.
Denotes the inhabitants of Namibia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Namibia.
Denotes the inhabitants of Nigeria, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Nigeria.
Denotes the inhabitants of the Democratic Republic of the Congo (formerly Zaire), a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Zaire.
Denotes the inhabitants of Tokelau, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Guam or the Mariana Islands.
Denotes the inhabitants of the Northern Mariana Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Marshall Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Palau, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Caroline Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Kosrae, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Pohnpei, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Saipan Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Kiribati, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Chuuk, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Yap, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Solomon Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the islands of Vanuatu, a person from there, or their descendants elsewhere.
Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Europe.
Denotes the inhabitants of Armenia, a person from there, or their descendants elsewhere.
Denotes the inhabitants of England, a person from there, or their descendants elsewhere.
Denotes the inhabitants of France, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Germany, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Ireland, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Italy, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Poland, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Scotland, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Russia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Russia.
Denotes the inhabitants of Sweden, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Norway, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Ukraine, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Mongolia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Mongolia.
Denotes the inhabitants of Finland, a person from there, or their descendants elsewhere.
Denotes a person from any of the countries of southwest Asia and northeastern Africa; this region includes those countries east of Egypt and south of Turkey and extending to Iran in the east.
A collective term used to identify indigenous peoples of northern Iraq and neighboring areas of Syria and Turkey, who also identify themselves as Aramaeans and Chaldeans. They are the survivors of the formerly extensive Aramaic- or Syriac- speaking Christian community of northern Iraq, southeastern Turkey, and northwestern Iran.
Denotes the inhabitants of Egypt, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Iran, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Iraq, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Lebanon, a person from there, or their descendants elsewhere.
Denotes those persons of mainly Arabic speakers who regard themselves as a distinct branch of the Arabic-speaking peoples, with family origin in Palestine being the defining characteristic.
Denotes the inhabitants of Syria, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Afghanistan, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Israel, a person from there, or their descendants elsewhere.
Denotes a person with ethnic origins in the Semitic people originally from the Arabian peninsula and surrounding territories in the Middle East and northern Africa.
A person having origins in any of the original peoples of the Arabian peninsula and surrounding territories in the Middle East and northern Africa.
Denotes a person having origins in one of the indigenous peoples of North America, who lived on the continent prior to the European colonization. The term includes individuals belonging to a large number of tribes, states, and ethnic groups, many of them still enduring as communities.
The native people inhabiting the territory spanning the Norton Sound on the Bering Sea to the Canadian border.
The native Yupik people inhabiting the coast of the Chukchi Peninsula in the far northeast of the Russian Federation and on St. Lawrence Island in Alaska.
The native people inhabiting western, southwestern, and southcentral Alaska and the Russian Far East.
Central Council of Tlingit and Haida Tribes
The mean pressure of the blood within the arterial circulation. The arterial pressure may be directly measured by insertion of an intra-arterial catheter connected to a transducer. The mean arterial pressure (MAP) can be calculated by subsequent analysis of the waveform. MAP can be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure.
The mean pressure of the blood within the arterial circulation. The arterial pressure may be directly measured by insertion of an intra-arterial catheter connected to a transducer. The mean arterial pressure (MAP) can be calculated by subsequent analysis of the waveform. MAP can be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure. (NCI)
The pressure of the circulating blood against the walls of the blood vessels.
The force of circulating blood on the walls of the arteries. Blood pressure is taken using two measurements: systolic (measured when the heart beats, when blood pressure is at its highest) and diastolic (measured between heart beats, when blood pressure is at its lowest). Blood pressure is written with the systolic blood pressure first, followed by the diastolic blood pressure (for example 120/80).
A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life.
Having ancestors of several or various races.
A person living in the United States of Mexican, Puerto Rican, Cuban, Central or South American, or other Spanish culture or origin. The concept does not include Brazilian Americans or Portuguese Americans.
A person of Puerto Rican culture or origin, regardless of race.
Denotes an american citizen of Mexican descent.
A person of Mexican and American descent.
Denotes a person from or of Cuba or an American citizen of Cuban descent.
Denotes the inhabitants of the Dominican Republic, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the Dominican Republic.
Denotes a person from the area between north and south America including persons from Belize, Costa Rica, El Salvador, Guatemala, Honduras, Nicaragua, Panama, and the Panama Canal zone.
Denotes a person from Spain or of Spanish descent.
A person from Spain or of Spanish descent.
Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day.
Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day.
An adult who has smoked 100 cigarettes in his or her lifetime and who currently smokes cigarettes. Includes daily smokers and non-daily smokers (also known as occasional smokers).
A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life.
Indicates a person who is known to have smoked but whose current smoking status is unknown.
Indicates that a person's smoking status is unknown.
Denotes the inhabitants of the Bahamas, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the Bahamas.
A person who inhales or has inhaled combustible products of organic material during their lifetime.
The age of a person at the start of a specific event.
The age of a patient on the first occurrence of an event, such as the first use of a medication.
The age of a person who is the subject in a study.
Age of patient who is the subject of observations.
A demographic parameter indicating the amount of earnings made by a family.
The first weight of a newborn obtained after birth.
A measured weight of a newborn obtained immediately or shortly after birth.
Denotes a person having origins in one of the indigenous people of South or Central America such as Mayans or Incas.
Denotes a person having origins in one of the indigenous people of the Caribbean.
Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe.
A person having origins in any of the original peoples of the countries surrounding the Mediterranean sea.
Denotes a person of European, Middle Eastern, or North African ancestral origins whose family settled in a North American country such as the United States of America or Canada.
Denotes a person having origins in a northern country of Africa such as Egypt, Sudan, Libya, Algeria, Morocco, or Tunisia.
A person having origins in any of the original peoples of North Africa.
Denotes a person having origins in any of the countries of northern Europe such as Belgium, Denmark, Austria, Switzerland, Norway, Sweden, or Great Britain.
A person having origins in any of the original peoples of Northern Europe.
Denotes a person having origins in any of the black racial groups of Africa whose family settled in a South or Central American country such as Argentina, Brazil, or Mexico.
Denotes a person with European, Middle Eastern, or North African ancestral origin whose family settled in the Caribbean region.
A person having origins in the original peoples of Europe, the Middle East, or North Africa, and the Caribbean.
Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France.
A person having origins in any of the original peoples of Western Europe.
Denotes a person of European ancestral origins whose family settled in a South or Central American country such as Argentina, Brazil, or Mexico.
Denotes a person having origins in any of the countries of Eastern Europe such as Czechoslovakia, Poland, Croatia, Hungary, Slovenia, Former Soviet Union, or Finland. It also includes persons who call themselves Gypsies from this region.
A person having origins in any of the original peoples of Eastern Europe.
Denotes a person having origins in the region of southwest Asia, between the India subcontinent and Europe, including Kuwait, Turkey, Lebanon, Israel, Iraq, Iran, Jordan, Saudi Arabia, lands east of Pakistan or the other countries of the Arabian Peninsula. Also includes people of Jewish ethnicity including Sephardic and Ashkenazic.
A person having origins in any of the original peoples of the Middle East.
A person's total income before taxes, exclusions, and deductions.
A general term for a group of culturally similar indigenous peoples inhabiting the Arctic regions of Canada, Greenland, Russia and the United States. In Alaska, the term Eskimo is commonly used, because it includes both Yupik and Inupiat, while Inuit is not accepted as a collective term. In Canada and Greenland, the term Eskimo has fallen out of favor, as it is considered pejorative by the natives and has been replaced by the term Inuit.
The systolic and diastolic blood pressure of the newborn upon examination; the normal range of the systolic blood pressure is 60 - 90, while the normal range of the diastolic blood pressure is 20-60.
The weight of a subject at a specified end point.
The weight of a subject at a specified end point. (NCI)
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
WEB: http://en.wikipedia.org/wiki/Adverse_event
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
WEB: http://wiki.answers.com/Q/What_is_medical_intervention
a medical intervention where a patient is administered with a drug
an adverse event that has an outcome of abnormal sign in a musculoskeletal or connective tissue.
musculoskeletal and connective tissue disorder AE
WEB: http://www.cdc.gov/niosh/programs/msd/
A musculoskeletal disorder is an injury or disorder of the muscles, nerves, tendons, joints, cartilage, or supporting structures of the upper or lower limbs, neck, or lower back that are caused, precipitated, or exacerbated by sudden exertion or prolonged exposure to physical factors such as repetition, force, vibration, or awkward posture
an adverse event that shows a complication that occurs after a medical procedure and is directly related to the precedure itself.
a procedure complication AE that occurs after a surgery.
The key difference between a surgery and a procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. Technically speaking, a surgery is a specific type of procedure. A procedure is a broad general term that refers to any series of pre-defined steps that should be followed to achieve a desired result. Therefore, a “surgical procedure” is synonymous with a “surgery.” See more: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm.
Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery.
WEB: http://en.wikipedia.org/wiki/Surgery
WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
a musculoskeletal and connective tissue AE that displays an outcome of fistula, a permanent abnormal passageway between two organs in the body or between an organ and the exterior of the body.
WEB: http://medical-dictionary.thefreedictionary.com/fistula
a serious AE that is due to an allergic brochospasm, which causes a serious problem with breathing and requires treatment in an emergency room.
URL: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
URL: https://en.wikipedia.org/wiki/Bronchospasm
allergic brochospasm AE that requires treatment in emergency
a sensory capability AE that has an outcome of pain in a patient
a sudden death AE that occurs to an infant.
According to the Vaccine Adverse Event Reporting System (VAERS), 'sudden infant death' is an adverse event that was mentioned in 808 VAERS reports (0.6%) during1991-2001 (Reference: PMID: 12825543).
an AE that occurs in cardiovascular system.
an adverse event that has an outcome of an abnormal behavior and neurological phenotype.
WEB: http://www.psychguides.com/guides/behavioral-disorder-symptoms-causes-and-effects/
any anomaly in the actions, reactions, or performance of an organism in response to external or internal stimuli compared to controls
a behavior and neurological AE that has an outcome of inability or altered ability to respond to a sensory stimulus
a urinary system AE that results in the presence of blood in the urine
UMLS CUI: C0018965 (hematuria AND haematuria); UMLS CUI: C0947999 (blood urine presence)
WEB: http://kidney.niddk.nih.gov/kudiseases/pubs/hematuria/
Hematuria AE can be caused by menstruation, vigorous exercise, sexual activity, viral illness, trauma, or infection, such as a urinary tract infection (UTI), along with more serious disorders such as cancer, disease, and clotting.
an adverse event that has an outcome of urinary system AE is a functional anomaly of any of the organs involved in the production or excretion of urine
serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death.
WEB: http://en.wikipedia.org/wiki/Serious_adverse_event
WEB: http://www.google.ca/url?sa=t&source=web&ct=res&cd=1&ved=0CA4QFjAA&url=http%3A%2F%2Fwww.irrd.ca%2Fethics%2Fimages%2FAdverse-event-definition.doc&ei=eqFMS-yFNZSoswOt6siKAQ&usg=AFQjCNGnQcwI8OXH7dqxwo4RgZEEn8X6lg&sig2=UNngkCdO5ZTFvbIB1pKuaA
a serious adverse event that has an outcome of death.
a serious AE that is suspected to put the patient at substantial risk of dying at the time of the adverse event, or that the use or continued use of the device or other medical product might have resulted in the death of the patient.
a serious adverse event that leads to hospitalization. Such an adverse event resulted in an admission to the hospital or prolongation of hospitalization.
adverse event leading to hospitalization
a serious adverse event that leads to disability or permanent damage. Such an adverse event results in a substantial disruption of a person's ability to conduct normal life functions, i.e., the adverse event resulted in a significant, persistent or permanent change, impairment, damage or disruption in the patient's body function/structure, physical activities and/or quality of life.
a serious adverse event that resulted in congenital anomaly and bith defect, leading to suspicions that an exposure to a medical product prior to conception or during pregnancy resulted in an adverse outcome in the child.
adverse event leading to congenital anomaly
WEB: http://www.thefreedictionary.com/birth+defect
a serious adverse event which is an adverse event that requires intervention to prevent permanent impairment or damage leads to suspicions that the use of a medical product may result in a condition which requires a medical or surgical intervention to preclude permanent impairment or damage to a patient.
adverse event that requires intervention to prevent permanent impairment or damage
an cardiovascular adverse event that is a collection of blood outside the blood vessels, generally the result of hemorrhage, or more specifically, internal bleeding. It is commonly called a bruise.
YH: MedDRA ID: 10018852 is for "haematoma"; MedDRA ID: 10019428 is for "hematoma".
WEB: http://en.wikipedia.org/wiki/Hematoma
CTCAE: E13775 (hematoma); CTCAE: E11666 (brruising)
NCIt: C37921 (Bruising); NCIt: C50579 (Hematoma)
an adverse event that has an outcome of disease in the biological tissue that supports, binds together and protects organs
WEB: http://medical-dictionary.thefreedictionary.com/connective+tissue+disease
a connective tissue disorder AE that occurs in the non-skeletal tissue, usually subcutaneous and muscle tissue
WEB: http://www.reference.md/files/D018/mD018461.html
a death AE that has an outcome of unexpected death, 1 to 24 hours after the onset of symptoms
WEB: http://medical-dictionary.thefreedictionary.com/sudden+death
a process quality that represents the level of severity of an adverse event.
severity of adverse event
a severity of AE that shows sign and symptom within normal limits.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_0_Adverse_Event
Note the AE severity Grade 0 equals to CTCAE G0 AE severity.
AE severity G0
a severity of AE that shows asymptomatic, or involves mild or minor symptoms, or is of marginal clinical relevance, or consists of clinical or diagnostic observations alone, or where intervention is not indicated, or where only non-prescription intervention is indicated.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_1_Adverse_Event
Note the AE severity Grade 1 equals to CTCAE G1 AE severity.
AE severity G1
a severity of AE for which only minimal, local, or noninvasive intervention (e.g. packing, cautery) is indicated, or that limits instrumental activities of daily living (ADLs, e.g., shopping, laundry, transportation, or ability to conduct finances).
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_2_Adverse_Event
Note the AE severity Grade 2 equals to CTCAE G2 AE severity.
AE severity G2
a severity of AE that shows an outcome which is medically significant but not life-threatening; or for which inpatient care or prolongation of hospitalization are indicated; or that is an important medical event that does not result in hospitalization, but may jeopardize the patient or may require intervention either to prevent hospitalization, to prevent the AE from becoming life-threatening or causing death; or that is disabling; or that results in persistent or significant disability, incapacity, or limitation of self care activities of daily living (ADLs, getting in and out of bed, dressing, eating, getting around inside, bathing, or using the toilet).
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_3_Adverse_Event
Note the AE severity Grade 3 equals to CTCAE G3 AE severity.
AE severity G3
a severity of AE that has life-threatening consequences, for which urgent intervention is indicated, that puts the patient is at risk of death at the time of the event if immediate intervention is not undertaken, or that causes blindness or deafness (need to decide if unilateral or bilateral).
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_4_Adverse_Event
Note the AE severity Grade 4 equals to CTCAE G4 AE severity.
AE severity G4
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_5_Adverse_Event
Note the AE severity Grade 5 equals to CTCAE G5 AE severity.
AE severity G5
a hospitalization AE that leads to an intial hospitalization.
initial hospitalization AE
a hospitalization AE that leads to a prolonged hospitalization.
prolonged hospitalization AE
an adverse event that shows a result of injury or procedural complication.
injury or procedural complication AE
a pain AE that has marked discomfort sensation on the lateral side of the body in the region below the ribs and above the hip.
a death AE that has death in utero; failure of the product of conception to show evidence of respiration, heartbeat, or definite movement of a voluntary muscle after expulsion from the uterus, without possibility of resuscitation.
a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
medical procedure
a behavioral quality where the behavior in an organism is abnormal.
WEB: https://en.wikipedia.org/wiki/Abnormality_(behavior)
behavior abnormal quality
a death AE that has cessation of life occurring during the first 28 days of life.
An adverse event of hematoma in the subcapsular space of the kidney. This event occurs after a medical intervention, and may be caused by a tumor, trauma, vasculitis, renal infarction, or other disease process.
subcapsular hematoma AE
An adverse event of hematoma occurring around the kidney.
perinephric hematoma AE
arteriovenous fistula AE
An adverse event of surgery that leads to the puncturing of an adjacent organ. For example, a needle to the kidney may puncture the adjacent organs.
puncturing of adjacent organ AE
A date of specimen collection for the first collection of blood from a donor.
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
A date of specimen collection for the first collection of a tissue from a donor.
A date of specimen collection on which the surgery was performed during which the specimen was collected.
A data item that indicates the time when the collection of a specimen occurred.
Alice Nzinga
date of specimen preparation
It is denoted by Date in ISO-standard (8601) time format.
date of specimen collection
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
a worker role comprised of handling the administrative duties of a trial or study.
Person:Jennifer Fostel
clinical research coordinator role
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
OBI branch derived
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
PlanAndPlannedProcess Branch
measuring
scientific observation
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
Jennifer Fostel
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
GROUP:Role Branch
OBI, CDISC
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
patient role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation role
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Person: Jennifer Fostel
responsible party role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker role
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
sponsor role
a responsible party role involved with any of the following activities: initiating, managing and funding a study
CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
analyte role
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
9 March 09 from discussion with PA branch
material to be added role
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
hypothesis driven investigation
is an investigation with the goal to test one or more hypothesis
hypothesis generating investigation
is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
transfer function
A transfer function is a function to displace a material from one location to another.
Taped, glued, pinned, dried or molecularly bonded to a solid support
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
A planned process with the objective to produce a processed material which will have a function for future use.
A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters.
An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
the sodium and chloride ions in a glass of salt water
A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
scattered molecular aggregate
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
is an objective to obtain an output material that contains several input materials.
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material entity that has the material sample role
An objective specification maintains some or all of the qualities of a material over time.
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
A person or organization that has a manufacturer role.
A planned process with the objective to maintain some or all of the characteristics of an input material over time.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
Establishment of HeLa immortal cell line
is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal
Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line
4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective.
'establishing immortal cell line through directed genetic modification'
A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line.
A measurement datum that is reported on a categorical scale
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An device that is used to determine the order of amino acids in protein sequences.
genetically modified material
a material entity, organism or cell, that is the output of a genetic transformation process.
PERSON: Jie Zheng
GROUP: OBI
term is proposed by BP on Oct 25, 2010 dev call
genetic transformation objective
a material transformation objective aims to create genetically modified organism or cell
Person: Jie Zheng
suggested to be added by BP and AR during Oct 25, 2010 dev call
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
Services performing DNA sequencing or Cell Analysis
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
Person: Chris Stoeckert, Jie Zheng
specimen ID
NIAID GSCID-BRC metadata working group
selection criterion
rats should be aged between 6 and 8 weeks and weight between 180-250grams
A directive information entity which defines and states a principle of standard by which selection process may take place.
Person: Philippe Rocca-Serra
selection rule
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides.
PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi
specimen repository organization
An organization that provides a service to store and distribute specimens
sequencing facility organization
An organization that provides sequence determination service
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
A cultured cell population that is derived through one or more passages in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
An immortal cell line derived from a transformed cell that was part of a malignant tumor.
a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
selection
PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
selection process
A value specification that is specifies one category out of a fixed number of nominal categories
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
molecular analysis facility organization
An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
An organization that provides molecular analysis service.
An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
chemotherapy treatment exclusion criterion
An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
chemotherapy treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years.
An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
radiation treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years.
An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process.
history of metastatic cancer exclusion criterion
An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
intravenous drug use exclusion criterion
Donor eligibility based on history of intravenous drug abuse in the last 5 years.
An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of blood borne infection exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of intravenous drugs exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process.
exposure to blood borne infectious disease exclusion criterion
Donor eligibility based on whether the donor has been exposed to HIV/AIDS.
An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
health status inclusion criterion
‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
MIABIS2.0
clinically relevant lifestyle inclusion criterion
'smoking behavior’
An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process.
clinically relevant exposure inclusion criterion
'exposure to cigarette smoke’, ‘exposure to lead through drinking water'
An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process.
gravidity inclusion criterion
'pregnant’, ‘not pregnant'
An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process.
inclusion based on age, sex, and living region (rural area or specified city).
An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
defined population inclusion criterion
age group inclusion criterion
"18-33 years old"
An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
minimum age value specification
A value specifcation that specifies the youngest age when specifying an age range.
maximum age value specification
A value specifcation that specifies the oldest age when specifying an age range.
use of medication inclusion criterion
"received at least 2 days of vancomycin"
An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
hospital patient inclusion criterion
"included hospital patients"
An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
family status inclusion criterion
"included married and unmarried patients", "included divorced individuals"
An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
sex inclusion criterion
"included males and females", "included male patients"
An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
country of residence inclusion criteria
"include US residents"
An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
ethnicity inclusion criterion
"include only Hispanic individuals"
An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
reactant role
A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction.
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
an organism that is the output of a genetic transformation process
OBI Biomaterial
genetically modified organism
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
inclusion condition
inclusion rule
exclusion rule
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
human subject enrollment
enlisting familiy members of HIV patients into a study
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
As with group assignment, should the specified output here be an organism which bears a role
IEDB
criteria come from plan / clinical trial branch
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
administering substance in vivo
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
A planned process with the objective to keep cells alive in a defined environment outside of an organism.
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
cell culture splitting
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
genetic transformation
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
the introduction. alteration or integration of genetic material into a cell or organism
PERSON:Kevin Clancy
genetic modification
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
A specimen that is derived from some bodily fluid
Christian Stoeckert ORCID:0000-0002-5714-991X
A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
WEB: http://en.wikipedia.org/wiki/Genome
genome
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.
gene
a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition".
gene disposition
a gene disposition that a gene can be used as a blueprint for generating a protein (i.e., a gene encodes for a protein).
protein-coding gene disposition
a gene disposition that is the disposition of a gene that encodes for a tRNA.
RNA gene disposition
a RNA gene disposition that is for a gene that encodes for a ncRNA.
ncRNA gene disposition
a gene disposition that is "other", i.e., the gene is for a gene product that is not listed for another other gene type.
Note: The other gene disposition originates from automated generation using terms imported from the NCBI Gene resource (http://www.ncbi.nlm.nih.gov/books/NBK3841/ ). However the use of such an information-related term is not fully compliant with the Foundry Principles. Before we can find a better solution, we will for now keep them in the OGG.
other gene disposition
The genome of an organism of Proteobacteria
The genome of an organism of Gammaproteobacteria
The genome of an organism of Homo sapiens
The genome of an organism of Pseudomonas aeruginosa PAO1
A gene of an organism of Gammaproteobacteria
A gene of an organism of Pseudomonas aeruginosa PAO1
A gene of Homo sapiens that has a protein-coding gene disposition
A gene of Pseudomonas aeruginosa PAO1 that has a protein-coding gene disposition
protein-coding gene of Pseudomonas aeruginosa PAO1
A gene of Homo sapiens that has a ncRNA gene disposition
A gene of Homo sapiens that has a RNA gene disposition
A gene of Homo sapiens that has a other gene disposition
gene of Homo sapiens with other gene disposition
Other designations: acrosin light and heavy chain prepropeptide|preproacrosin|proacrosin
Other designations: actin, alpha skeletal muscle|nemaline myopathy type 3
Other designations: actin, aortic smooth muscle|alpha-cardiac actin|cell growth-inhibiting gene 46 protein
Other designations: F-actin cross-linking protein|actinin alpha4 isoform|alpha-actinin-4|focal segmental glomerulosclerosis 1|non-muscle alpha-actinin 4
Other designations: AC-III|ATP pyrophosphate-lyase 3|adenylate cyclase type 3|adenylate cyclase type III|adenylate cyclase, olfactive type|adenylyl cyclase 3|adenylyl cyclase, type III
Other designations: G protein coupled receptor|adrenergic, alpha-1A-, receptor variant 1|adrenergic, alpha-1A-, receptor variant 11|adrenergic, alpha-1A-, receptor variant 3|adrenergic, alpha-1A-, receptor variant 5|adrenergic, alpha-1A-, receptor variant 8|alpha-1A adrenergic receptor|alpha-1A adrenoceptor|alpha-1A adrenoreceptor|alpha-1C adrenergic receptor
Other designations: type-1 angiotensin II receptor|type-1B angiotensin II receptor
Other designations: aldolase 2|aldolase B, fructose-bisphosphatase|fructose-bisphosphate aldolase B|liver-type aldolase
aldo-keto reductase family 1, member B1 (aldose reductase)
Other designations: Lii5-2 CTCL tumor antigen|aldehyde reductase 1|aldo-keto reductase family 1 member B1|aldose reductase|low Km aldose reductase
Other designations: bikunin|complex-forming glycoprotein heterogeneous in charge|growth-inhibiting protein 19|inter-alpha-trypsin inhibitor light chain|protein AMBP|protein HC|trypstatin|uristatin|uronic-acid-rich protein
Other designations: ANG-2|Tie2-ligand|angiopoietin-2|angiopoietin-2B|angiopoietin-2a
Other designations: annexin I (lipocortin I)|annexin-1|calpactin II|calpactin-2|chromobindin-9|lipocortin I|p35|phospholipase A2 inhibitory protein
Other designations: apo-AIV|apoA-IV|apolipoprotein A4
Other designations: apo-E|apolipoprotein E3
Other designations: aquaporin 1 (channel-forming integral protein, 28kDa, CO blood group)|aquaporin-1|aquaporin-CHIP|channel-like integral membrane protein, 28-kDa|urine water channel|water channel protein for red blood cells and kidney proximal tubule
Other designations: ADH water channel|AQP-2|aquaporin-2|aquaporin-CD|collecting duct water channel protein|water channel protein for renal collecting duct|water-channel aquaporin 2
Other designations: aquaglyceroporin-3|aquaporin 3 (GIL blood group)|aquaporin-3
Other designations: AQP-6|aquaporin 2-like, kidney specific|aquaporin-6|aquaporin-6, kidney specific|hKID|kidney-specific aquaporin
Other designations: protein MemB|ras homolog gene family, member E|rho-related GTP-binding protein Rho8|rho-related GTP-binding protein RhoE|small GTP binding protein Rho8
Other designations: SCCL vasopressin subtype 1a receptor|V1-vascular vasopressin receptor AVPR1A|V1a vasopressin receptor|antidiuretic hormone receptor 1A|vascular/hepatic-type arginine vasopressin receptor|vasopressin V1a receptor
Other designations: AVPR V2|antidiuretic hormone receptor|renal-type arginine vasopressin receptor|vasopressin V2 receptor
Other designations: AXL oncogene|AXL transforming sequence/gene|tyrosine-protein kinase receptor UFO
Other designations: beta chain of MHC class I molecules|beta-2-microglobin
Other designations: biglycan proteoglycan|bone/cartilage proteoglycan I|bone/cartilage proteoglycan-I|dermatan sulphate proteoglycan I|small leucine-rich protein 1A
betaine--homocysteine S-methyltransferase
Other designations: betaine--homocysteine S-methyltransferase 1|epididymis secretory sperm binding protein Li 61p
Other designations: osteogenic protein 1
complement component 1, q subcomponent, A chain
Other designations: complement C1q subcomponent subunit A|complement component 1, q subcomponent, alpha polypeptide|complement component C1q, A chain
complement component 1, q subcomponent, B chain
Other designations: complement C1q subcomponent subunit B|complement component 1, q subcomponent, beta polypeptide|complement component C1q, B chain|complement subcomponent C1q chain B
Other designations: C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1|C3a anaphylatoxin|acylation-stimulating protein cleavage product|complement C3|complement component C3|complement component C3a|complement component C3b|epididymis secretory sperm binding protein Li 62p|prepro-C3
Other designations: complement component C7
Other designations: carbonate dehydratase II|carbonic anhydrase 2|carbonic anhydrase B|carbonic anhydrase C|carbonic dehydratase|epididymis luminal protein 76
Other designations: D-28K|RTVL-H protein|calbindin|calbindin 1, (28kD)|calbindin D28|vitamin D-dependent calcium-binding protein, avian-type
Other designations: alpha-type CGRP|calcitonin|calcitonin 1|calcitonin gene-related peptide I|calcitonin/calcitonin-related polypeptide, alpha|katacalcin
caspase 1, apoptosis-related cysteine peptidase
Other designations: CASP1 nirs variant 1|IL-1 beta-converting enzyme|IL1B-convertase|caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)|caspase-1|interleukin 1, beta, convertase|interleukin 1-B converting enzyme
caspase 3, apoptosis-related cysteine peptidase
Other designations: CASP-3|CPP-32|PARP cleavage protease|SREBP cleavage activity 1|apopain|caspase 3, apoptosis-related cysteine protease|caspase-3|cysteine protease CPP32|procaspase3|protein Yama
Other designations: extracellular calcium-sensing receptor|parathyroid Ca(2+)-sensing receptor 1|parathyroid cell calcium-sensing receptor 1
Other designations: CBF-alpha-3|PEA2 alpha C|PEA2-alpha C|PEBP2 alpha C|PEBP2-alpha C|SL3-3 enhancer factor 1 alpha C subunit|SL3/AKV core-binding factor alpha C subunit|acute myeloid leukemia 2 protein|acute myeloid leukemia gene 2|core-binding factor subunit alpha-3|core-binding factor, runt domain, alpha subunit 3|oncogene AML-2|polyomavirus enhancer-binding protein 2 alpha C subunit|transcription factor AML2
Other designations: G2/mitotic-specific cyclin B1|G2/mitotic-specific cyclin-B1
Other designations: CD1C antigen, c polypeptide|T-cell surface glycoprotein CD1c|cortical thymocyte antigen CD1C|differentiation antigen CD1-alpha-3
Other designations: CD1E antigen, e polypeptide|R2G1|T-cell surface glycoprotein CD1e, membrane-associated|differentiation antigen CD1-alpha-3|hCD1e|leukocyte differentiation antigen|thymocyte antigen CD1E
Other designations: CD3 antigen, delta subunit|CD3 delta|CD3d antigen, delta polypeptide (TiT3 complex)|OKT3, delta chain|T-cell receptor T3 delta chain|T-cell surface glycoprotein CD3 delta chain
Other designations: CD3g antigen, gamma polypeptide (TiT3 complex)|CD3g molecule, epsilon (CD3-TCR complex)|T-cell antigen receptor complex, gamma subunit of T3|T-cell receptor T3 gamma chain|T-cell surface glycoprotein CD3 gamma chain
Other designations: CD247 antigen, zeta subunit|CD3Z antigen, zeta polypeptide (TiT3 complex)|CD3zeta chain|T-cell antigen receptor complex, zeta subunit of CD3|T-cell receptor T3 zeta chain|T-cell surface glycoprotein CD3 zeta chain|TCR zeta chain
Other designations: CD4 antigen (p55)|CD4 receptor|T-cell surface antigen T4/Leu-3|T-cell surface glycoprotein CD4
Other designations: CD8 antigen, alpha polypeptide (p32)|Leu2 T-lymphocyte antigen|OKT8 T-cell antigen|T cell co-receptor|T-cell antigen Leu2|T-cell surface glycoprotein CD8 alpha chain|T-lymphocyte differentiation antigen T8/Leu-2|T8 T-cell antigen
Other designations: CD8 antigen, beta polypeptide 1 (p37)|T lymphocyte surface glycoprotein beta chain|T-cell surface glycoprotein CD8 beta chain
Other designations: monocyte differentiation antigen CD14|myeloid cell-specific leucine-rich glycoprotein
membrane-spanning 4-domains, subfamily A, member 1
Other designations: B-lymphocyte antigen CD20|B-lymphocyte cell-surface antigen B1|CD20 antigen|CD20 receptor|leukocyte surface antigen Leu-16
Other designations: B-lymphocyte activation antigen B7|CD80 antigen (CD28 antigen ligand 1, B7-1 antigen)|CTLA-4 counter-receptor B7.1|T-lymphocyte activation antigen CD80|activation B7-1 antigen|costimulatory factor CD80|costimulatory molecule variant IgV-CD80
Other designations: CD34 antigen|hematopoietic progenitor cell antigen CD34
Other designations: CD36 antigen (collagen type I receptor, thrombospondin receptor)|GPIIIB|PAS IV|PAS-4 protein|cluster determinant 36|fatty acid translocase|glycoprotein IIIb|leukocyte differentiation antigen CD36|platelet glycoprotein 4|platelet glycoprotein IV|scavenger receptor class B, member 3
Other designations: ADP-ribosyl cyclase 1|ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase|CD38 antigen (p45)|NAD(+) nucleosidase|cADPr hydrolase 1|cyclic ADP-ribose hydrolase 1
Other designations: CD40 antigen ligand|CD40-L|T-B cell-activating molecule|T-cell antigen Gp39|TNF-related activation protein|tumor necrosis factor (ligand) superfamily member 5
Other designations: CD68 antigen|macrophage antigen CD68|macrosialin|scavenger receptor class D, member 1
Other designations: C-type lectin domain family 2, member C|CD69 antigen (p60, early T-cell activation antigen)|activation inducer molecule (AIM/CD69)|early T-cell activation antigen p60|early activation antigen CD69|early lymphocyte activation antigen|leukocyte surface antigen Leu-23
CD79a molecule, immunoglobulin-associated alpha
Other designations: B-cell antigen receptor complex-associated protein alpha chain|CD79a antigen (immunoglobulin-associated alpha)|MB-1 membrane glycoprotein|ig-alpha|membrane-bound immunoglobulin-associated protein|surface IgM-associated protein
Other designations: cell cycle controller CDC2|cell division control protein 2 homolog|cell division cycle 2, G1 to S and G2 to M|cell division protein kinase 1|p34 protein kinase
Other designations: T1-cadherin|cadherin-9
chitinase 3-like 1 (cartilage glycoprotein-39)
Other designations: 39 kDa synovial protein|cartilage glycoprotein 39|chitinase-3-like protein 1
cytokine inducible SH2-containing protein
Other designations: cytokine-inducible SH2-containing protein|cytokine-inducible inhibitor of signaling type 1B|suppressor of cytokine signaling
CDC28 protein kinase regulatory subunit 2
Other designations: CDC28 protein kinase 2|CKS-2|CKS1(S. cerevisiae Cdc28/Cdc2 kinase subunit) homolog-2|cyclin-dependent kinases regulatory subunit 2
Other designations: chloride channel Ka|chloride channel protein ClC-Ka|chloride channel, kidney, A
Other designations: aging-associated protein 4|apolipoprotein J|complement cytolysis inhibitor|complement lysis inhibitor|complement-associated protein SP-40,40|ku70-binding protein 1|sulfated glycoprotein 2|testosterone-repressed prostate message 2
Other designations: C-C CKR-1|C-C chemokine receptor type 1|CC-CKR-1|CCR-1|LD78 receptor|MIP-1alpha-R|RANTES receptor|RANTES-R|macrophage inflammatory protein 1-alpha receptor
Other designations: cannabinoid receptor 2|testis-dominant CNR2 isoform CB2
Other designations: alpha-1 type I collagen|collagen alpha 1 chain type I|collagen alpha-1(I) chain|collagen alpha-1(I) chain preproprotein|collagen of skin, tendon and bone, alpha-1 chain|pro-alpha-1 collagen type 1
Other designations: alpha 2(I)-collagen|alpha-2 type I collagen|collagen I, alpha-2 polypeptide|collagen alpha-2(I) chain|collagen of skin, tendon and bone, alpha-2 chain|type I procollagen
collagen, type IV, alpha 3 (Goodpasture antigen)
Other designations: collagen IV, alpha-3 polypeptide|collagen alpha-3(IV) chain|tumstatin
Other designations: collagen alpha-1(V) chain
Other designations: alpha 1 (VI) chain (61 AA)|collagen VI, alpha-1 polypeptide|collagen alpha-1(VI) chain
Other designations: alpha 1 type XVI collagen|collagen XVI, alpha-1 polypeptide|collagen alpha-1(XVI) chain
Other designations: mast cell carboxypeptidase A|tissue carboxypeptidase A
Other designations: CPH|carboxypeptidase H|cobalt-stimulated chromaffin granule carboxypeptidase|enkephalin convertase|insulin granule-associated carboxypeptidase|prohormone-processing carboxypeptidase
Other designations: CPE-R 2|CPE-receptor 2|Clostridium perfringens enterotoxin receptor 2|claudin-3|ventral prostate.1 protein homolog|ventral prostate.1-like protein
complement component (3d/Epstein Barr virus) receptor 2
Other designations: EBV receptor|complement C3d receptor|complement receptor type 2|epstein-Barr virus receptor
Other designations: alpha-crystallin B chain|epididymis secretory protein Li 101|heat shock protein beta-5|heat-shock 20 kD like-protein|renal carcinoma antigen NY-REN-27|rosenthal fiber component
colony stimulating factor 1 (macrophage)
Other designations: lanimostim|macrophage colony-stimulating factor 1
Other designations: CD115 antigen|CSF-1 receptor|FMS proto-oncogene|McDonough feline sarcoma viral (v-fms) oncogene homolog|macrophage colony stimulating factor I receptor|macrophage colony-stimulating factor 1 receptor|proto-oncogene c-Fms
colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)
Other designations: CD116 antigen|GM-CSF receptor alpha subunit|GMCSFR-alpha|GMR-alpha|colony stimulating factor 2 receptor alpha subunit|granulocyte-macrophage colony-stimulating factor receptor alpha chain|granulocyte-macrophage colony-stimulating factor receptor subunit alpha
colony stimulating factor 3 receptor (granulocyte)
Other designations: CD114 antigen|G-CSF receptor|G-CSF-R|granulocyte colony-stimulating factor receptor
Other designations: chondroitin sulfate proteoglycan 2|chondroitin sulfate proteoglycan core protein 2|glial hyaluronate-binding protein|large fibroblast proteoglycan|versican core protein|versican proteoglycan
Other designations: bA218C14.4 (cystatin C)|cystatin 3|cystatin-3|cystatin-C|gamma-trace|neuroendocrine basic polypeptide|post-gamma-globulin
Other designations: cystatin AS|cystatin-A
Other designations: CCN family member 2|IBP-8|IGF-binding protein 8|IGFBP-8|hypertrophic chondrocyte-specific protein 24|insulin-like growth factor-binding protein 8
Other designations: carboxypeptidase LB|cathepsin B2|cathepsin IV|cathepsin P|cathepsin X|cathepsin Y|cathepsin Z1|cysteine-type carboxypeptidase|lysosomal carboxypeptidase B|preprocathepsin P
Other designations: CGD91-phox|NADPH oxidase 2|cytochrome b(558) subunit beta|cytochrome b-245 heavy chain|cytochrome b558 subunit beta|heme-binding membrane glycoprotein gp91phox|neutrophil cytochrome b 91 kDa polypeptide|p22 phagocyte B-cytochrome|superoxide-generating NADPH oxidase heavy chain subunit
cytochrome P450, family 4, subfamily B, polypeptide 1
Other designations: cytochrome P450 4B1|cytochrome P450, subfamily IVB, polypeptide 1|cytochrome P450-HP|microsomal monooxygenase
Other designations: PG-S2|bone proteoglycan II|decorin proteoglycan|dermatan sulphate proteoglycans II|proteoglycan core protein|small leucine-rich protein 1B
Other designations: C/EBP zeta|CCAAT/enhancer-binding protein homologous protein|DDIT-3|DNA damage-inducible transcript 3 protein|c/EBP-homologous protein 10|growth arrest and DNA damage-inducible protein GADD153
Other designations: DNase I, lysosomal|Dornase alfa|deoxyribonuclease-1|human urine deoxyribonuclease I
Other designations: DNase I homolog protein 2|DNase I homolog protein DHP2|DNase I-like 3|DNase gamma|LS-DNase|Liver and spleen DNase|deoxyribonuclease I-like III|deoxyribonuclease gamma
Other designations: diphtheria toxin receptor (heparin-binding EGF-like growth factor)|diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor)|heparin-binding epidermal growth factor|proheparin-binding EGF-like growth factor
Other designations: MAP kinase phosphatase 1|dual specificity protein phosphatase 1|dual specificity protein phosphatase hVH1|mitogen-activated protein kinase phosphatase 1|protein-tyrosine phosphatase CL100|serine/threonine specific protein phosphatase
Other designations: dual specificity protein phosphatase 2|dual specificity protein phosphatase PAC-1|dual-specificity phosphatase 2|serine/threonine specific protein phosphatase
Other designations: endothelin-1|preproendothelin-1
Other designations: beta-urogastrone|pro-epidermal growth factor
Other designations: EGR-1|early growth response protein 1|nerve growth factor-induced protein A|transcription factor ETR103|transcription factor Zif268|zinc finger protein 225|zinc finger protein Krox-24
Other designations: fatty acid-binding protein 1|fatty acid-binding protein, liver|liver-type fatty acid-binding protein
Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide
Other designations: Fc IgE receptor, alpha polypeptide|Fc epsilon RI alpha-chain|Fc-epsilon RI-alpha|high affinity immunoglobulin epsilon receptor alpha-subunit|high affinity immunoglobulin epsilon receptor subunit alpha|igE Fc receptor subunit alpha|immunoglobulin E receptor, high-affinity, of mast cells, alpha polypeptide
membrane-spanning 4-domains, subfamily A, member 2
Other designations: Fc fragment of IgE, high affinity I, receptor for; beta polypeptide|High affinity immunoglobulin epsilon receptor beta-subunit (FcERI) (IgE Fc receptor, beta-subunit) (Fc epsilon receptor I beta-chain)|high affinity IgE receptor beta subunit|high affinity immunoglobulin epsilon receptor subunit beta|igE Fc receptor subunit beta|immunoglobulin E receptor, high affinity, beta polypeptide
Fc fragment of IgG, low affinity IIIa, receptor (CD16a)
Other designations: CD16a antigen|Fc fragment of IgG, low affinity III, receptor for (CD16)|Fc gamma receptor III-A|Fc-gamma RIII-alpha|Fc-gamma RIIIa|Fc-gamma receptor III-2 (CD 16)|Fc-gamma receptor IIIb (CD16)|FcgammaRIIIA|fc-gamma RIII|igG Fc receptor III-2|immunoglobulin G Fc receptor III|low affinity immunoglobulin gamma Fc region receptor III-A|neutrophil-specific antigen NA
Fc fragment of IgG, low affinity IIIb, receptor (CD16b)
Other designations: Fc-gamma receptor IIIb (CD 16)|fc-gamma RIII-beta|fc-gamma RIIIb|igG Fc receptor III-1|low affinity immunoglobulin gamma Fc region receptor III-B
ficolin (collagen/fibrinogen domain containing) 1
Other designations: M-ficolin|collagen/fibrinogen domain-containing protein 1|ficolin (collagen/fibrinogen domain-containing) 1|ficolin-1|ficolin-A|ficolin-alpha
Other designations: FREAC-1|Forkhead, drosophila, homolog-like 5|forkhead box protein F1|forkhead-related activator 1|forkhead-related protein FKHL5|forkhead-related transcription factor 1
Other designations: Forkhead, drosophila, homolog-like 8|forkhead box protein D1|forkhead-like 8|forkhead-related activator 4|forkhead-related protein FKHL8|forkhead-related transcription factor 4
Other designations: HNF-3/fork-head homolog 3|HNF-3/fork-head homolog-3|forkhead box protein I1|forkhead-like 10|forkhead-related activator 6|forkhead-related protein FKHL10|forkhead-related transcription factor 6|hepatocyte nuclear factor 3 forkhead homolog 3
Other designations: fms-like tyrosine kinase 1|fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)|tyrosine-protein kinase FRT|tyrosine-protein kinase receptor FLT|vascular endothelial growth factor receptor 1|vascular permeability factor receptor
Other designations: CD135 antigen|FL cytokine receptor|STK-1|fetal liver kinase 2|fms-like tyrosine kinase 3|growth factor receptor tyrosine kinase type III|receptor-type tyrosine-protein kinase FLT3|stem cell tyrosine kinase 1
Other designations: cold-insoluble globulin|fibronectin|migration-stimulating factor
FBJ murine osteosarcoma viral oncogene homolog
Other designations: FBJ murine osteosarcoma viral (v-fos) oncogene homolog (oncogene FOS)|G0/G1 switch regulatory protein 7|activator protein 1|cellular oncogene c-fos|proto-oncogene c-Fos
Other designations: N-formylpeptide chemoattractant receptor|fMLP receptor|fMet-Leu-Phe receptor
Other designations: ferritin L subunit|ferritin L-chain|ferritin light chain|ferritin light polypeptide-like 3
Other designations: interferon alpha-inducible protein 6|interferon, alpha-inducible protein clone IFI-6-16|interferon-induced protein 6-16
Other designations: GATA-binding factor 3|trans-acting T-cell-specific transcription factor GATA-3
glycine amidinotransferase (L-arginine:glycine amidinotransferase)
Other designations: L-arginine:glycine amidinotransferase|glycine amidinotransferase, mitochondrial|transamidinase
Other designations: connexin 40|gap junction alpha-5 protein
Other designations: glypican proteoglycan 3|glypican-3|heparan sulphate proteoglycan|intestinal protein OCI-5|secreted glypican-3
Other designations: GLI-Kruppel family member GLI1|glioma-associated oncogene 1|glioma-associated oncogene homolog 1 (zinc finger protein)|oncogene GLI|zinc finger protein GLI1
Other designations: neuronal membrane glycoprotein M6-a
Other designations: N-arachidonyl glycine receptor|NAGly receptor
glutathione peroxidase 2 (gastrointestinal)
Other designations: gastrointestinal glutathione peroxidase|glutathione peroxidase 2|glutathione peroxidase-related protein 2
Other designations: GPx-3|extracellular glutathione peroxidase|glutathione peroxidase 3|plasma glutathione peroxidase
Other designations: C-X-C motif chemokine 2|GRO2 oncogene|MGSA beta|MIP2-alpha|gro-beta|growth-regulated protein beta|macrophage inflammatory protein 2-alpha|melanoma growth stimulatory activity beta
granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)
Other designations: CTL tryptase|Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)|HF|cytotoxic T-lymphocyte proteinase 1|fragmentin-1|granzyme A|h factor
granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)
Other designations: C11|CTLA-1|T-cell serine protease 1-3E|cathepsin G-like 1|cytotoxic T-lymphocyte proteinase 2|cytotoxic serine protease B|fragmentin 2|fragmentin-2|granzyme B|human lymphocyte protein
Other designations: NK-Tryp-2|NK-tryptase-2|fragmentin-3|granzyme 3|granzyme K|granzyme K (serine protease, granzyme 3; tryptase II)|granzyme-3|tryptase II
Other designations: hematopoietic cell kinase|p59-HCK/p60-HCK|tyrosine-protein kinase HCK
Other designations: H factor 1 (complement)|H factor 2 (complement)|adrenomedullin binding protein|age-related maculopathy susceptibility 1|beta-1-H-globulin|beta-1H|factor H|factor H-like 1
hepatocyte growth factor (hepapoietin A; scatter factor)
Other designations: fibroblast-derived tumor cytotoxic factor|hepatocyte growth factor|hepatopoeitin-A|hepatopoietin-A|lung fibroblast-derived mitogen
Other designations: MSTP131|glial growth factor|heregulin, alpha (45kD, ERBB2 p185-activator)|neu differentiation factor|neuregulin 1 type IV beta 1a|neuregulin 1 type IV beta 3|pro-NRG1|pro-neuregulin-1, membrane-bound isoform|sensory and motor neuron derived factor
major histocompatibility complex, class II, DQ alpha 1
Other designations: DC-1 alpha chain|DC-alpha|HLA class II histocompatibility antigen, DQ alpha 1 chain|HLA class II histocompatibility antigen, DQ(W3) alpha chain|HLA-DCA|MHC HLA-DQ alpha|MHC class II DQA1|MHC class II HLA-D alpha glycoprotein|MHC class II HLA-DQ-alpha-1|MHC class II antigen|MHC class II surface glycoprotein|leucocyte antigen DQA1|leukocyte antigen alpha chain
major histocompatibility complex, class II, DQ beta 1
Other designations: HLA class II histocompatibility antigen, DQ beta 1 chain|MHC DQ beta|MHC class II DQ beta chain|MHC class II HLA-DQ beta glycoprotein|MHC class II antigen DQB1|MHC class II antigen HLA-DQ-beta-1|MHC class2 antigen|lymphocyte antigen
major histocompatibility complex, class II, DR alpha
Other designations: HLA class II histocompatibility antigen, DR alpha chain|MHC cell surface glycoprotein|MHC class II antigen DRA|histocompatibility antigen HLA-DR alpha
major histocompatibility complex, class II, DR beta 1
Other designations: DW2.2/DR2.2|HLA class II histocompatibility antigen, DR-1 beta chain|MHC class II HLA-DR beta 1 chain|MHC class II HLA-DR-beta cell surface glycoprotein|MHC class II HLA-DRw10-beta|MHC class II antigen|human leucocyte antigen DRB1|lymphocyte antigen DRB1
Other designations: heat shock protein, 32-kD|heme oxygenase 1
nuclear receptor subfamily 4, group A, member 1
Other designations: ST-59|TR3 orphan receptor|early response protein NAK1|growth factor-inducible nuclear protein N10|hormone receptor|nerve growth factor IB nuclear receptor variant 1|nuclear hormone receptor NUR/77|nuclear receptor subfamily 4 group A member 1|orphan nuclear receptor HMR|orphan nuclear receptor TR3|steroid receptor TR3|testicular receptor 3
hydroxysteroid (11-beta) dehydrogenase 2
Other designations: -HSD11 type II|11-DH2|11-beta-HSD2|11-beta-hydroxysteroid dehydrogenase type 2|11-beta-hydroxysteroid dehydrogenase type II|NAD-dependent 11-beta-hydroxysteroid dehydrogenase|corticosteroid 11-beta-dehydrogenase isozyme 2|short chain dehydrogenase/reductase family 9C member 3
Other designations: heat shock 70 kDa protein 6|heat shock 70 kDa protein B'|heat shock 70kD protein 6 (HSP70B')
DnaJ (Hsp40) homolog, subfamily B, member 1
Other designations: DnaJ (Hsp40) homolog, subfmaily B, member 1|dnaJ homolog subfamily B member 1|dnaJ protein homolog 1|hDj-1|heat shock 40 kDa protein 1|heat shock 40kD protein 1|heat shock protein 40|human DnaJ protein 1|radial spoke 16 homolog B
Other designations: GP 150-225|cytotactin|deafness, autosomal dominant 56|glioma-associated-extracellular matrix antigen|hexabrachion (tenascin)|myotendinous antigen|neuronectin|tenascin|tenascin-C additional domain 1|tenascin-C isoform 14/AD1/16
Other designations: ICAM-1|cell surface glycoprotein P3.58|intercellular adhesion molecule 1 (CD54), human rhinovirus receptor|major group rhinovirus receptor
inhibitor of DNA binding 1, dominant negative helix-loop-helix protein
Other designations: DNA-binding protein inhibitor ID-1|class B basic helix-loop-helix protein 24|dJ857M17.1.2 (inhibitor of DNA binding 1, dominant negative helix-loop-helix protein)|inhibitor of differentiation 1
Other designations: 2310061N23Rik|ISG12(a)|interferon alpha-induced 11.5 kDa protein|interferon alpha-inducible protein 27, mitochondrial|interferon-stimulated gene 12a protein
insulin-like growth factor 1 (somatomedin C)
Other designations: IGF-IA|IGF-IB|MGF|insulin-like growth factor I|insulin-like growth factor IA|insulin-like growth factor IB|mechano growth factor|somatomedin-C
insulin-like growth factor binding protein 7
Other designations: IGF-binding protein 7|IGFBP-rP1|PGI2-stimulating factor|angiomodulin|insulin-like growth factor-binding protein 7|prostacyclin-stimulating factor|tumor-derived adhesion factor
Other designations: CCN family member 1|IBP-10|IGF-binding protein 10|IGFBP-10|cysteine-rich heparin-binding protein 61|cysteine-rich, anigogenic inducer, 61|insulin-like growth factor-binding protein 10|protein CYR61
immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides
Other designations: IgJ chain|immunoglobulin J chain
interleukin 3 receptor, alpha (low affinity)
Other designations: CD123 antigen|IL-3 receptor alpha SP2 isoform|IL-3 receptor subunit alpha|IL-3R subunit alpha|IL-3R-alpha|IL-3RA|interleukin-3 receptor subunit alpha
Other designations: CD125 antigen|IL-5 receptor subunit alpha|IL-5R subunit alpha|interleukin 5 receptor type 3|interleukin-5 receptor alpha chain|interleukin-5 receptor subunit alpha
Other designations: B-cell differentiation factor|B-cell stimulatory factor 2|BSF-2|CDF|CTL differentiation factor|IFN-beta-2|hybridoma growth factor|interferon beta-2|interferon, beta 2|interleukin 6 (interferon, beta 2)|interleukin BSF-2|interleukin-6
Other designations: CD127 antigen|IL-7 receptor subunit alpha|IL-7R subunit alpha|IL-7RA|interleukin 7 receptor alpha chain|interleukin 7 receptor isoform H5-6|interleukin-7 receptor subunit alpha
Other designations: T-cell chemotactic factor|alveolar macrophage chemotactic factor I|beta endothelial cell-derived neutrophil activating peptide|beta-thromboglobulin-like protein|chemokine (C-X-C motif) ligand 8|emoctakin|granulocyte chemotactic protein 1|interleukin-8|lung giant cell carcinoma-derived chemotactic protein|lymphocyte derived neutrophil activating peptide|monocyte-derived neutrophil chemotactic factor|monocyte-derived neutrophil-activating peptide|neutrophil-activating peptide 1|small inducible cytokine subfamily B, member 8|tumor necrosis factor-induced gene 1
Other designations: T-cell growth inhibitory factor|cytokine synthesis inhibitory factor|interleukin-10
Other designations: CTLA-8|cytotoxic T-lymphocyte-associated antigen 8|cytotoxic T-lymphocyte-associated protein 8|interleukin 17 (cytotoxic T-lymphocyte-associated serine esterase 8)|interleukin-17A
Other designations: IFN-gamma-inducing factor|IL-1 gamma|iboctadekin|interleukin 18 (interferon-gamma-inducing factor)|interleukin-1 gamma|interleukin-18
Other designations: Inhibin, beta-2|activin AB beta polypeptide|activin beta-B chain|inhibin beta B chain
Other designations: 10 kDa interferon gamma-induced protein|C-X-C motif chemokine 10|gamma IP10|gamma-IP10|interferon-inducible cytokine IP-10|protein 10 from interferon (gamma)-induced cell line|small inducible cytokine subfamily B (Cys-X-Cys), member 10|small-inducible cytokine B10
Other designations: IR-related receptor|insulin receptor-related protein
integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)
Other designations: GPalpha IIb|integrin alpha-IIb|platelet fibrinogen receptor, alpha subunit|platelet membrane glycoprotein IIb|platelet-specific antigen BAK
integrin, alpha 5 (fibronectin receptor, alpha polypeptide)
Other designations: CD49 antigen-like family member E|VLA-5|fibronectin receptor subunit alpha|fibronectin receptor, alpha subunit|integrin alpha-5|integrin alpha-F|very late activation protein 5, alpha subunit
integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)
Other designations: CD11 antigen-like family member A|LFA-1 alpha|LFA-1A|antigen CD11A (p180), lymphocyte function-associated antigen 1, alpha polypeptide|integrin alpha-L|integrin gene promoter|leukocyte adhesion glycoprotein LFA-1 alpha chain|leukocyte function-associated molecule 1 alpha chain|lymphocyte function-associated antigen 1
integrin, alpha M (complement component 3 receptor 3 subunit)
Other designations: CD11 antigen-like family member B|CR-3 alpha chain|antigen CD11b (p170)|cell surface glycoprotein MAC-1 subunit alpha|integrin alpha-M|leukocyte adhesion receptor MO1|macrophage antigen alpha polypeptide|neutrophil adherence receptor alpha-M subunit
integrin, alpha X (complement component 3 receptor 4 subunit)
Other designations: CD11 antigen-like family member C|integrin alpha-X|integrin, alpha X (antigen CD11C (p150), alpha polypeptide)|leu M5, alpha subunit|leukocyte adhesion glycoprotein p150,95 alpha chain|leukocyte adhesion receptor p150,95|leukocyte surface antigen p150,95, alpha subunit|myeloid membrane antigen, alpha subunit|p150 95 integrin alpha chain
Other designations: CD104 antigen|GP150|integrin beta-4|integrin beta-4 subunit
Other designations: Jun activation domain binding protein|activator protein 1|enhancer-binding protein AP1|jun oncogene|p39|proto-oncogene c-Jun|transcription factor AP-1|v-jun avian sarcoma virus 17 oncogene homolog|v-jun sarcoma virus 17 oncogene homolog
potassium voltage-gated channel, Isk-related family, member 1
Other designations: IKs producing slow voltage-gated potassium channel subunit beta Mink|cardiac delayed rectifier potassium channel protein|delayed rectifier potassium channel subunit IsK|minimal potassium channel|potassium voltage-gated channel subfamily E member 1|potassium voltage-gated channel, Isk-related subfamily, member 1|voltage gated potassiun channel accessory subunit
potassium inwardly-rectifying channel, subfamily J, member 1
Other designations: ATP-regulated potassium channel ROM-K|ATP-sensitive inward rectifier potassium channel 1|inward rectifier K(+) channel Kir1.1|inwardly rectifying K+ channel|potassium channel, inwardly rectifying subfamily J member 1
potassium channel, subfamily K, member 2
Other designations: K2P2.1 potassium channel|TREK-1 K(+) channel subunit|TWIK-related potassium channel 1|outward rectifying potassium channel protein TREK-1|potassium channel subfamily K member 2|potassium channel subfamily k member 2 variant 1|potassium channel subfamily k member 2 variant 2|potassium inwardly-rectifying channel, subfamily K, member 2|tandem-pore-domain potassium channel TREK-1|two pore domain potassium channel TREK-1|two pore potassium channel TPKC1|two-pore potassium channel 1
v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog
Other designations: mast/stem cell growth factor receptor Kit|p145 c-kit|piebald trait protein|proto-oncogene c-Kit|proto-oncogene tyrosine-protein kinase Kit|soluble KIT variant 1|tyrosine-protein kinase Kit|v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene-like protein
Other designations: glandular kallikrein 1|kallikrein 1, renal/pancreas/salivary|kallikrein serine protease 1|kallikrein-1|kidney/pancreas/salivary gland kallikrein|tissue kallikrein
Other designations: 58 kda cytokeratin|CK-5|cytokeratin-5|epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types|keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)|keratin, type II cytoskeletal 5|type-II keratin Kb5
Other designations: cytokeratin 8|cytokeratin-8|keratin, type II cytoskeletal 8|type-II keratin Kb8
Other designations: 25 kDa alpha-2-microglobulin-related subunit of MMP-9|lipocalin-2|migration-stimulating factor inhibitor|neutrophil gelatinase-associated lipocalin|oncogene 24p3|p25|siderocalin LCN2
low density lipoprotein receptor-related protein 2
Other designations: Heymann nephritis antigen homolog|LRP-2|calcium sensor protein|glycoprotein 330|low-density lipoprotein receptor-related protein 2|megalin
Other designations: KSPG lumican|keratan sulfate proteoglycan lumican|lumican proteoglycan
Other designations: CD180 antigen|lymphocyte antigen 64|lymphocyte antigen-64, radioprotective, 105kDa|radioprotective 105 kDa protein
v-yes-1 Yamaguchi sarcoma viral related oncogene homolog
Other designations: lck/Yes-related novel protein tyrosine kinase|tyrosine-protein kinase Lyn
tumor-associated calcium signal transducer 2
Other designations: 40kD glycoprotein, identified by monoclonal antibody GA733|cell surface glycoprotein TROP2|cell surface glycoprotein Trop-2|epithelial glycoprotein-1|gastrointestinal tumor-associated antigen GA7331|membrane component chromosome 1 surface marker 1|membrane component, chromosome 1, surface marker 1|pancreatic carcinoma marker protein GA733-1|pancreatic carcinoma marker protein GA7331
Other designations: membrane component chromosome 3 surface marker 1|membrane component, chromosome 3, surface marker 1|transmembrane 4 L6 family member 1|transmembrane 4 superfamily member 1|tumor-associated antigen L6
myristoylated alanine-rich protein kinase C substrate
Other designations: myristoylated alanine-rich C-kinase substrate|myristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L)|phosphomyristin|protein kinase C substrate, 80 kDa protein, light chain
Other designations: MAX-binding protein|antagonizer of myc transcriptional activity|max dimerization protein 1|max dimerizer 1
Other designations: Gicerin|S-endo 1 endothelial-associated antigen|cell surface glycoprotein MUC18|cell surface glycoprotein P1H12|melanoma adhesion molecule|melanoma-associated antigen A32|melanoma-associated antigen MUC18
class II, major histocompatibility complex, transactivator
Other designations: MHC class II transactivator|MHC class II transactivator type III|NLR family, acid domain containing|nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing
matrix metallopeptidase 3 (stromelysin 1, progelatinase)
Other designations: matrix metalloproteinase 3 (stromelysin 1, progelatinase)|matrix metalloproteinase-3|proteoglycanase|stromelysin-1|transin-1
matrix metallopeptidase 7 (matrilysin, uterine)
Other designations: matrilysin|matrin|matrix metalloproteinase 7 (matrilysin, uterine)|matrix metalloproteinase-7|pump-1 protease|uterine matrilysin|uterine metalloproteinase
matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)
Other designations: 92 kDa gelatinase|92 kDa type IV collagenase|macrophage gelatinase|matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)|matrix metalloproteinase-9|type V collagenase
myeloid cell nuclear differentiation antigen
Other designations: C-type lectin domain family 13 member D|macrophage mannose receptor 1|macrophage mannose receptor 1-like protein 1|mannose receptor, C type 1-like 1
Other designations: macrophage acetylated LDL receptor I and II|macrophage scavenger receptor type III|macrophage scavenger receptor types I and II|scavenger receptor class A member 1|scavenger receptor class A, member 1
myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)
Other designations: interferon-induced GTP-binding protein Mx1|interferon-induced protein p78|interferon-regulated resistance GTP-binding protein MxA|myxoma resistance protein 1
growth arrest and DNA-damage-inducible, beta
Other designations: growth arrest and DNA damage-inducible protein GADD45 beta|myeloid differentiation primary response protein MyD118|negative growth regulatory protein MyD118
Other designations: myosin heavy chain 11|myosin heavy chain, smooth muscle isoform|myosin, heavy polypeptide 11, smooth muscle|myosin-11
Other designations: antigen recognized by monoclonal antibody 5.1H11|neural cell adhesion molecule, NCAM
Other designations: 67 kDa neutrophil oxidase factor|NADPH oxidase activator 2|chronic granulomatous disease, autosomal 2|neutrophil NADPH oxidase factor 2|neutrophil cytosol factor 2|neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)
Other designations: G-CSF-induced gene 1 protein|GIG-1 protein|granule membrane protein 17|granule membrane protein of 17 kDa|natural killer cell group 7 sequence|natural killer cell protein 7|protein NKG7
Other designations: NOS type I|constitutive NOS|neuronal NOS|nitric oxide synthase, brain|peptidyl-cysteine S-nitrosylase NOS1
nephrosis 1, congenital, Finnish type (nephrin)
Other designations: nephrin|renal glomerulus-specific cell adhesion receptor
Other designations: 5'-NT|5'-nucleotidase|Purine 5-Prime-Nucleotidase|ecto-5'-nucleotidase
neurotrophic tyrosine kinase, receptor, type 1
Other designations: Oncogene TRK|TRK1-transforming tyrosine kinase protein|gp140trk|high affinity nerve growth factor receptor|tropomyosin-related kinase A|tyrosine kinase receptor A
neurotrophic tyrosine kinase, receptor, type 3
Other designations: ETS related protein-neurotrophic receptor tyrosine kinase fusion protein|ETV6-NTRK3 fusion|GP145-TrkC|NT-3 growth factor receptor|tyrosine kinase receptor C
2'-5'-oligoadenylate synthetase 1, 40/46kDa
Other designations: (2-5')oligo(A) synthase 1|(2-5')oligo(A) synthetase 1|2',5'-oligo A synthetase 1|2',5'-oligoadenylate synthetase 1, 40/46kDa|2'-5' oligoadenylate synthetase 1 p48 isoform|2'-5' oligoadenylate synthetase 1 p52 isoform|2'-5'-oligoadenylate synthase 1|2'-5'-oligoisoadenylate synthetase 1|2-5A synthase 1|2-5A synthetase 1|E18/E16|p46/p42 OAS
Other designations: natural killer cell-enhancing factor A|natural killer-enhancing factor A|peroxiredoxin-1|proliferation-associated gene A|proliferation-associated gene protein|thioredoxin peroxidase 2|thioredoxin-dependent peroxide reductase 2
Other designations: paired box homeotic gene 2|paired box protein Pax-2
Other designations: procollagen C-endopeptidase enhancer 1|procollagen C-proteinase enhancer 1|procollagen COOH-terminal proteinase enhancer 1|procollagen, type 1, COOH-terminal proteinase enhancer|type 1 procollagen C-proteinase enhancer protein|type I procollagen COOH-terminal proteinase enhancer
platelet-derived growth factor beta polypeptide
Other designations: PDGF subunit B|PDGF, B chain|becaplermin|platelet-derived growth factor 2|platelet-derived growth factor B chain|platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)|platelet-derived growth factor subunit B|platelet-derived growth factor, beta polypeptide (oncogene SIS)|proto-oncogene c-Sis
platelet-derived growth factor receptor, beta polypeptide
Other designations: CD140 antigen-like family member B|PDGF-R-beta|PDGFR-beta|beta-type platelet-derived growth factor receptor|platelet-derived growth factor receptor 1|platelet-derived growth factor receptor beta
solute carrier family 26 (anion exchanger), member 4
Other designations: pendrin|sodium-independent chloride/iodide transporter|solute carrier family 26, member 4
Other designations: CFTR-associated protein of 70 kDa|Na(+)/H(+) exchange regulatory cofactor NHE-RF3|PDZ-containing kidney protein 1|na/Pi cotransporter C-terminal-associated protein 1|naPi-Cap1|sodium-hydrogen exchanger regulatory factor 3
platelet/endothelial cell adhesion molecule 1
Other designations: CD31 antigen|platelet endothelial cell adhesion molecule
serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2
Other designations: glia-derived nexin|glial-derived neurite promoting factor|peptidase inhibitor 7|protease nexin I|serpin E2
Other designations: alteplase|plasminogen activator, tissue type|reteplase|t-plasminogen activator|tissue plasminogen activator (t-PA)|tissue-type plasminogen activator
plasminogen activator, urokinase receptor
Other designations: monocyte activation antigen Mo3|u-plasminogen activator receptor form 2|urokinase plasminogen activator surface receptor|urokinase-type plasminogen activator (uPA) receptor
serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2
Other designations: alpha-2-AP|alpha-2-antiplasmin|alpha-2-plasmin inhibitor|serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2|serpin F2
Other designations: GCTM-2 antigen|podocalyxin|podocalyxin-like protein 1
Other designations: B-cell-specific coactivator OBF-1|BOB-1|OCA-B|OCT-binding factor 1|POU domain class 2-associating factor 1|POU domain, class 2, associating factor 1
pro-platelet basic protein (chemokine (C-X-C motif) ligand 7)
Other designations: C-X-C motif chemokine 7|CXC chemokine ligand 7|beta-thromboglobulin|connective tissue-activating peptide III|leukocyte-derived growth factor|low-affinity platelet factor IV|macrophage-derived growth factor|neutrophil-activating peptide 2|neutrophil-activating peptide-2|platelet basic protein|small inducible cytokine B7|small inducible cytokine subfamily B, member 7|small-inducible cytokine B7|thrombocidin 1|thrombocidin 2|thromboglobulin, beta-1
Other designations: homeobox prospero-like protein PROX1|prospero homeobox protein 1|prospero-related homeobox 1
Other designations: HB-GAM|HBBM|HBGF-8|HBNF-1|OSF-1|heparin affin regulatory protein|heparin binding growth factor 8|heparin-binding brain mitogen|heparin-binding growth factor 8|heparin-binding growth-associated molecule|heparin-binding neurite outgrowth-promoting factor 1|neurite growth-promoting factor 1|osteoblast-specific factor 1|pleiotrophin (heparin binding growth factor 8, neurite growth-promoting factor 1)
protein tyrosine phosphatase, receptor type, C
Other designations: CD45 antigen|T200 glycoprotein|T200 leukocyte common antigen|protein tyrosine phosphatase, receptor type, c polypeptide|receptor-type tyrosine-protein phosphatase C
protein tyrosine phosphatase, receptor-type, Z polypeptide 1
Other designations: protein tyrosine phosphatase, receptor-type, zeta polypeptide 1|protein-tyrosine phosphatase receptor type Z polypeptide 2|receptor-type tyrosine phosphatase beta/zeta|receptor-type tyrosine-protein phosphatase zeta
Other designations: rap1 GTPase-activating protein 1
Other designations: CRBP-I|cellular retinol-binding protein I|retinol-binding protein 1|retinol-binding protein 1, cellular
Other designations: PRBP|RBP|plasma retinol-binding protein|retinol-binding protein 4|retinol-binding protein 4, interstitial
Other designations: angiotensin-forming enzyme|angiotensinogenase|renin precursor, renal
Other designations: GTP-binding protein Rit1|GTP-binding protein Roc1|Ric-like, expressed in many tissues|ras-like protein expressed in many tissues|ras-like without CAAX protein 1
ribonuclease, RNase A family, 1 (pancreatic)
Other designations: HP-RNase|RIB-1|RNase 1|RNase A|RNase upI-1|ribonuclease 1|ribonuclease A C1|ribonuclease pancreatic
roundabout, axon guidance receptor, homolog 1 (Drosophila)
Other designations: deleted in U twenty twenty|roundabout homolog 1
roundabout, axon guidance receptor, homolog 2 (Drosophila)
Other designations: roundabout homolog 2
Other designations: RAR-related orphan nuclear receptor variant 2|nuclear receptor ROR-gamma|nuclear receptor RZR-gamma|nuclear receptor subfamily 1 group F member 3|retinoic acid-binding receptor gamma|retinoid-related orphan receptor gamma
Other designations: ribonucleoside-diphosphate reductase subunit M2|ribonucleotide reductase M2 polypeptide|ribonucleotide reductase small chain|ribonucleotide reductase small subunit
Other designations: S100 calcium-binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog)|fibroblast-specific protein-1|leukemia multidrug resistance associated protein|malignant transformation suppression 1|placental calcium-binding protein|protein Mts1|protein S100-A4
Other designations: MLN 4|S100 calcium-binding protein A6 (calcyclin)|calcyclin|growth factor-inducible protein 2A9|prolactin receptor-associated protein|protein S100-A6
Other designations: MRP-8|S100 calcium-binding protein A8 (calgranulin A)|calgranulin A|calgranulin-A|calprotectin L1L subunit|cystic fibrosis antigen|leukocyte L1 complex light chain|migration inhibitory factor-related protein 8|protein S100-A8|urinary stone protein band A
Other designations: MRP-14|S100 calcium-binding protein A9 (calgranulin B)|calgranulin B|calgranulin-B|calprotectin L1H subunit|leukocyte L1 complex heavy chain|migration inhibitory factor-related protein 14|protein S100-A9
sodium channel, voltage-gated, type II, alpha subunit
Other designations: HBSC II|sodium channel protein brain II subunit alpha|sodium channel protein type 2 subunit alpha|sodium channel protein type II subunit alpha|sodium channel protein, brain type 2 alpha subunit|sodium channel, voltage-gated, type II, alpha 1 polypeptide|sodium channel, voltage-gated, type II, alpha 2 polypeptide|voltage-gated sodium channel subtype II|voltage-gated sodium channel subunit alpha Nav1.2
sodium channel, voltage-gated, type VII, alpha subunit
Other designations: putative voltage-gated sodium channel subunit alpha Nax|sodium channel protein cardiac and skeletal muscle subunit alpha|sodium channel protein type 7 subunit alpha|sodium channel protein type VII subunit alpha|sodium channel, voltage-gated, type VI, alpha polypeptide|voltage-dependent sodium channel alpha subunit
sodium channel, non-voltage-gated 1, gamma subunit
Other designations: ENaC gamma subunit|amiloride-sensitive epithelial sodium channel gamma subunit|amiloride-sensitive sodium channel gamma-subunit|amiloride-sensitive sodium channel subunit gamma|epithelial Na(+) channel subunit gamma|gamma-ENaC|gamma-NaCH|nonvoltage-gated sodium channel 1 subunit gamma|sodium channel, nonvoltage-gated 1, gamma
Other designations: C-C motif chemokine 2|monocyte chemoattractant protein 1|monocyte chemoattractant protein-1|monocyte chemotactic and activating factor|monocyte chemotactic protein 1|monocyte secretory protein JE|small inducible cytokine A2 (monocyte chemotactic protein 1, homologous to mouse Sig-je)|small inducible cytokine subfamily A (Cys-Cys), member 2|small-inducible cytokine A2
Other designations: C-C motif chemokine 4|G-26 T-lymphocyte-secreted protein|MIP-1-beta(1-69)|PAT 744|SIS-gamma|T-cell activation protein 2|lymphocyte activation gene 1 protein|macrophage inflammatory protein 1-beta|secreted protein G-26|small inducible cytokine A4 (homologous to mouse Mip-1b)
Other designations: C-C motif chemokine 5|T-cell specific protein p288|beta-chemokine RANTES|eosinophil chemotactic cytokine|regulated upon activation, normally T-expressed, and presumably secreted|small inducible cytokine subfamily A (Cys-Cys), member 5
Other designations: C-C motif chemokine 19|CC chemokine ligand 19|CK beta-11|EBI1 ligand chemokine|EBI1-ligand chemokine|MIP-3-beta|beta chemokine exodus-3|beta-chemokine exodus-3|epstein-Barr virus-induced molecule 1 ligand chemokine|exodus-3|macrophage inflammatory protein 3 beta|macrophage inflammatory protein 3-beta|small inducible cytokine subfamily A (Cys-Cys), member 19|small-inducible cytokine A19
Other designations: C-C motif chemokine 21|Efficient Chemoattractant for Lymphocytes|beta chemokine exodus-2|secondary lymphoid tissue chemokine|small inducible cytokine subfamily A (Cys-Cys), member 21
Other designations: C-X-C motif chemokine 6|Small inducible cytokine subfamily B (Cys-X-Cys), member b|chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2)|chemokine alpha 3|granulocyte chemotactic protein 2|small inducible cytokine subfamily B (Cys-X-Cys), member 6 (granulocyte chemotactic protein 2)|small-inducible cytokine B6
Other designations: CD138 antigen|heparan sulfate proteoglycan fibroblast growth factor receptor|syndecan proteoglycan 1|syndecan-1
Other designations: CD62 antigen-like family member E|E-selectin|ELAM-1|endothelial adhesion molecule 1|endothelial leukocyte adhesion molecule 1|leukocyte endothelial cell adhesion molecule 2|leukocyte-endothelial cell adhesion molecule 2
Other designations: SARP-1|sFRP-2|secreted apoptosis related protein 1|secreted apoptosis-related protein 1
Other designations: SH3 domain protein 2C|SH3 domain-containing GRB2-like protein 3|endophilin-3|endophilin-A3
solute carrier family 3 (amino acid transporter heavy chain), member 1
Other designations: B(0,+)-type amino acid transport protein|SLC3A1 variant B|SLC3A1 variant C|SLC3A1 variant D|SLC3A1 variant E|SLC3A1 variant F|SLC3A1 variant G|amino acid transporter 1|neutral and basic amino acid transport protein rBAT|solute carrier family 3 (cystine, dibasic and neutral amino acid transporters), member 1|solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1|solute carrier family 3 member 1
solute carrier family 4 (anion exchanger), member 1 (Diego blood group)
Other designations: Diego blood group|Froese blood group|Swann blood group|Waldner blood group|Wright blood group|anion exchange protein 1|anion exchanger 1|anion exchanger-1|band 3 anion transport protein|erythrocyte membrane protein band 3|erythroid anion exchange protein|solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)|solute carrier family 4, anion exchanger, number 1
solute carrier family 4 (anion exchanger), member 2
Other designations: AE 2|anion exchange protein 2|anion exchanger 2 type a|anion exchanger 2 type b1|anion exchanger 2 type b2|erythrocyte membrane protein band 3-like 1|non-erythroid band 3-like protein|solute carrier family 4 member 2
solute carrier family 5 (sodium/glucose cotransporter), member 2
Other designations: Na(+)/glucose cotransporter 2|low affinity sodium-glucose cotransporter|sodium/glucose cotransporter 2|solute carrier family 5 (sodium/glucose transporter), member 2|solute carrier family 5 member 2
solute carrier family 8 (sodium/calcium exchanger), member 1
Other designations: Na(+)/Ca(2+)-exchange protein 1|Na+/Ca++ exchanger|Na+/Ca2+ exchanger|sodium/calcium exchanger 1|solute carrier family 8 member 1
solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3
Other designations: NHE-3|Na(+)/H(+) exchanger 3|sodium/hydrogen exchanger 3|solute carrier family 9 (sodium/hydrogen exchanger)|solute carrier family 9 (sodium/hydrogen exchanger), member 3|solute carrier family 9 member 3
solute carrier family 12 (sodium/potassium/chloride transporter), member 1
Other designations: NKCC2A variant A|Na-K-2Cl cotransporter|bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2|kidney-specific Na-K-Cl symporter|solute carrier family 12 (sodium/potassium/chloride transporters), member 1|solute carrier family 12 member 1
solute carrier family 12 (sodium/chloride transporter), member 3
Other designations: Na-Cl cotransporter|Na-Cl symporter|NaCl electroneutral thiazide-sensitive cotransporter|solute carrier family 12 member 3|thiazide-sensitive Na-Cl cotransporter|thiazide-sensitive sodium-chloride cotransporter
solute carrier family 13 (sodium/sulfate symporter), member 1
Other designations: Na(+)/sulfate cotransporter|hNaSi-1|renal sodium/sulfate cotransporter|solute carrier family 13 (sodium/sulfate symporters), member 1|solute carrier family 13 (sodium/sulphate symporters), member 1|solute carrier family 13 member 1
solute carrier family 14 (urea transporter), member 1 (Kidd blood group)
Other designations: Kidd blood group|SLC14A1 JK|urea transporter 1|urea transporter JK glycoprotein|urea transporter, erythrocyte|urea transporter-B1
solute carrier family 17 (organic anion transporter), member 1
Other designations: Na(+)/PI cotransporter 1|na/Pi-4|renal Na(+)-dependent phosphate cotransporter 1|renal sodium-dependent phosphate transport protein 1|renal sodium-phosphate transport protein 1|sodium phosphate transporter|sodium-dependent phosphate transport protein 1|sodium/phosphate cotransporter 1|sodium/phosphate type I cotransporter|solute carrier family 17 (sodium phosphate), member 1|solute carrier family 17 (vesicular glutamate transporter), member 1|solute carrier family 17 member 1
solute carrier family 34 (type II sodium/phosphate contransporter), member 1
Other designations: Na(+)-dependent phosphate cotransporter 2A|Na(+)/Pi cotransporter 2A|Na+-phosphate cotransporter type II|naPi-2a|renal sodium-dependent phosphate transporter|sodium-dependent phosphate transport protein 2A|sodium-phosphate transport protein 2A|sodium/phosphate co-transporter|sodium/phosphate cotransporter 2A|solute carrier family 17 (sodium phosphate), member 2|solute carrier family 34 (sodium phosphate), member 1|solute carrier family 34 member 1
Other designations: HUSI-1|WAP four-disulfide core domain protein 4|antileukoproteinase|mucus proteinase inhibitor|protease inhibitor WAP4|secretory leukocyte protease inhibitor (antileukoproteinase)|seminal proteinase inhibitor
Other designations: extracellular superoxide dismutase [Cu-Zn]
Other designations: SRY (sex-determining region Y)-box 9 protein|SRY-related HMG-box, gene 9|transcription factor SOX-9
Other designations: SPP1/CALPHA1 fusion|early T-lymphocyte activation 1|nephropontin|osteopontin|osteopontin/immunoglobulin alpha 1 heavy chain constant region fusion protein|secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1)|urinary stone protein|uropontin
Other designations: synaptotagmin 1|synaptotagmin-1|sytI
Other designations: 22 kDa actin-binding protein|SM22-alpha|smooth muscle protein 22-alpha|transgelin variant 2
Other designations: T-box 1 transcription factor C|T-box transcription factor TBX1|Testis-specific T-box protein|brachyury
nuclear receptor subfamily 2, group F, member 2
Other designations: ADP-ribosylation factor related protein 1|COUP transcription factor 2|COUP transcription factor II|apolipoprotein A-I regulatory protein 1|apolipoprotein AI regulatory protein 1|chicken ovalbumin upstream promoter transcription factor 2|chicken ovalbumin upstream promoter-transcription factor I
Other designations: polypeptide P1.B|trefoil factor 3
Other designations: TGF-beta-1|latency-associated peptide|prepro-transforming growth factor beta-1|transforming growth factor beta-1
Other designations: TGF-beta-3|prepro-transforming growth factor beta-3|transforming growth factor beta-3
transforming growth factor, beta-induced, 68kDa
Other designations: RGD-CAP|RGD-containing collagen-associated protein|beta ig-h3|kerato-epithelin|transforming growth factor-beta-induced protein ig-h3
Other designations: CD141 antigen|fetomodulin
Other designations: TIMP-1|collagenase inhibitor|erythroid potentiating activity|erythroid-potentiating activity|fibroblast collagenase inhibitor|metalloproteinase inhibitor 1|tissue inhibitor of metalloproteinases 1
Other designations: TIMP-2|metalloproteinase inhibitor 2|tissue inhibitor of metalloproteinase 2|tissue inhibitor of metalloproteinases 2
Other designations: toll/interleukin 1 receptor-like 4|toll/interleukin-1 receptor-like protein 4
Other designations: TMDVCF|claudin-5|transmembrane protein deleted in VCFS|transmembrane protein deleted in velocardiofacial syndrome
Other designations: DNA gyrase|DNA topoisomerase (ATP-hydrolyzing)|DNA topoisomerase 2-alpha|DNA topoisomerase II, 170 kD|DNA topoisomerase II, alpha isozyme
Other designations: Epstein-Bar virus-induced protein 6
Other designations: E3 ubiquitin-protein ligase TRAF2|tumor necrosis factor type 2 receptor associated protein 3|tumor necrosis factor type 2 receptor-associated protein 3
Other designations: Tamm-Horsfall urinary glycoprotein|uromucoid
Other designations: uroplakin II|uroplakin-2
Other designations: uroplakin III|uroplakin-3a
Other designations: CD106 antigen|vascular cell adhesion protein 1
Other designations: vascular permeability factor
Other designations: neuro-endocrine specific protein VGF|neurosecretory protein VGF
Other designations: epididymis luminal protein 113
wingless-type MMTV integration site family member 2
Other designations: Int-1-related protein|int-1-like protein 1|protein Wnt-2|secreted growth factor
Other designations: Wilms tumor protein|amino-terminal domain of EWS|last three zinc fingers of the DNA-binding domain of WT1
nephrosis 2, idiopathic, steroid-resistant (podocin)
Other designations: C-X-C chemokine receptor type 4|CD184 antigen|SDF-1 receptor|fusin|leukocyte-derived seven transmembrane domain receptor|lipopolysaccharide-associated protein 3|neuropeptide Y receptor Y3|seven transmembrane helix receptor|seven-transmembrane-segment receptor, spleen|stromal cell-derived factor 1 receptor
Other designations: placental protein 5|retinal pigment epithelium cell factor 1
cubilin (intrinsic factor-cobalamin receptor)
Other designations: 460 kDa receptor|cubilin|cubilin precursor variant 1|cubilin precursor variant 2|intestinal intrinsic factor receptor|intrinsic factor-vitamin B12 receptor
Other designations: phosphatonin|tumor-derived hypophosphatemia inducing factor
solute carrier family 14 (urea transporter), member 2
Other designations: solute carrier family 14 member 2|urea transporter 2|urea transporter, kidney|urea transporter-2
Other designations: axin-2|axin-like protein|axis inhibition protein 2|conductin
Other designations: neuropilin-1|transmembrane receptor|vascular endothelial cell growth factor 165 receptor
aldehyde dehydrogenase 1 family, member A2
Other designations: RALDH 2|retinal dehydrogenase 2|retinaldehyde-specific dehydrogenase type 2
sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A
Other designations: sema F|semaphorin F|semaphorin-5A|semaphorin-F
Other designations: anaphase spindle elongation 1 homolog|protein regulating cytokinesis 1
Other designations: claudin-1|senescence-associated epithelial membrane protein 1
Other designations: G2/mitotic-specific cyclin-B2
Other designations: interleukin-32|interleukin-32 eta|interleukin-32 small|interleukin-32 theta|natural killer cell transcript 4|natural killer cells protein 4|tumor necrosis factor alpha-inducing factor
Other designations: neuronal protein 3.1|neuronal regeneration related protein homolog|neuronal regeneration-related protein|protein p311
Other designations: hemoglobin scavenger receptor|macrophage-associated antigen|scavenger receptor cysteine-rich type 1 protein M130
solute carrier family 22 (organic anion transporter), member 6
Other designations: PAH transporter|hPAHT|hROAT1|organic anion transporter 1|para-aminohippurate transporter|renal organic anion transporter 1|solute carrier family 22 member 6
solute carrier family 22 (organic anion transporter), member 8
Other designations: hOAT3|organic anion transporter 3|solute carrier family 22 member 8
Other designations: neurexin I|neurexin-1-beta
solute carrier family 22 (organic anion/urate transporter), member 13
Other designations: organic cation transporter-like 3|organic cationic transporter-like 3|organic-cation transporter like 3|solute carrier family 22 (organic anion transporter), member 13|solute carrier family 22 member 13|solute carrier family 22, member 13
Other designations: ASP4|TA01/TA02|asp 4|aspartyl protease 4|kidney-derived aspartic protease-like protein|napsin-1|napsin-A|pronapsin A
ADAM metallopeptidase with thrombospondin type 1 motif, 2
Other designations: A disintegrin and metalloproteinase with thrombospondin motifs 2|a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2|procollagen I N-proteinase|procollagen I/II amino propeptide-processing enzyme|procollagen N-endopeptidase
apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B
Other designations: DNA dC->dU-editing enzyme APOBEC-3B|apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3B|cytidine deaminase|phorbolin 2|phorbolin 3|phorbolin-1-related protein|phorbolin-2/3|probable DNA dC->dU-editing enzyme APOBEC-3B
Other designations: GTPase activating protein|H_DJ1108A12.1|S914|WUGSC:H_DJ0283M22.1|WUGSC:H_DJ1108A12.1|regulator of G-protein signalling 6
Ras association (RalGDS/AF-6) domain family member 2
Other designations: Ras association (RalGDS/AF-6) domain family 2|centromere protein 34|ras association domain-containing protein 2
Other designations: SMAD interacting protein 1|Smad-interacting protein 1|zinc finger E-box-binding homeobox 2|zinc finger homeobox 1b
purinergic receptor P2Y, G-protein coupled, 14
Other designations: G protein coupled receptor for UDP-glucose|G protein-coupled receptor 105|G-protein coupled receptor 105|P2Y purinoceptor 14|P2Y(14) receptor|P2Y14 receptor|UDP-glucose receptor
collagen, type IV, alpha 3 (Goodpasture antigen) binding protein
Other designations: StAR-related lipid transfer (START) domain containing 11|ceramide transfer protein|ceramide transporter|collagen type IV alpha-3-binding protein|hCERT|lipid-transfer protein CERTL
Other designations: ADP ribosylation factor-like protein 7|ADP-ribosylation factor-like 7|ADP-ribosylation factor-like protein 4C|ADP-ribosylation factor-like protein 7|ADP-ribosylation factor-like protein LAK
Other designations: CD96 antigen|T cell activation, increased late expression|T-cell surface protein tactile|cell surface antigen CD96|t cell-activated increased late expression protein
receptor (G protein-coupled) activity modifying protein 2
Other designations: CRLR activity-modifying protein 2|calcitonin receptor-like receptor activity modifying protein 2|calcitonin-receptor-like receptor activity-modifying protein 2|receptor (calcitonin) activity modifying protein 2|receptor activity modifying protein 2|receptor activity-modifying protein 2|receptor-activity-modifying protein 2
receptor (G protein-coupled) activity modifying protein 3
Other designations: CRLR activity-modifying protein 3|calcitonin receptor-like receptor activity modifying protein 3|calcitonin-receptor-like receptor activity-modifying protein 3|receptor (calcitonin) activity modifying protein 3|receptor activity modifying protein 3|receptor activity-modifying protein 3|receptor-activity-modifying protein 3
leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2
Other designations: CD85 antigen-like family member D|Ig-like transcript 4|leukocyte immunoglobulin-like receptor subfamily B member 2|monocyte/macrophage immunoglobulin-like receptor 10
Other designations: A20-binding inhibitor of NF-kappa-B activation 1|HIV-1 Nef-interacting protein|Nef-associated factor 1 SNP|TNFAIP3-interacting protein 1|virion-associated nuclear shuttling protein
Other designations: WAP domain containing protein HE4-V4|WAP four-disulfide core domain protein 2|epididymal protein 4|epididymal secretory protein E4|epididymis-specific, whey-acidic protein type, four-disulfide core|major epididymis-specific protein E4|putative protease inhibitor WAP5
brain abundant, membrane attached signal protein 1
Other designations: 22 kDa neuronal tissue-enriched acidic protein|brain acid soluble protein 1|brain acid-soluble protein 1|neuronal axonal membrane protein NAP-22|neuronal tissue-enriched acidic protein
interferon induced transmembrane protein 3
Other designations: dispanin subfamily A member 2b|interferon-induced transmembrane protein 3|interferon-inducible protein 1-8U
C-type lectin domain family 10, member A
Other designations: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13 (macrophage-derived)|C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 14 (macrophage-derived)|C-type lectin domain family 10 member A|macrophage lectin 2 (calcium dependent)
cAMP responsive element binding protein 3
Other designations: CREB-3|basic leucine zipper protein|cAMP-responsive element-binding protein 3|cyclic AMP response element (CRE)-binding protein/activating transcription factor 1|cyclic AMP-responsive element-binding protein 3|leucin zipper proitein|leucine zipper protein|transcription factor LZIP-alpha
Other designations: developmental arteries and neural crest EGF-like protein|fibulin-5|urine p50 protein
Other designations: B-cell chemoattractant|B-cell-attracting chemokine 1|B-cell-homing chemokine (ligand for Burkitt's lymphoma receptor-1)|B-lymphocyte chemoattractant|C-X-C motif chemokine 13|CXC chemokine BLC|b cell-attracting chemokine 1|b lymphocyte chemoattractant|chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant)|small inducible cytokine B subfamily (Cys-X-Cys motif), member 13 (B-cell chemoattractant)|small-inducible cytokine B13
Other designations: T-cell activation protein 519|T-lymphocyte activation gene 519|lymphocyte-activation gene 2|lymphokine LAG-2
interferon induced transmembrane protein 2
Other designations: dispanin subfamily A member 2c|interferon-induced transmembrane protein 2|interferon-inducible protein 1-8D
Other designations: osteoblast specific factor 2 (fasciclin I-like)|periodontal ligament-specific periostin|periostin
solute carrier family 17 (organic anion transporter), member 3
Other designations: Na(+)/PI cotransporter 4|sodium-dependent phosphate transport protein 4|sodium/phosphate cotransporter 4|solute carrier family 17 (sodium phosphate), member 3
solute carrier family 22 (organic anion transporter), member 7
Other designations: hOAT2|liver-specific transporter|novel liver transporter|organic anion transporter 2|solute carrier family 22 member 7
Other designations: fibrinogen-like protein 2|fibroleukin
Other designations: tetraspanin-21|tspan-21|uroplakin Ia|uroplakin-1a
Other designations: cyclin-selective ubiquitin carrier protein|mitotic-specific ubiquitin-conjugating enzyme|ubiquitin-conjugating enzyme E2 C|ubiquitin-protein ligase C
Other designations: LIM domain-binding protein 3|PDZ and LIM domain 6|Z-band alternatively spliced PDZ motif protein|Z-band alternatively spliced PDZ-motif protein|cardiomyopathy, dilated 1C (autosomal dominant)|protein cypher
ADAM metallopeptidase with thrombospondin type 1 motif, 6
Other designations: A disintegrin and metalloproteinase with thrombospondin motifs 6|a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6
Other designations: YLSR571|axon guidance molecule|laminet 1|laminet-1|netrin G1f|netrin-G1
Other designations: EMILIN-4|elastin microfibril interface located protein 4|elastin microfibril interfacer 4|endothelial cell multimerin|glycoprotein Ia*|multimerin-1
Other designations: ELL-related RNA polymerase II, elongation factor|RNA polymerase II elongation factor ELL2
Other designations: extracellular sulfatase Sulf-1|sulfatase FP
sel-1 suppressor of lin-12-like 3 (C. elegans)
Other designations: protein sel-1 homolog 3|suppressor of lin-12-like protein 3
Other designations: DNA-binding protein SATB2|SATB family member 2|special AT-rich sequence-binding protein 2
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
Other designations: DEAD box protein 58|DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide|RIG-1|RIG-I-like receptor 1|RNA helicase RIG-I|probable ATP-dependent RNA helicase DDX58|retinoic acid inducible gene I|retinoic acid-inducible gene 1 protein|retinoic acid-inducible gene I protein
Other designations: Cas ligand with multiple Src homology 3 (SH3) domains|adapter protein CMS|cas ligand with multiple SH3 domains
Other designations: T cell immunoglobin domain and mucin domain protein 1|T-cell immunoglobulin mucin family member 1|T-cell immunoglobulin mucin receptor 1|T-cell membrane protein 1|kidney injury molecule 1
Other designations: DC-lysosome-associated membrane glycoprotein|lysosome-associated membrane glycoprotein 3
dickkopf WNT signaling pathway inhibitor 3
Other designations: RIG-like 5-6|RIG-like 7-1|dickkopf 3 homolog|dickkopf homolog 3|dickkopf-3|dickkopf-related protein 3|dkk-3|hDkk-3|regulated in glioma
Other designations: C2H2 zinc finger protein SALL3|hSALL3|sal-like protein 3|spalt-like zinc finger protein|zinc finger protein 796
Other designations: B cell adaptor containing SH2 domain|B cell linker protein|B-cell activation|B-cell adapter containing a SH2 domain protein|B-cell adapter containing a Src homology 2 domain protein|B-cell linker protein|Src homology 2 domain-containing leukocyte protein of 65 kDa|Src homology [SH2] domain-containing leukocyte protein of 65 kD|cytoplasmic adapter protein
Other designations: T-box expressed in T cells|T-box protein 21|T-box transcription factor TBX21|T-cell-specific T-box transcription factor T-bet|transcription factor TBLYM
Other designations: C-type lectin domain family 4 member L|C-type lectin domain family 4, member L|CD209 antigen|HIV gpl20-binding protein|dendritic cell-specific ICAM-3-grabbing non-integrin 1|dendritic cell-specific intracellular adhesion molecules (ICAM)-3 grabbing non-integrin
Other designations: EH domain containing 3|EH domain-containing protein 3|PAST homolog 3
Other designations: FOXP3delta7|forkhead box protein P3|immune dysregulation, polyendocrinopathy, enteropathy, X-linked|immunodeficiency, polyendocrinopathy, enteropathy, X-linked|scurfin
Other designations: chemokine-like factor 1|chemokine-like factor 2|chemokine-like factor 3|chemokine-like factor 4|transmembrane proteolipid
marginal zone B and B1 cell-specific protein
Other designations: HSPC190|caspase-2 binding protein|marginal zone B- and B1-cell-specific protein|mesenteric estrogen-dependent adipose 7|mesenteric oestrogen-dependent adipose gene- 7|plasma cell-induced ER protein 1|plasma cell-induced resident ER protein|plasma cell-induced resident endoplasmic reticulum protein|proapoptotic caspase adapter protein|proapoptotic caspase adaptor protein
Other designations: 19 kDa FK506-binding protein|19 kDa FKBP|FK506-binding protein 11|FKBP-11|FKBP-19|PPIase FKBP11|peptidyl-prolyl cis-trans isomerase FKBP11|rotamase
Other designations: IL-23 subunit alpha|IL-23-A|IL-23p19|JKA3 induced upon T-cell activation|interleukin 23 p19 subunit|interleukin-23 subunit alpha|interleukin-23 subunit p19|interleukin-six, G-CSF related factor
Other designations: NAG/BC035112 fusion|NAG/FAM49A fusion|neuroblastoma-amplified gene protein|neuroblastoma-amplified sequence
Other designations: MUC-14|endomucin-2|gastric cancer antigen Ga34|mucin-14
Other designations: chloride intracellular channel protein 5
FXYD domain containing ion transport regulator 4
Other designations: FXYD domain-containing ion transport regulator 4|channel-inducing factor
Other designations: cytokeratin 20|cytokeratin-20|keratin, type I cytoskeletal 20|keratin-20|protein IT
Other designations: CP-Mac carboxypeptidase|VCP-like protein|carboxypeptidase WUG|probable serine carboxypeptidase CPVL|vitellogenic carboxypeptidase-like protein
Other designations: PC12 ETS domain-containing transcription factor 1|fifth Ewing variant protein|protein FEV
Other designations: paralemmin-like protein|paralemnin-like protein
Other designations: MI oxygenase|aldehyde reductase (aldose reductase) like 6|aldehyde reductase-like 6|inositol oxygenase|kidney-specific protein 32|renal-specific oxidoreductase
transient receptor potential cation channel, subfamily V, member 5
Other designations: ECaC|calcium transport protein 2|calcium transporter 2|epithelial calcium channel 1|osm-9-like TRP channel 3|transient receptor potential cation channel subfamily V member 5
HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2
Other designations: E3 ubiquitin-protein ligase HECW2|HECT, C2 and WW domain-containing protein 2|NEDD4-like E3 ubiquitin-protein ligase 2|NEDD4-related E3 ubiquitin ligase NEDL2
Other designations: RNA-binding protein RBP|SURP and G-patch domain-containing protein 1|splicing factor 4
pleckstrin homology domain containing, family B (evectins) member 1
Other designations: PH domain containing protein in retina 1|PH domain containing, retinal 1|PH domain-containing family B member 1|PH domain-containing protein in retina 1|evectin-1|pleckstrin homology domain retinal protein 1|pleckstrin homology domain-containing family B member 1
Other designations: kidney and liver proline oxidase 1|probable proline dehydrogenase 2|probable proline oxidase 2
Other designations: pappalysin-2|placenta-specific 3|pregnancy-associated plasma preproprotein-A2|pregnancy-associated plasma protein E1
piezo-type mechanosensitive ion channel component 2
Other designations: family with sequence similarity 38, member A pseudogene|family with sequence similarity 38, member B2|piezo-type mechanosensitive ion channel component 1 pseudogene|protein PIEZO2
interferon induced with helicase C domain 1
Other designations: CADM-140 autoantigen|DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide|RIG-I-like receptor 2|RNA helicase-DEAD box protein 116|clinically amyopathic dermatomyositis autoantigen 140 kDa|helicard|helicase with 2 CARD domains|interferon-induced helicase C domain-containing protein 1|melanoma differentiation associated protein-5|melanoma differentiation-associated protein 5|murabutide down-regulated protein
membrane-spanning 4-domains, subfamily A, member 6A
Other designations: CD20 antigen-like 3|CD20-like precusor|HAIRB-iso|MS4A6A-polymorph|four-span transmembrane protein 3|four-span transmembrane protein 3.1|four-span transmembrane protein 3.2|membrane-spanning 4-domains subfamily A member 6A
Other designations: SRY-related HMG-box transcription factor SOX17|transcription factor SOX-17
Other designations: DNA replication complex GINS protein PSF3
solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3
Other designations: Na(+)/dicarboxylate cotransporter 3|hNaDC3|naDC-3|sodium-dependent high affinity dicarboxylate transporter 3|sodium-dependent high-affinity dicarboxylate transporter 2|solute carrier family 13 member 3
poliovirus receptor related immunoglobulin domain containing
Other designations: poliovirus receptor-related immunoglobulin domain-containing protein|transmembrane protein PVRIG
Other designations: multiple C2 and transmembrane domain-containing protein 1|multiple C2-domains with two transmembrane regions 1
Other designations: CAR-like membrane protein|adipocyte adhesion molecule|adipocyte-specific adhesion molecule|coxsackie- and adenovirus receptor-like membrane protein
Other designations: coiled-coil domain-containing protein 102B
Other designations: DENN domain-containing protein 2D|RP5-1180E21.2
Other designations: Fc receptor-like protein 5|fc receptor homolog 5|fcR-like protein 5|immune receptor translocation-associated protein 2|immunoglobulin superfamily receptor translocation associated 2 (IRTA2)
Other designations: fenestrated endothelial-linked structure protein|fenestrated-endothelial linked structure protein; PV-1 protein|plasmalemma vesicle protein 1|plasmalemma vesicle-associated protein
solute carrier family 4, sodium bicarbonate cotransporter, member 9
Other designations: anion exchange protein 4|anion exchanger 4|sodium bicarbonate cotransporter 5|solute carrier family 4, sodium bicarbonate cotransporter-like, member 9
solute carrier family 4, sodium borate transporter, member 11
Other designations: bicarbonate transporter related protein 1|sodium bicarbonate transporter-like protein 11|sodium-coupled borate cotransporter 1|solute carrier family 4, sodium bicarbonate transporter-like, member 11
protein phosphatase 1, regulatory (inhibitor) subunit 1B
Other designations: dopamine and cAMP-regulated neuronal phosphoprotein 32|protein phosphatase 1 regulatory subunit 1B
major facilitator superfamily domain containing 2A
Other designations: major facilitator superfamily domain-containing protein 2A
Other designations: acyl-CoA:glycine N-acyltransferase-like protein 1|glutamine N-acyltransferase|glycine N-acyltransferase-like protein 1
Other designations: SP140L-1 protein|SP140L-2 protein|SP140L-3 protein|nuclear body protein SP140-like protein
Other designations: NACHT domain-, leucine-rich repeat-, and PYD-containing protein 3|NACHT, LRR and PYD containing protein 3|NACHT, LRR and PYD domains-containing protein 3|PYRIN-containing APAF1-like protein 1|caterpiller protein 1.1|cold autoinflammatory syndrome 1 protein|cryopyrin|nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3
solute carrier family 26 (anion exchanger), member 7
Other designations: anion exchange transporter|solute carrier family 26, member 7|sulfate anion transporter
solute carrier family 5 (sodium/inositol cotransporter), member 11
Other designations: Na(+)/myo-inositol cotransporter 2|homolog of rabbit KST1|putative sodium-coupled cotransporter RKST1|sodium-dependent glucose cotransporter|sodium/glucose cotransporter KST1|sodium/myo-inositol cotransporter 2|sodium/myo-inositol transporter 2|solute carrier family 5 (sodium/glucose cotransporter), member 11
Other designations: 2-acylglycerol O-acyltransferase 1|acyl-CoA:monoacylglycerol acyltransferase 1|diacylglycerol O-acyltransferase 2 like 1|diacylglycerol O-acyltransferase candidate 2|diacylglycerol acyltransferase 2-like protein 1|hDC2
family with sequence similarity 129, member A
Other designations: cell growth-inhibiting gene 39 protein|protein Niban
acyl-CoA synthetase medium-chain family member 2A
Other designations: Homolog of rat kidney-specific (KS)|acyl-coenzyme A synthetase ACSM2A, mitochondrial|butyrate--CoA ligase 2A|butyryl-coenzyme A synthetase 2A|middle-chain acyl-CoA synthetase 2A
ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3
Other designations: ATPase, H+ transporting, lysosomal (vacuolar proton pump) subunit G3|V-ATPase 13 kDa subunit 3|V-ATPase G subunit 3|V-ATPase G3 subunit|V-ATPase subunit G 3|V-type proton ATPase subunit G 3|vacuolar ATP synthase subunit G 3|vacuolar proton pump G subunit 3|vacuolar proton pump subunit G 3|vacuolar proton pump, subunit G3
Other designations: GATA binding factor-5|GATA-binding factor 5|GATA-binding protein 5|transcription factor GATA-5
Other designations: TBC/LysM-associated domain-containing protein 2|TLD domain containing 2|TLD domain-containing protein 2
transient receptor potential cation channel, subfamily M, member 6
Other designations: channel kinase 2|melastatin-related TRP cation channel 6|transient receptor potential cation channel subfamily M member 6
Other designations: solute carrier family 35 member F3
solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12
Other designations: electroneutral sodium monocarboxylate cotransporter|low-affinity sodium-lactate cotransporter|sodium-coupled monocarboxylate transporter 2|sodium-iodide related cotransporter|solute carrier family 5 (sodium/glucose cotransporter), member 12|solute carrier family 5 member 12
Other designations: BDCA-2|C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 11|C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7|C-type lectin domain family 4 member C|C-type lectin superfamily member 7|blood dendritic cell antigen 2 protein|dendritic cell lectin b|dendritic lectin
Other designations: genethonin-2|myopodin|synaptopodin-2
Other designations: choline transporter-like protein 5
ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2
Other designations: V-ATPase subunit d 2|V-type proton ATPase subunit d 2|vacuolar proton pump subunit d 2
ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2
Other designations: V-ATPase C2 subunit|V-ATPase subunit C 2|V-type proton ATPase subunit C 2|vacuolar proton pump subunit C 2
Other designations: IL-27 p28 subunit|IL-27 subunit alpha|IL-27-A|IL27-A|interleukin 30|interleukin-27 subunit alpha
Other designations: mitotic kinetics regulator
Other designations: immunoglobulin superfamily member 4D|immunoglobulin superfamily, member 4D|nectin-like 3|nectin-like protein 3|synaptic cell adhesion molecule 2
MPV17 mitochondrial membrane protein-like
Other designations: M-LP homolog|Mpv17-like protein type 1|Mpv17-like protein type 2|mpv17-like protein
long intergenic non-protein coding RNA 521
Other designations: C-type lectin domain family 9 member A|HEEE9341
Other designations: crumbs homolog 2|crumbs-like protein 2|protein crumbs homolog 2
Other designations: ceh-10 homeo domain containing homolog|ceh-10 homeodomain-containing homolog|homeobox protein CHX10
acyl-CoA synthetase medium-chain family member 2B
Other designations: acyl-CoA synthetase medium-chain family member 2|acyl-coenzyme A synthetase ACSM2B, mitochondrial|butyrate--CoA ligase 2B|butyryl-coenzyme A synthetase 2B|middle-chain acyl-CoA synthetase 2B|xenobiotic/medium-chain fatty acid-CoA ligase HXM-A|xenobiotic/medium-chain fatty acid:CoA ligase
Other designations: Nogo-66 receptor homolog 1|nogo receptor-like 3|nogo-66 receptor-related protein 2|reticulon-4 receptor-like 2
protein tyrosine phosphatase, receptor type, Q
Other designations: phosphatidylinositol phosphatase PTPRQ|phosphotidylinositol phosphatase PTPRQ|protein-tyrosine phosphatase, receptor-type, expressed by glomerular mesangial cells
Other designations: notch-regulated ankyrin repeat-containing protein
Other designations: CD24 antigen (small cell lung carcinoma cluster 4 antigen)|signal transducer CD24
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A representation of an image that supports an inference to an assertion about some quality of a patient.
A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A process in which at least one bodily component of an organsim participates.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060
A bodily process that is clinically abnormal.
The representation of a conclusion of a diagnostic process.
TODO: Define.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure.
At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.
A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes.
social security number
A social role inhering in a human being.
human social role
party to a legal entity
party to a legal proceeding
party to a legal agreement
party to a marriage contract
party to a power of attorney
A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
male gender
male gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
female gender
female gender role
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
health care role
human health care role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
Amanda Hicks
patient
CAFE domain expert working group.
In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
physician
physician role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
nurse
based on: http://en.wikipedia.org/wiki/Nursing
nurse role
Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division).
health care provider organization role
person health care provider role
A health care provider organization role that inheres in an organization consisting of two or more physicians.
physician practice
A health care provider organization role that inheres in an organization that is comprised of other organizations.
integrated delivery network
An object aggregate of organisms.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
collection of organisms
An object aggregate all of whose components are human beings.
collection of humans
A role inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A role in human social processes that inheres in an organization.
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
organization social role
A role in human social processes that inheres in an organism.
William R. Hogan Mathias Brochhausen
Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
Previous definition: A role in human social processes played by an organism.
organism social role
An organization social role that is realized by a health care process.
Previous definition: An organization social role played by an organization in health care processes.
organization health care role
A patient role that inheres in a human being.
human patient role
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
A role that inheres in an organism and is realized by habitually smoking tobacco products.
smoker role
material entity role
A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
hospital role
An organization social role that inheres in an organization and is realized by providing formal education to students.
school role
An organization that is the bearer of a school role.
school organization
A human social role that is realized by the process of formal education that the bearer undergoes.
student role
nursery school role
primary school role
secondary school role
A trauma patient role that inheres in a homo sapiens who is under the age of 15 years.
pediatric trauma patient
The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years."
pediatric trauma patient role
A patient role that inheres an organism suffering one or more injuries.
injured patient
The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries.
injured patient role
A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn.
The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn.
burn patient
burn patient role
A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient.
physiatrist
The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine.
Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.
physiatrist role
A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury.
trauma patient
The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury.
trauma patient role
A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
residence function
A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function.
household
employee role
A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person.
http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015
US Census reference person role
A role that concretizes a socio-lega generically dependent continuant
socio-legal human social role
A socio-legal human social role that concretizes a socio-legally generically dependent continuat that was created by a declaration performed by an organization.
human role within an organization
employer role
payer role
party to an insurance policy
A US Census unemployed role is a human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff.
US Census unemployed role
A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon.
US physician assistant role
A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication.
anesthesiologist role
surgeon role
A surgeon role realized by its bearer using performing neurosurgery.
neurosurgereon role
A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products.
heavy smoker role
A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products.
light smoker role
employment data
income data
government assistance health care plan data
health care plan data
government assistance income data
WIC data
socio-economic data
A planned process that achieves the planned objective of precision medicine objective. Specifically, it is a medical process that includes the customization of healthcare, with medical decisions, treatments, practices, or products being tailored to the individual patient.
precision medicine process
An investigation that is targeted for precision medicine
precision medicine investigation
the number of people living together supported jointly by an household income
We may use IRS's definition: https://www.healthcare.gov/income-and-household-information/household-size/
household size
more than 5.5 pounds (2500 grams) birth weight
less than 5.5 pounds (2500 grams) birth weight
unknown birth weight
birth weight declined to answer
individual plan insurance (paid by the member)
group plan insurance through employee union
USA government health plan insurance
no insurance status
body temperature measured orally
body temprature by ear (tempanic, aural)
body temprature by forhead
arterial line body temperature
body temprature by other measurement
An education level that indicates a grade of higher than 7th but lower than 12 as the highest level of educational achievement.
higher than 7th but less than 12th Grade education level
direct serum bilirubin level
precision medicine objective
An education level that indicates the 7th grade complete or less as the highest level of educational achievement.
less than 8th Grade education level
An education level that indicates that the highest level of education achievement for a person is a high school completion, GED, or equivalent
high school completion, GED or equivalent
An information content entity that is the answer to a specific question
answer to question
An answer to question where the answer is Yes.
yes answer to question
An answer to question where the answer is No.
no answer to question
An answer to question that indicates the response to the specified question is unknown.
unknown answer to question
A do not know answer to question that is answered due to data unavailable
do not know due to data unavailable answer to question
An answer to question where one declines to answer the specified question.
declined to answer to question
An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box
other answer to question
An answer to question that is not listed in the whole list of response options
none answer to question
A textual entity that is a question presented in text
textual question
medical history form
A form with questions that is used to assess a person's eligibility to participate in a specific study (e.g., kidney precision medicine project).
eligibility assessment form
A form with questions that includes statistical data related to particular groups within a population where a person belongs to
demographic information form
physical measurement form
A textual question that includes a list of enumerated answers
question with enumerated responses
A question that has two primary and definitive answers: Yes and No, and there may be other given options like Don't know or Decline to answer.
question with yes and no responses
A question with enumerated responses where one can only choose one answer.
question with enumerated responses where only one answer chosen
A question with enumerated responses where one can choose multiple answers.
question with enumerated responses where multiple answers may be chosen
A case report form (or CRF) is a paper or electronic questionnaire specifically used in clinical trial research
Oliver He, Edison Ong, Fred Dowd, Hong Yu
case report form
laboratory result form
new patient form
biopsy procedure form
kidney biopsy procedure form
consent form
paper form
Medical records release form is usually required to be a paper form that should be signed by the patient who agrees to have his/her medical records released.
paper form with signature required
A public health process that involves clean drinking water and adequate treatment and disposal of human and animal excreta and sewage.
sanitation
A form that includes the information of contact for a person
contact information form
biosample collection form
clinic reception form
medications form
participant study status form
hospitalization form
personal history form
AKI hospitalization form
CKD hospitalization form
participant reported outcome measures form
health literacy questionnaire form
biopsy safety checklist form
post biopsy form
A clinical report form that covers the information about the tracking of biopsied tissue
tissue tracking form
pathology images upload form
diagnostic core .jpg images QC form
diagnostic core - disease categories form
central path quality metrics assessment Dx core form
central path quality metrics assessment interrogation core form
post-biopsy patient experience survey form
adverse event entry form
month of year
The first month of the year in the Gregorian calendar
January
The second month of the year in the Gregorian calendar.
February
The third month of the year in the Gregorian calendar.
March
The4th month of the year in the Gregorian calendar
April
The 5th month of the year in the Gregorian calendar
May
The 6th month of the year in the Gregorian calendar
June
The 7th month of the year in the Gregorian calendar
July
The 8th month of the year in the Gregorian calendar
August
The 9th month of the year in the Gregorian calendar
September
The 10th month of the year in the Gregorian calendar
October
The 11th month of the year in the Gregorian calendar
November
The 12th month of the year in the Gregorian calendar
December
A day of a calendar week that includes covers 24 hours each day.
day of week
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
A day when an organism (e.g., a human) is born.
day of birth
the anniversary of the birth of a person
There is a difference between birthday and birthdate: The former, such as February 29, occurs each year, while the latter is the exact date a person was born (e.g., January 15, 2001).
birthday
information associated with an individual
personal information
A name of a person, which can have different types
person name
person first name
person last name
person middle name
患者本人在公安户籍管理部门正式登记注册的姓氏和名称
Suyuan Peng, Hong Yu, Yongqun He
《电子病历基本数据集 第10部分：住院病案首页》WS 445.10-2014
person full name
A person name that identifies a person for legal, administrative and other official purposes
person legal name
birth name
A person name that is used for a person to access a computer system.
person login username
maiden name
A person name that is fictitious and generated for a person to perform a particular social role.
pseudonym
Personal information that indicates a person's status in marriage
marital status
married marital status
single marrital status
divorced marrital status
A marital status that indicates no marriage status due to the death of his/her spouse and no remarriage.
widowed marrital status
legally separated marital status
not married marital status
An education level that indicates that the highest level of education achievement for a person.
education level
A telephone number is a sequence of digits assigned to a fixed-line telephone subscriber station connected to a telephone line or to a wireless electronic telephony device, such as a radio telephone or a mobile telephone, or to other devices for data transmission via the public switched telephone network (PSTN) or other public and private networks.
telephone number
A telephone number used for a phone at home
home telephone number
A telephone number used for a phone at work
work telephone number
A telephone number that is used in a cellular device
cell phone number
The status of actively looking for employment, but not being currently employed.
unemployment status
home postal address
work postal address
A series of letters or digits or both, sometimes including spaces or punctuation, included in a postal address for the purpose of sorting mail.
postal code
A ZIP Code is a postal code used by the United States Postal Service (USPS). The term ZIP is an acronym for Zone Improvement Plan.
ZIP code
The personal information that indicates an individual's or his/her family's economic and social position in relation to others, based on income, education, and occupation.
socioeconomic status
An socioeconomic status that indicates the status of being employed in an occupation to perform an activity or service for wage or salary. It is the status of a worker in a company or institute on the basis of the contract of work or duration of work done.
employment status
A state of employment in which a person works for a minimum number of hours defined as full-time by their employer.
full time employment status
a status of employment that carries fewer hours per week than a full-time job.
part time employment status
an employment status where the work is arranged and paid on a hourly basis.
hourly employment status
The state of working for oneself rather than an employer.
self-employment status
An employment situation where the working arrangement is limited to a certain period of time based on the needs of the employing organization.
temporary employment status
An education level that indicates that the highest level of education achievement for a person is a Master's degree.
Master's degree education level
An education level that indicates that the highest level of education achievement for a person is an academic Doctorate degree
academic Doctorate degree education level
An education level that indicates that a person does not have formal school education.
no formal school education level
An education level that indicates that the highest level of education achievement for a person is a high school completion.
high school education level
An education level that indicates that the highest level of education achievement for a person is a Bachelor's degree
Bachelor's degree education level
An education level that indicates that a person has obtained a degree allowing them to practice a profession, such as law, medicine, music, or ministry.
professional doctorate degree education level
M.D. completion education level
Pharmacy complete education level
An education level that indicates that the highest level of education achievement for a person is kindergarten completion.
kindergarten completion education level
An education level that indicates that the highest level of education achievement for a person is preschool.
preschool completion education level
An education level that indicates that the highest level of education achievement for a person is the pass of a General Education Development (GED) tests. The GED tests are a group of four subject tests which, when passed, provide certification that the test taker has United States or Canadian high school-level academic skills.
GED education level
An education level that indicates that the highest level of education achievement for a person is the 1st Grade elementary school completion.
1st Grade education level
An education level that indicates that the highest level of education achievement for a person is the second Grade elementary school completion.
2nd Grade education level
An education level that indicates that the highest level of education achievement for a person is the third Grade elementary school completion.
3rd Grade education level
An education level that indicates that the highest level of education achievement for a person is the 4th Grade elementary school completion.
4th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 5th Grade elementary school completion.
5th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 6th Grade elementary school completion.
6th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 7th Grade elementary school completion.
7th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 8th Grade elementary school completion.
8th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 9th Grade elementary school completion.
9th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 10th Grade elementary school completion.
10th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 11th Grade elementary school completion.
11th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 12th Grade elementary school completion.
12th Grade education level
An education level that indicates that the highest level of education achievement for a person is a degree from a 2 year college program.
associate academic degree education level
An education level that indicates that the highest level of education achievement for a person is a degree from an occupational, technical, or vocational program
vocational program completion education level
The code in the specific coding system for the payment method of the expenses incurred in a single hospitalization of the patient
患者单次住院诊疗所发生费用的支付方式的特定编码体系中的代码
医疗付费方式
health insurance plan
A joint federal and state program that helps with medical costs for some people with limited income and resources.
Medicaid
Medicare is a national health insurance program in the United States, begun in 1966 under the Social Security Administration and now administered by the Centers for Medicare and Medicaid Services (CMS).
Medicare
private health insurance plan
worker compensation insurance plan
body weight
A body weight that is obtained immediately after birth
birth weight
emergency contact phone number
care provider
primary care provider
a centrally registered identifier symobol that refers to a specific study
centrally registered study identifier symbol
secondary care provider
tertiary care provider
An email address that is used secondary after the de fault first email address.
2nd email address
age question
A textual question that asks whether a person's age is less than 18 years old
Whether age less than 18 years old
An eligibility assessment form that is designed and used by the Kidney Precision Medicine Project (KPMP; http://kpmp.org) organization.
KPMP eligibility assessment form
BMI question
Whether BMI greater than 40 kg per m2
BMI greater than 40 kg per m2
question about blood transfusion
Whether unwilling to receive blood transfusion
pregnancy question
A pregnancy question that asks whether a person is pregnant at the moment of being questioned
Whether pregnant
transplant question
A transplant question that asks whether a person has received some transplant (includes solid transplant and bone marrow). Example transplants are kidney transplant and heart transplant.
Whether transplant recipient
A transplant question that asks whether a person has received a kidney transplant.
Whether kidney transplant recipient
KPMP clinical report form
A biopsy procedure form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP biopsy procedure form
A biosample collection form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP biosample collection form
An adverse event entry form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP adverse event entry form
A biopsy safety checklist form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP biopsy safety checklist form
A clinic reception form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP clinic reception form
A contact information form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP contact information form
KPMP demographic information form
KPMP health literacy questionnaire form
A textual question that is about eligibility of a person to participate in a project.
eligibility question
KPMP AKI hospitalization form
KPMP CKD hospitalization form
KPMP laboratory result form
KPMP medical history form
This form is the end of a successful screening process
KPMP consent form
KPMP medications form
KPMP new patient form
KPMP participant reported outcome measures form
KPMP participant study status form
KPMP pathology images upload form
KPMP patient experience survey form
KPMP personal history form
KPMP physical measurement form
KPMP post biopsy form
KPMP tissue tracking form
KPMP Dx core - .jpg images QC form
KPMP Dx core - disease categories form
KPMP central path quality metrics assessment Dx core form
KPMP central path quality metrics assessment interrogation core form
The last four digits of a social security number, which is often asked in a survey form.
last four digits of social security number
A question in a survey form may ask whether a provided email address belongs to self
The self is an individual person as the object of his or her own reflective consciousness.
self
email question
An email question that asks the exact email address
What email address
An email question that asks whether the email address provided belongs to the person being surveyed.
Whether self owns email address
Who owns email address
A textual question that asks the birthday of the person being surveyed
What is your birthday
The textual name of the contact person or organization
contact name
The textual name of the contact person or organization that will be contacted during emergency
emergency contact name
Who owns the 2nd email address
Who owns the 3rd email address
physician information
physician specialty information
Health care or healthcare is the maintenance or improvement of health via the prevention, diagnosis, and treatment of disease, illness, injury, and other physical and mental impairments in human beings.
health care
A health care rendered for the benefit of a patient.
patient care
Primary care refers to the work of health professionals who act as a first point of consultation for all patients within the health care system
primary care
Secondary care includes acute care: necessary treatment for a short period of time for a brief but serious illness, injury, or other health condition. This care is often found in a hospital emergency department. Secondary care also includes skilled attendance during childbirth, intensive care, and medical imaging services.
secondary care
Tertiary care is specialized consultative health care, usually for inpatients and on referral from a primary or secondary health professional, in a facility that has personnel and facilities for advanced medical investigation and treatment, such as a tertiary referral hospital.
tertiary care
The term quaternary care is sometimes used as an extension of tertiary care in reference to advanced levels of medicine which are highly specialized and not widely accessed.
quaternary care
A patient care that is provided in hospital.
It is sometimes the synonym of secondary care. However, many secondary care providers, such as psychiatrists, clinical psychologists, occupational therapists, most dental specialties or physiotherapists do not necessarily work in hospitals. Some primary care services are delivered within hospitals. Depending on the organization and policies of the national health system, patients may be required to see a primary care provider for a referral before they can access secondary care.
hospital care
nephrology care
endocrinology care
physician question
What physician's specialty
hospital question
what name of hospital
address question
What street name
What city
What state
What Zip code
What street number and name
What apartment
What country
Do you have physician who provides your usual medical care?
Whether have physician for usual medical care
nephrology care provider
patient condition question
Whether diabetic kidney disease (DKD)
Whether hypertensive CKD (H-CKD)
Whether diabetic nephropathy resisters percutaneous biopsy
Whether AKI percutaneous biopsy
Whether AKI open biopsy
Whether biopsy
CRF filled up by patient
What postal code
CRF filled up by research coordinator
CRF filled up by biopsy operator
biopsy-related CRF
post biopsy hospitlization form
A clinical report form that is related to the processing and analysis of tissue of diseased patient.
pathology CRF
screening and patient tracking CRF
enrollment CRF
A eligibility question that asks whether a patient is eligible to consent to participate in a project.
Whether patient eligible to consent
HIPAA release
Whether patient signed HIPPA release form
When HIPAA release form signed
Whether scanned HIPAA release form uploaded
A chronic kidney disease that is accompanied with elevated blood pressure or hypertension
Oliver note: This term is not shown in MONDO or DOID. May request an addition.
hypertensive chronic kidney disease
a process that obtains a tissue from a living body in order to discover the presence, cause, or extent of a disease, or perform further biomeidcal investigation
biopsy
A systematized collection of patient and population electronically-stored health information in a digital format
NCIT definition: A digital version of a patient's medical history. [def-source: NCI]
electronic health record
A biopsy that takes a small piece of tissue out of a living body through the skin, using only a tiny incision
percutaneous biopsy
AKi percutaneous biopsy
A biopsy process in which a surgical incision (cut) is made through the skin to expose and remove tissues
open biopsy
AKI open biopsy
diabetic nephropathy resisters percutaneous biopsy
The state of being free from illness or injury
health status
The medical state or condition of a patient
medical condition
Whether diseased
Whether kidney diseased
the date or time on which a visit occurs
visit temporal region
a machine-readable centrally registered identifier that is represented in a visual format on a surface
barcode
a barcode that represents a specific specimen
specimen barcode
A planned process that tracks the tissue specimen including tissue vial number, storage location, time of vial arrival to storage, storage temperature, etc.
tissue tracking
A centrally registered identifier that is assigned for a specific clinical trial registered in the ClinicalTrials.gov. The format for the ClinicalTrials.gov registry number is “NCT” followed by an 8-digit number, e.g.: NCT00000419.
Qingliang Leon Li, Asiyah Yu Lin, Oliver He
USA National Clinical Trial identifier
A textual entity that is the title of a clinical trial
title of clinical trial
A title of clinical trial that is recorded as official
official title of clinical trial
A title of clinical trial that is meant for lay people understanding
lay title of clinical trial
A person who performs an investigation task and takes the role of an investigator role.
investigator
An investigator who is involved in a clinical trial and is responsible for ensuring that an investigation is conducted according to the signed investigator statement, the investigational plan, and applicable regulations; for protecting the rights, safety, and welfare of subjects under the investigator's care; and for the control of drugs under investigation.
clinical investigator
study start date
The (estimated) date on which the clinical study is open for recruitment of participants, or the actual date on which the first participant is enrolled.
clinical trial start date
study completion date
The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated.
clinical trial study completion date
The date that the final participant was examined or received an intervention for the purposes of final collection of data for the primary outcome, whether the clinical study concluded according to the pre-specified protocol or was terminated. In the case of clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all of the primary outcomes.
clinical trial primary completion date
The main objective of the intervention(s) being evaluated by the clinical trial.
clinical trial primary purpose specification
date of registration
A primary outcome measure used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment.
primary health outcome measurement datum
The current stage of a clinical study and whether it is or will be open for enrollment
recruitment status
A case report form that is presented in an electronic format
electronic case report form
A human being who is a candidate to participant in a clinical study
clinical study participant candidate
answering textual question
today's date
CRF filled up by participant candidate
pregnancy test positive
hemoglobin test finding
In KPMP, the hemoglobin < 9 g/dl is considered as hemoblobin test positive.
hemoglobin test positive with result < 9 g/dl
a date when a test is performed at the first time
date of first test
date of test
a date when a test is performed at the second time
date of second test
A person name that includes both the first and last name
person first and last name
sign date
status
study status
patient status
a selection criterion (rule) which defines and states the exclusion condition for an entity to be considered as suitable for a given task or participation in a process.
exclusion criterion - obsolete
An exclusion criterion that relates to the process of bleeding
bleeding exclusion criteria
A case report form of PROMIS: Patient-Reported Outcomes Measurement Information System. PROMIS is a set of person-centered measures that evaluates and monitors physical, mental, and social health in adults and children. It can be used with the general population and with individuals living with chronic conditions.
PROMIS form
kit identifier
A centrally registered identifier that is for a kit used in biopsy
biopsy kit identifier
A PROMIS form that is designed and used by the KPMP project (http://kpmp.org).
KPMP PROMIS form
biopsy pass
needle biopsy
A textual question about health condition
health status question
A health status question that asks about the condition of a person's heath, which can be a selection from different options such as Excellent, Very good, Good, Fair, or Poor.
what health status
excellent health status
very good health status
good health status
fair health status
poor health status
quality of life
excellent quality of life
very good quality of life
good quality of life
fair quality of life
poor quality of life
consent status
A consent status that indicates a participant unwilling to receive a procedure of blood transfusion
unwilling to receive a blood transfusion
A consent status that indicates a participate willing to receive a procedure of blood transfusion
willing to receive a blood transfusion
year
A textual quesition thta is about medical history of a person
medical history question
What birth weight
Japan clinical trial identifier
A Japan clinical trial identifier provided by the University Hospital Medical Information Network Center (UMIN-CTR)
UMIN-CTR clinical trial identifier
JAPIC clinical trial identifier
JMACCT clinical trial identifier
European clinical trial registry identifier
A clinical trial that covers both Phase 1 and 2
Phase I/II clinical trial
combinational intervention
The quality of a clinical trial that studies a drug or biological product. The phase is based on the study's objective, the number of participants, and other characteristics. According to USA FDA, there are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4.
clinical trial phase
A clinical trial phase that represents the first-in-man trial, which tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects.
clinical trial phase 1
A clinical trial phase that is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI]
clinical trial phase 2
A clinical trial phase that is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI]
clinical trial phase 3
A clinical trial phase that is designed for a randomized, controlled trial to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed. [def-source: NCI]
clinical trial phase 4
A clinical trial phase that is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI]
clinical trial phase 0
A clinical trial that covers both Phase 2 and 3
Phase II/III clinical trial
genetic intervention
A medical intervention that involves a behavioral process to control, prevent, or treat a behavior problem.
behavioral intervention
study accession identifier
title of study
A livinging individual who is or becomes a participant in research, either as a recipient of a test article or as a control. A subject may be either a healthy human or a patient. Based on the NIH definition, a living individual about whom an investigator (whether professional or student) conducting the following research: (1) Obtains information or biospecimens through intervention or interaction with the individual, and uses, studies, or analyzes the information or biospecimens; or (2) Obtains, uses, studies, analyzes, or generates identifiable private information or identifiable biospecimens.
human subject
In clinicaltrials.gov, contact information character limits: First Name: 62 characters Last Name: 62 characters Degree: 30 characters Phone: 30 characters Phone Ext: 14 characters Email: 254 characters Citation: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials
A person who serves as a contact role and has disclosed specified information to be reached. Usually the contact information, such as email and phone number, is provided.,
Leon, Asiyah, Oliver: Since each contact needs to provide some contact information, we may need to define the contact information.
contact person
A contact person for each facility participating in a study.
facility contact
biosample identifier
GSM identiifier
ImmPort biosample identifier
Person to contact if Facility Contact is not available (that is, a second contact person).
facility contact backup
contact of scientific queries
An investigation agent role that is taken by a human individual
investigator role
a role taken by a person who serves as a contact for some process.
contact person role
Topical ocular hypotensive eye drops
contact for public queries
A person who is responsible for the overall scientific leadership of the protocol, including study principal investigator
overall study official
A person to whom questions concerning enrollment at any location of the study can be addressed.
central contact person of study
A person to contact if Central Contact is not available.
central contact backup of study
information content entity about a contact person
contact person information
A sponsor role taken by an individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. The Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder.
primary sponsor role
A sponsor role taken by an additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship.
A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. by WHO (https://www.who.int/ictrp/network/trds/en/)
In clinicaltrials.gov, the secondary sponsor role can be taken by a project collaborator (Reference: https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf). However, a secondary sponsor may serve as a collaborator role, but a collaborator may not serve as a secondary sponsor role.
secondary sponsor role
An investigator role taken by an individual who is designated as responsible party by the sponsor
principal investigator role
An investigator role taken by an individual who both initiates and conducts the study
sponsor investigator role
An investigation agent role taken by an agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them.
A secondary sponsor may serve as a collaborator role. However, a collaborator may not serve as a secondary sponsor role.
investigation collaborator role
a selection criterion (rule) which defines and states the inclusion condition for an entity to be considered as suitable for a given task or participation in a process.
Oliver He, Edison Ong, Leon Li, Asiyah Lin
inclusion criterion - obsolete
A centrally registered unique identifier assigned by the primary registry to a study including a clinical trial.
primary registry identifier
An individual, organization, group or other legal entity that involves with any of the following activities: initiating, managing and funding a study
sponsor
investigation agent
The individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. In clinical trial, the Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder.
primary sponsor
An additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship.
A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. Reference: https://www.who.int/ictrp/network/trds/en/
secondary sponsor
A centrally registered unique identifier besides the primary registry identifier allocated by the Primary Registry, if any.
secondary registry identifier
An agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them.
collaborator
An investigator who is designated as responsible party by the sponsor
principal investigator
sponsor investigator
A role taken by a string (which may have mixed integer and text) that serves as a unique record.
identifier role
obsolete class
An identifier role that inheres in a unique record which provides an identifier secondary to the primary registry identifier.
secondary registry identifier role
An identifier role that is assigned by a primary registry and provides a unique record.
primary registry identifier role
a human who is a recipient of a health care service performed by healthcare professionals.
A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research.
human subject study
A collection of humans who share a defining characteristic, typically those who are collectively experiencing a common event (e.g., a clincal trial study) in a selected period.
human cohort
A process of a dynamic system that produces an identiical or similar copy of itself.
self-replication
organic chemical entity
A measurement datum that is about the age of human subject
human subject age data
For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, a child is defined as an individual under the age of 18 years.
child age data of human subject (by NIH)
The regular aged adult group is defined here as an individual over 18 years of age.
adult age data of human subject
For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, an older adult is defined as an individual 65 years of age or older.
older adult data of human subject (by NIH)
The representation of a positive conclusion of a diagnostic process, which indicates that the patient is diagnozed as positive for a hypothetic disease.
positive diagnosis
The representation of a negative conclusion of a diagnostic process, which indicates that the patient is diagnozed as negative for a hypothetic disease.
negative diagnosis
The representation of a presumptive positive conclusion of a diagnostic process, which indicates that the patient is diagnozed as presumptive positive for a hypothetic disease.
presumptive positive diagnosis
A human subject classified as adult, which is defined by NIH as an individual under the age of 18 years. For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, a child is defined as an individual under the age of 18 years.
child human subject
A human subject classified as adult, which is defined by NIH as an individual 65 years of age or older. For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, an older adult is defined as an individual 65 years of age or older.
older adult human subject
A human subject classified as adult, which is defined by NIH as an individual over 18 years of age.
adult human subject
Yingtong Liu, Anthony Huffman, Oliver He
biomarker role
immune signature role
cytokine signature role
inflammatory cytokine signature role
A material entity that has a measurable quality or process profile(s), which can be used as an indicator of an underlying biological state or identity.
The NIH Biomarkers and Surrogate Endpoint Working Group defined a biomarker as “A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention” (https://pubmed.ncbi.nlm.nih.gov/11240971/). However, the definition of 'characteriistc' is unclear, so we do not use the exact definintion in the ontology.
biomarker
A biomarker that is indicative of an immune response
immune biomarker
cytokine biomarker
inflammatory cytokine biomarker
disease biomarker role
A biomarker that is indicative of a disease
disease biomarker
A biomarker that is an indicator of a cell lineage or cell type
cell lineage biomarker
molecular biomarker
Cellular biomarkers are marked cells that can be isolated, sorted, quantified and characterized by their morphology and physiology, and used in both clinical and laboratory settings for different biomarker applications. An example of a cellular biomarker sorting technique is Fluorescent-activated cell sorting.
cellular biomarker
imaging biomarker
A biomarker that can predict clincal outcome.
predictive biomarker
A biomarker that provides information about the patient's overall outcome, regardless of therapy.
prognostic biomarker
A biomarker that can serve a role in narrowing down diagnosis, which can lead to diagnosis that is significantly more specific to individual patients.
diagnostic biomarker
A molecular biomarker at the DNA gene level
DNA biomarker
RNA biomarker
A molecular biomarker at the protein level
protein biomarker
A biomarker that is indicative of a disease and achieved through imaging.
imaging disease biomarker
A disposition that a material entity (e.g., gene or protein) is susceptible to be up or down-regulated in an organism or virus.
susceptibility to biological regulation
imaging disease biomarkers by magnetic resonance imaging
imaging disease biomarkers by MRI
A biomarker that is indicative of the presence of cancer in the body
cancer marker
A disposition that a material entity (e.g., gene or protein) is susceptible to be up-regulated in an organism or virus.
susceptibility to biological up-regulation
A disposition that a material entity (e.g., gene or protein) is susceptible to be down-regulated in an organism or virus.
susceptibility to biological down-regulation
A Unified Social Credit Identifier is issued to registered companies and other types of organization by the Chinese government.
Unified Social Credit Identifier
healthcare organization
A centrality registered identifier for a medical record.
medical record number
A centrally registered identifier that is uniquely assigned to a person.
person ID
指患者在本医疗机构住院诊治的次数
Suyuan Peng, Hong Yu, Oliver He
《卫生部关于修订住院病案首页的通知》卫医政发〔2011〕84号
住院次数
number of hospital admissions
A time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's admission to a hospital
指患者实际入病房的接诊时间
《住院病案首页数据填写质量规范（暂行）》国卫办医发〔2016〕24号
入院时间
date of hospital admission
A year when an organism (e.g., a human) is born.
year of birth
A month when an organism (e.g., a human) is born.
month of birth
This term is generated to be equivalent to the "birth_datetime" in OMOP. Also note: in OMOP v6.0, DATETIME fields were made mandatory and date fields were made optional. Reference: https://ohdsi.github.io/CommonDataModel/cdm60.html#PERSON
birth datetime
A time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's discharge from a hospital
出院时间是指患者治疗结束或终止治疗离开病房的时间，其中死亡患者是指其死亡时间；记录时间应当精确到分钟
The number of health card for residents of the People's Republic of China
在已统一发放“中华人民共和国居民健康卡”的地区填写健康卡号码，尚未发放“健康卡”的地区填写“-”
健康卡号
residents health card number
birth-related time
A care site is a uniquely identified institutional (physical or organizational) unit where healthcare delivery is practiced, for example, office, ward, hospital, clinic, etc.
According to OMOP, care site does not consider the provider (human) information such a specialty. Instead, care site is considered at the institutional level.
care site
A centrally registered identifier that refers to where the care provider typically provides the primary care.
care site identifier
A medical occurrence where a person engages with the healthcare system for a duration of time.
medical visit
A centrally registered identifier that refers to a specific visit occurrence. This identifier identifies a unique interaction between a person and the health care system.
visit occurrence identifier
A vist ocurrence in which the patient's condition requires admission to a hospital.
inpatient visit
A vist ocurrence in which a patient attends an outpatient clinic with no plan to stay beyond the duration of the visit.
outpatient visit
emergency room visit
The date on which a visit starts. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction.
visit start date
The date on which a visit ends. For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.
visit end date
A temporal region that covers the time period from the visit start time to the visit end time.
visit duration
The date and time on which a visit starts. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction.
visit start datetime
The date and time on which a visit ends. For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.
visit end datetime
A visit occurrence that occurs for the person prior to the given visit. There could be a few days or a few years in between.
preceding medical visit
A vist ocurrence that includes a visit to the emergency room followed by a subsequent inpatient visit.
emergency room and inpatient visit
A visit to a dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock
non-hospital institution visit
A visit where a provider visits a person, without a care site, within one day, delivering service
home medical visit
A visit in which a patient engages with a Provider through communication media. A patient can use digital information and communication technologies, such as computers and mobile devices, to access health care services remotely and manage their health care.
telehealth visit
A visit to the pharmacy for dispensing of drug, at a care site, within one day
pharmacy visit
A visit to a dedicated institution, at a care site, within one day, for the purpose of a measurement. The visit is carried out in a medical laboratory or clinical laboratory where tests are carried out on clinical specimens to obtain information about the health of a patient to aid in diagnosis, treatment, and prevention of disease
laboratory medical visit
A medical visit occurrence that involves an interaction with the healthcare system, without a care site, within a day, with no providers involved, for the administrative purpose of patient case management.
case management visit
A site that is used as a permanent or semi-permanent residence for one or many humans.
home
A centrally registered identifier that refers to the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS). NPI is assigned for use in all administrative and financial transactions specified by HIPAA.
National Provider Identifier
A centrally registered identifier that is issued by the Drug Enforcement Administration (DEA), a US federal agency, that allows a provider to write prescriptions for controlled substances.
DEA identifier
A medicl occurrence that is ordered by, or carried out by, a healthcare provider on a patient with a diagnostic or therapeutic purpose.
medical procedure occurrence
A centrally registered identifier that refers to a procedure occurrence, which is an activity or process that is ordered by, or carried out by, a healthcare provider on a patient with a diagnostic or therapeutic purpose.
procedure occurrence identifier
A temporal region that is associated with a procedure
procedure temporal region
procedure start date
The date and time when a procedure starts
procedure start datetime
procedure end date
procedure end datetime
The information content entity that represents the origin of record such as the clinical form as the origin record of death.
provenance of record
As part of the OMOP CDM, PROCEDURE TYPE CONCEPT best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’.
A provenance of record that determines the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
provenance of procedure record
death diagnosis status
A provenance of record that designates the source (provenance) of the cost data.
provenance of cost record
As part of the OMOP CDM, use the type concept that be reflects the source of the death record. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.
A provenance of record that determines the provenance of the death record, i.e., where it came from.
provenance of death record
A provenance of record that determines the provenance of the record, as in whether the record is from administrative claims or EHR.
provenance of device record
As part of the OMOP CDM, choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug.
A provenance of record that determines the provenance of a drug prescription, which delineates prescriptions written, prescriptions dispensed, medication history, patient-reported exposure, etc.
provenance of drug record
A provenance of record that determines the provenance of the Episode record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
provenance of episode record
A provenance of record that determines the provenance of the Measurement record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
provenance of measurement record
As part of the OMOP CDM, the provenance of the notes most likely will be EHR.
A provenance of record that determines the provenance of the note.
provenance of note record
A provenance of record that determines the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.
provenance of observation record
A provenance of record that determines the source of the specimen record, as in an EHR system.
provenance of specimen record
As part of the OMOP CDM, populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim.
A provenance of record that determines the provenance of the visit record, or where the record comes from.
provenance of visit record
A provenance of record that determines the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources.
provenance of condition occurrence record
The primary diagnosis refers to the patient condition that demands the most provider resources during the patient’s stay.
There is often confusion surrounding primary and principal diagnoses and, consequently, the terms are commonly used interchangeably. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis
primary diagnosis status
A medicl occurrence where a person presents a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient.
medical condition occurrence
the date or time on which a condition occurs
condition temporal region
condition end date
The date and time on which a clinical condition ends.
condition end datetime
condition start date
The date and time on which a condition starts.
In OMOP CDM, most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. Reference: https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE
condition start datetime
The state or status at the point during the visit the diagnosis was given (admitting diagnosis, final diagnosis), whether the diagnosis was determined due to laboratory findings, if the diagnosis was exclusionary, or if it was a preliminary diagnosis, among others.
In OPMI, we treated medical condition status as a status, which is a realizable entitry. One major section of the branch is various diagnosis condition status. There are basically two types of diagnosis: one type diagnosis is treated as a condition status, the other is diagnosis (OGMS_0000073) as a type of clinical data item. One good example to illustrate the difference is the difference between primary and principal diagnoses. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes and is a type of medical condition status. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis
medical condition status
An action specification that indicates why a Condition is no longer valid with respect to the purpose specified within the source data.
In OMOP CDM, a Stop Reason does not necessarily imply that the condition is no longer occurring.
medical condition stop reason specification
The status of have the primary admission diagnosis
primary admission diagnosis status
confirmed diagnosis status
Principal diagnosis describes the underlying cause behind a patient’s initial hospital admission and is assigned only after a physician has completed necessary tests and examinations.
principal diagnosis
A discharge diagnosis is a final diagnosis given a patient before release from the hospital after all testing, surgery, and workup are complete.
discharge diagnosis status
A postoperative diagnosis is a diagnosis or diagnoses discovered or confirmed during the surgery. Often it is the same as the preoperative diagnosis.
postoperative diagnosis status
preliminary diagnosis status
A preoperative diagnosis is a surgical diagnosis or diagnoses that are assigned to the patient before the surgical procedure, and is the reason for the surgery. A preoperative diagnosis is, in the opinion of the surgeon, the diagnosis that will be confirmed during surgery.
preoperative diagnosis status
An admitting diagnosis is defined as the initial working diagnosis documented by the patient's admitting or attending physician who determined that inpatient care was necessary.
admission diagnosis status
A cause of death is an official determination of conditions resulting in a human's death, which may be recorded on a death certificate. A cause of death is determined by a medical examiner.
cause of death status
primary referral diagnosis status
A referral is a written request from one health professional to another health professional or health service, asking them to diagnose or treat you for a particular condition.
referral diagnosis status
A secondary diagnosis is a condition that coexists at the time of admission, that develops subsequently, or that affects the treatment received and/or length of stay.
secondary diagnosis status
secondary discharge diagnosis status
secondary referral diagnosis status
preliminary admission diagnosis status
preliminary discharge diagnosis status
condition to be diagnosed by procedure status
A contributory cause of death is a significant condition that unfavourably influences the course of the morbid process and thus contributes to the fatal outcome, but which is not related to the disease or condition directly causing death.
contributory cause of death status
An immediate cause of death is a final disease, injury, or complication directly causing the death
immediate cause of death status
A process of a person’s exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).
medical device exposure
primary discharge diagnosis status
the date or time on which a device exposure occurs
device exposure temporal region
The date on which a device exposure ends.
"Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure end date
The date and time on which a device exposure ends.
"If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure end datetime
secondary admission diagnosis status
A medical condition status in which the subject is not presently experiencing the condition or situation and there is a negligible perceived risk of the condition or situation returning.
resolved condition status
The underlying cause of death refers to the disease or injury that initiated the train of morbid events leading directly to death or the circumstances of the accident or violence that produced the injury.
underlying cause of death status
The date on which a device exposure starts.
"Valid entries include a start date of a procedure to implant a device, the date of a prescription for a device, or the date of device administration." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure start date
The date and time on which a device exposure starts.
"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure start datetime
the date or time on which a drug exposure occurs in a patient
drug exposure temporal region
The date on which a drug exposure starts.
"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE." http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure start date
The date and time on which a drug exposure starts.
"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure start datetime
The date on which a drug exposure ends for a patient.
drug exposure end date
The date and time on which a drug exposure ends for a patient.
"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)". http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure end datetime
The reason a person stopped a medication as it is represented in the source. Reasons include regimen completed, changed, removed, etc.
This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist. This field will be retired in v6.0 of the OMOP CDM, . http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure stop reason specification
An action specification that represents the intended refills at time of the prescription.
drug refills specification from prescription
This is only filled in when the record is coming from a prescription. http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug refills specification
The end date of a drug exposure as it appears in the source data
drug exposure verbatim end date
An exposure or contact of a person to a drug. The drug exposure includes drug dispensing or administration for a person.
This term is used in OMOP CDM. This term appears similar to 'drug administration'. However, drug exposure also covers involuntary, but drug administration usually means voluntary. More discussion is needed.
drug exposure
In drug exposure, the quantity refers to number of pieces, e.g. tablets. In the example: 20 Ingredient dose= quantity x amount_value [amount_unit_concept_id] Acetaminophen dose = 20 x 500mg = 10,000mg Daily dose = Acetaminophen dose/drug duration
The quantity of drug exposure refers to the number of drug pieces, e.g. tablets, that are exposed to a person.
quantity of drug exposure
This days of the supply of a drug that is given on the prescription.
days of drug supply
A period time when an observation is conducted.
In OMOP, the observation table contains records that defines spans of time during which two conditions are expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, and (ii) absense of records indicate such Events did not occur during this span of time.
observation period
A temporal region that is associated with an observation
observation temporal region
observation period start date
observation period end date
measurement time
measurement date
A datetime when a measurement is conducted.
measurement datetime
A unique key given to a Measurement record for a Person. Such record can be used in the ETL for how duplicate Measurements during the same Visit were handled.
clnical measurement identifier
Payer plan is a plan specification that captures the details of the period of time that a person is continuously enrolled under a specific health Plan benefit structure from a given payer. Each person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies.
payer plan
A temporal region that is associated with the payment process defined in a payer plan
payer plan temporal region
A period time of the payment that is covered by a payer plan for a person.
payer plan period
payer plan period start date
payer plan period end date
A process that a patient experiences over a period of time.
medical occurrence
An electronic health record that records the information of medical condition.
condition occurrence record
An electronic health record that records the information of medical cost.
electronic health cost record
An electronic health record that records the information of the death record of a person.
electronic death record
An electronic health record that records the information of medical device usage.
electronic device record
An electronic health record that records the information of drug usage including drug prescriptions written, prescriptions dispensed, medication history, patient-reported exposure, etc.
electronic drug record
A data item that captures clinical facts about a patient obtained in the context of examination, questioning or a procedure.
This term is dervied from OMOP:Observation term. Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc.
medical observation data
An electronic health record that records the information of medical Episode record.
electronic episode record
An electronic health record that records the information of medical measurement record.
electronic measurement record
An electronic health record that records the information of medical notes.
electronic health note record
An electronic health record that records the information of medical observational record.
electronic health observation record
An electronic health record that records the information of Procedure record.
electronic health procedure record
An electronic health record that records the information of the specimen record.
electronic specimen record
An electronic health record that records the information of medical visit.
electronic medical visit record
preliminary diagnosis
preliminary admission diagnosis
preliminary discharge diagnosis
The primary diagnosis is a diagnosis of the patient condition that demands the most provider resources during the patient’s stay.
primary diagnosis
primary admission diagnosis
primary discharge diagnosis
primary referral diagnosis
A secondary diagnosis is a diagnosis made at the time of admission, that develops subsequently, or that affects the treatment received and/or length of stay.
secondary diagnosis
secondary admission diagnosis
secondary discharge diagnosis
secondary referral diagnosis
admission diagnosis
confirmed diagnosis
death diagnosis
discharge diagnosis
postoperative diagnosis
A medical occurrence in which a patience is exposed to a medical related material entity such as drug or medical device. Medical exposure refers primarily to exposure incurred by patients for the purpose of medical diagnosis or treatment.
medical exposure
preoperative diagnosis
referral diagnosis
A age quality that is measured by the value of less than 18 years old
age less than 18 years
GFR 30-59 mL/min/1.73m2
eGFR >=60 mL/min/1.73m2 with urine albumin excretion >= 30 mg/g creatinine
eGFR >= 60 mL/min/1.73m2 with urine protein excretion >= 150 mg/g creatinine
A role of a person (e.g., a study participant, participant's family member, or participant's physician) who provides the medical history information.
medical history information provider role
A role of a person who is a family member of a participant in an investigation study.
study participant's family member role
a role of a physician who takes care of a study participant
study participant's physician role
An age when a disease is first diagnosed
age at diagnosis of disease
age at diagnosis of kidney disease
Whether chronic kidney disease
Whether acute kidney injury
time of biopsy
year of kidney biopsy
time of kidney biopsy
month of kidney biopsy
age at the start of kidney stone
An age when a disease started in a patient
age at the start of disease
Whether diabetes
age at diagosis of diabetes
What disease
What type of diabetes
treatment question
medicatoin treatment question
surgical treatment question
Whether taking medication for diabetes
age at the start of medication
age at the start of taking medication for diabetes
What medication
What medication taken for diabetes
Whether insulin taken for diabetes
Whether diabetes during pregnancy
a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc.
clinical trial
A clinical trial that is at Early Phase 1 or Phase 0
A clinical trial that is at an Early Phase i or Phase 0, which is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI]
Early Phase 1 clinical trial
A clinical trial that is at Phase 1, which is often the first-in-man trial, and it tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects.
Phase 1 clinical trial
A clinical trial that is at Phase 2, which is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI]
Phase 2 clinical trial
A clinical trial that is at Phase 3, which is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI]
Phase 3 clinical trial
Phase 4 clinical trial
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
患者生理性别在特定编码体系中的代码
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
TODO: define this or obsolete it and move children somewhere else.
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
The number of entities of this type that are part of the whole organism.
This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
A physical quality inhering in a bearer that has mass near a gravitational body.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course.
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement.
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
A quality denoting the lack of an entity.
We recommend using the new absent terms (physical absence, absent anatomical entity, or absent process) instead of this class. This is a legacy term and will ultimately be obsoleted. See https://github.com/pato-ontology/pato/issues/331.
A quality inhering in a bearer by virtue of the bearer's existence.
A size quality which is relatively high.
A pattern where all the repeated elements are oriented in the same direction.
A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided.
A positional quality inhering in a bearer by virtue the bearer's being changed in abnormal position.
A spatial pattern inhering in a bearer by virtue of the bearer's involvement of only one part or side.
A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells.
A physical quality inhering in an organ or tissue by virtue of the bearer's exhibiting a decreased number of cells, typically associated with a decrease in size.
A structural quality inhering in a bearer by virtue of the bearer's undergoing unprogrammed cell death.
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
See comments of relational quality of a physical entity.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
A monadic quality of continuant that exists at the cellular level of organisation.
A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types.
A cellular potency that is the capacity to produce only one differentiated cell type.
Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells.
A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity.
Less potent than multipotent, often thought of as precursor or progenitor cell status.
A cellular potency that is the capacity to form multiple differentiated cell types.
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311).
A quality inhering in a bearer by virtue of the bearer's being present in two copies.
A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s).
A functionality quality held by the bearer when the latter is able to perform a regular function(s).
A disfunctional quality held by the bearer when the latter is unable to perform a regular function(s).
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
extra or missing physical or functional parts
A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity.
A quality of a process inhering in a bearer by virtue of the bearer's processual parts.
A size quality inhering in a bearer by virtue of the bearer's being made wider or larger in all dimensions.
A physical quality that is the ability to contract or shrink.
An oriented quality inhering in a bearer by virtue of the bearer's being relocated around an axis.
A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting.
A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s).
Structure quality that is the presence of at least one sac-like closed membranous structure containing one or more liquid or solid organism substances.
Structure quality that is the presence of closed epithelium bounded capsules containing one or more liquid or solid organism substances.
A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted.
This refers to the disposition of the bearer.
A structural quality inhering in a bearer by virtue of the bearer's being drawn together, compressed or squeezed physically.
A shape quality in a bearer by virtue of the bearer's curving inward.
A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter.
A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter U.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions.
A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance.
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
A quality that inheres in an entire organism or part of an organism.
The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type.
A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity.
Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2.
Surface shape that refers to the inward or outward curvature of the surface.
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
Use this term or an is_a child of this term when the entire shape of the object is known.
A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave.
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells.
A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces.
A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure.
A molecular quality that arises from the molecular attraction exerted between two atoms or compounds.
A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
A structure quality inhering in a bearer by virtue of the bearer's body containing more than one cyst - formations of sac-like closed membranous structures not associated with neoplasia.
A morphology quality inhering in a neoplastic cell by virtue of the bearer's exhibiting breakdown of cell-cell interaction maintaining tissue architecture, proliferative dysregulation and bizarre modification to nucleus size and shape.
An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific ph conditions.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions.
A disposition inhering in a tumour by virtue of the bearer's disposition not to progress, invade surrounding tissues or metastasize.
A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A disposition inhering in a tumour by virtue of the bearer's disposition to invade surrounding tissues.
A disposition inhering in a tumour by virtue of the bearer's disposition not to invade surrounding tissues.
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc.
A quality inhering in a bearer by virtue of its constitution.
A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.
A shape that inheres in a 3 dimensional entity.
A quality that has a value that is increased compared to normal or average.
A quality that has a value that is decreased compared to normal or average.
A quality of a process that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is decreased compared to normal or average.
A quality of a process that has a value that is increased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter.
Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope).
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions.
Eosin stains acidophilic structures, hence eosinophilic is the same as acidophilic.
Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry.
A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching.
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other.
A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array.
A complete coverage of this domain would subclasses homopolymeric, copolymeric, crystalline.
A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen.
A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio.
A high nuclear/cytolasmic ratio is 70% or higher.
A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components.
A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain.
An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions.
A material entity that consists of two or more organisms, viruses, or viroids.
A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.
ecological community
A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
community
A collection of organisms that consists of two or more organisms from at least two species.
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction.
A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved.
hematopoietic progenitor cell antigen CD34
A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage.
A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule.
receptor-type tyrosine-protein phosphatase C
An integrin alpha with A domain that is a translation product of the human ITGA2 gene or a 1:1 ortholog thereof.
An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1.
cell surface glycoprotein MAC-1 subunit alpha
An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis.
leukocyte adhesion glycoprotein p150,95 alpha chain
A receptor-type tyrosine-protein phosphatase C isoform CD45R that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8 or a 1:1 ortholog thereof.
Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C).
receptor-type tyrosine-protein phosphatase C isoform CD45RA
A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof.
T-cell surface antigen T3/Leu-4 epsilon chain
A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain.
A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration.
A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof.
A protein that is a type I transmembrane receptor with an N-terminal cysteine-rich domain, a single Fibronectin type II (FNII) domain (Pfam:PF00040) and eight to ten copies of the Lectin C-type domain (Pfam:PF00059) (CTLDs). The presence of multiple copies of the CTLD domain is a hallmark of this class.
C-type lectin with multiple lectin domains
A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
T-lymphocyte differentiation antigen T8/Leu-2
T-cell surface glycoprotein CD8 alpha chain
A protein that is a translation product of the human CD8B gene or a 1:1 ortholog thereof. CD8 is a transmembrane receptor that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain.
T-cell surface glycoprotein CD8 beta chain
A G-protein coupled receptor with a 7 transmembrane (secretin family) domain (Pfam:PF00002) preceded by an amino-terminal region containing one or more functional domains with adhesion-like motifs.
secretin receptor-like G-protein coupled receptor
Category=family. Classification based on GRAFS system. [PMID:12761335]
A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions.
rhodopsin-like G-protein coupled receptor
A rhodopsin-like G-protein coupled receptor that is a translation product of the human OPN1LW, OPN1MW, OPN1SW, RHO, OPN3, OPN4, or OPN5 genes, 1:1 orthologs thereof, or a semi-ortholog thereof in Metazoa. The active form binds a vitamin A-based retinaldehyde chromophore through a Schiff base linkage to a Lys residue in the seventh transmembrane alpha helix.
A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines.
Category=family. Note: Only those that have been unequivocally shown to activate a G-protein coupled signaling pathway appear on the official IUPHAR list.
A chemokine receptor that is a translation product of the human CCR1 or CCR3 genes, the mouse CCR1L1 gene, 1:1 orthologs thereof, or a semi-ortholog thereof.
A chemokine receptor that is a translation product of the human CCR2 gene or a 1:1 ortholog thereof. The preferred ligands include CCL2, CCL7, CCL8, CCL13.
monocyte chemoattractant protein 1 receptor
An endothelin receptor that is a translation product of the human EDNRB gene or a 1:1 ortholog thereof. The active form binds endothelin 1 (ET-1), ET-2, and ET-3 with equal affinity.
An animal opsin that is a translation product of the human OPN1MW, OPN1MW2, or OPN1MW3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof.
Category=gene. Note: The human OPN1MW, OPN1MW2, and OPN1MW3 genes encode identical proteins.
A chemokine receptor whose active form binds interleukin-8 with high affinity.
A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof.
macrophage inflammatory protein 1-alpha receptor-like 2
A high affinity interleukin-8 receptor that is a translation product of the human CXCR1 gene or a 1:1 ortholog thereof.
A high affinity interleukin-8 receptor that is a translation product of the human CXCR2 gene or a 1:1 ortholog thereof.
A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267).
A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof.
membrane-spanning 4-domains subfamily A member 1
A protein that is a translation product of the human CD209 gene or a 1:1 ortholog thereof.
dendritic cell-specific ICAM-3-grabbing non-integrin 1
Category=gene. This gene and CLEC4M are products of a recent gene duplication in the primate lineage. Independent duplications of an ancestral gene have given rise to several orthologs in rodents, including CD209A. Requested by=CL.
A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof.
GP90 lymphocyte homing/adhesion receptor
A protein that is a stand alone version of the Glycosyltransferase family 10 (fucosyltransferase) (Pfam:PF00852) domain. Proteins in this class may catalyze alpha-1,3 glycosidic linkages.
A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues.
A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof.
non-specific cross-reacting antigen NCA-95
carcinoembryonic antigen-related cell adhesion molecule 8
A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof.
ectonucleotide pyrophosphatase/phosphodiesterase 3
phosphodiesterase I/nucleotide pyrophosphatase 3
ectonucleotide pyrophosphatase/phosphodiesterase family member 3
A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III.
immunoglobulin gamma Fc receptor II/III/IV
A protein that is a translation product of the human IL18 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof.
high affinity IL-2 receptor subunit beta
A protein that is a translation product of the human CXCL8 gene or a 1:1 ortholog thereof.
monocyte-derived neutrophil chemotactic factor
monocyte-derived neutrophil-activating peptide
A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif.
An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof.
2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase
2'-phospho-cyclic-ADP-ribose transferase
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof.
An alpha-(1,3)-fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof.
A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds.
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof.
low affinity immunoglobulin gamma Fc region receptor II
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof.
low affinity immunoglobulin gamma Fc region receptor III
A protein that has a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region.
A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain.
A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof.
Category=gene. Requested by=CL. Pro-orthology refers to, in this case, after-speciation gene duplication in the non-human species (aka 1:many orthology). This gene is present as a single copy in human and has undergone a lineage-specific duplication in mouse. CD59 antigen has a core architecture consisting of one UPAR/Ly-6 domain (Pfam:PF00021), a small domain of about 70 amino acids and containing 5 conserved disulfide bonds. It is both N- and O-glycosylated and is a GPI-anchored protein that releases soluble forms in some tissues.
A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines.
CSF-1/PDGF receptor-type tyrosine-protein kinase
An adhesion G-protein coupled receptor that is a translation product of the human ADGRE1 gene or a 1:1 ortholog thereof.
EGF-like module-containing mucin-like hormone receptor-like 1
A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof.
A protein with core architecture consisting of a signal sequence, an extracellular region with Class I Histocompatibility antigen, domains alpha 1 and alpha two (Pfam:PF00129) and an Immunoglobulin C1-set domain (Pfam:PF07654), a single-pass transmembrane region, and a very short cytoplasmic region. Forms a heterodimer with beta-2 microglobulin.
A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ARG1 gene or a 1:1 ortholog thereof.
A cathepsin-like protease that is a translation product of the human CTSK gene or a 1:1 ortholog thereof.
A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725).
A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof.
interleukin-3 receptor class II alpha chain
interleukin-3 receptor class 2 alpha chain
A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL6ST gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof.
A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat.
A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof.
A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (Pfam:PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane.
A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof.
myeloid cell-specific leucine-rich glycoprotein
A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof.
common acute lymphocytic leukemia antigen
A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD36 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof.
small cell lung carcinoma cluster 4 antigen
Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL.
A protein that is a translation product of the human SDC1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ACP5 gene or a 1:1 ortholog thereof.
tartrate-resistant acid phosphatase type 5
A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof.
tumor necrosis factor ligand superfamily member 5
A protein that is a translation product of the human TNFRSF11A gene or a 1:1 ortholog thereof.
osteoclast differentiation factor receptor
tumor necrosis factor receptor superfamily member 11A
A protein that is a translation product of the human CD27 gene or a 1:1 ortholog thereof.
tumor necrosis factor receptor superfamily member 7
A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof.
urokinase plasminogen activator surface receptor
A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain.
vascular endothelial growth factor receptor
A T-cell surface glycoprotein CD1 that is a translation product of the human CD1A gene or a 1:1 ortholog thereof.
A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human CSF1R gene or a 1:1 ortholog thereof.
macrophage colony-stimulating factor 1 receptor
A lysosome-associated membrane protein that is a translation product of the human CD68 gene or a 1:1 ortholog thereof.
A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof.
A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof.
vascular endothelial growth factor receptor 2
A C-type lectin with multiple lectin domains that is a translation product of the human MRC1 gene or a 1:1 ortholog thereof.
C-type lectin domain family 13 member D-like
macrophage mannose receptor 1-like protein 1
A protein that is the translation product of any of the LY6 genes (LY6A-LY6I).
An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof.
An Ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof.
An Ly-6-like protein that is a translation product of the mouse Ly6c2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Ly76 gene in mouse.
Category=organism-gene. Requested by=CL.
A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure.
A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof.
V(D)J recombination-activating protein 1
A protein that is a translation product of the human RAG2 gene or a 1:1 ortholog thereof.
V(D)J recombination-activating protein 2
A protein that is a translation product of the human EGR2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ALPL gene or a 1:1 ortholog thereof.
alkaline phosphatase liver/bone/kidney isozyme
alkaline phosphatase, tissue-nonspecific isozyme
A protein that is a translation product of the human AMBP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human B4GALNT4 gene or a 1:1 ortholog thereof.
beta-1,4-N-acetylgalactosaminyltransferase IV
N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase 1
A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CST3 gene or a 1:1 ortholog thereof.
An IGFBP-related protein that is a translation product of the human CCN1 gene or a 1:1 ortholog thereof.
insulin-like growth factor-binding protein 10
A protein that is a translation product of the mouse Cd200r3 gene or a 1:1 ortholog thereof.
CD200 cell surface glycoprotein receptor-like 3
CD200 cell surface glycoprotein receptor-like b
cell surface glycoprotein OX2 receptor 3
cell surface glycoprotein CD200 receptor 3
A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof.
A fatty acid-binding protein that is a translation product of the human FABP1 gene or a 1:1 ortholog thereof.
An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof.
high affinity immunoglobulin epsilon receptor subunit alpha
A protein that is a translation product of the human FOS gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human FOXN1 gene or a 1:1 ortholog thereof.
hepatocyte nuclear factor 3 forkhead homolog 11
A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human HAVCR1 gene or a 1:1 ortholog thereof.
T cell immunoglobulin and mucin domain-containing protein 1
T-cell immunoglobulin and mucin domain-containing protein 1
A protein that is a translation product of the human IGFBP7 gene or a 1:1 ortholog thereof.
insulin-like growth factor-binding protein 7
An integrin beta that is a translation product of the human ITGB7 gene or a 1:1 ortholog thereof.
An L-lactate dehydrogenase, cytoplasmic that is a translation product of the human LDHAL6B gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human LTF gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human MMP9 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human MPO gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human MYB gene or a 1:1 ortholog thereof.
A protein that is a translation product of the mouse Mcpt1 gene or a 1:1 ortholog thereof.
A transcription factor NF-kappa-B subunit that is a translation product of the human NFKB2 gene or a 1:1 ortholog thereof.
lymphocyte translocation chromosome 10 protein
nuclear factor of kappa light polypeptide gene enhancer in B-cells 2
A protein that is a translation product of the human PRDX1 gene or a 1:1 ortholog thereof.
thioredoxin-dependent peroxide reductase 2
A protein that is a translation product of the human RBPJL gene or a 1:1 ortholog thereof.
recombining binding protein suppressor of hairless-like protein
An angiotensinogenase that is a translation product of the human REN gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human S100A6 gene or a 1:1 ortholog thereof.
A serpin that is a translation product of the human SERPINF2 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains
A protein that is a translation product of the human SLC9A3 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof.
class A basic helix-loop-helix protein 17
T-cell acute lymphocytic leukemia protein 1
A protein that is a translation product of the human TFF3 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TIMP2 gene or a 1:1 ortholog thereof.
tissue inhibitor of metalloproteinases 2
A protein that is a translation product of the human TMED1 gene or a 1:1 ortholog thereof.
putative T1/ST2 receptor-binding protein
transmembrane emp24 domain-containing protein 1
A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof.
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
A protein that is produced as the result of proteolytic processing of a longer protein.
A T-cell surface glycoprotein CD8 alpha chain that has had the signal peptide removed.
T-cell surface glycoprotein CD8 alpha chain, signal peptide removed form
A T-cell surface glycoprotein CD8 beta chain that has had the signal peptide removed.
T-cell surface glycoprotein CD8 beta chain, signal peptide removed form
An acrosin that has been processed by proteolytic cleavage.
A clusterin that has been processed by proteolytic cleavage.
A cystatin-C that has had the signal peptide removed.
A part of a protein that is removed during the protein maturation process.
A protein that was initially identified as an antibacterial enzyme located in egg whites of Embden goose, but is now known to exist in both mammals and fish. Lysozyme catalyzes hydrolysis of most bacterial cell walls by cleaving the beta-1,4 glycosidic bond between N-acetyl-d-glucosamine (NAG) and N-acetylmuramic acid (NAM) in the peptidoglycan layer. It contains one copy of the Transglycosylase SLT domain (Pfam:PF01464).
An alkaline phosphatase that has had the signal peptide removed.
alkaline phosphatase, signal peptide removed form
A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction.
A T-cell surface glycoprotein CD8 alpha chain that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P01732-1 or a 1:1 ortholog thereof. Having a single-pass transmembrane domain, this form is membrane bound.
T-cell surface glycoprotein CD8 alpha chain isoform 1
A T-cell surface glycoprotein CD8 beta chain that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P10966-1 or a 1:1 ortholog thereof.
T-cell surface glycoprotein CD8 beta chain isoform 1
A T-cell surface glycoprotein CD8 alpha chain isoform 1 that has had the signal peptide removed to yield the mature form.
T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed form
A T-cell surface glycoprotein CD8 beta chain isoform 1 that has had the signal peptide removed to yield the mature form.
T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed form
A T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed form that includes at least one glycosylated residue.
T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed glycosylated form
A T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed form that includes at least one glycosylated residue.
T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed glycosylated form
A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif.
Category=family. Integrins are heterodimeric complexes of an alpha and a beta subunit. They are a structurally elaborate family of adhesion molecules that transmit signals bidirectionally across the plasma membrane by undergoing large-scale structural rearrangements. By regulating cell-cell and cell-matrix contacts, integrins participate in a wide-range of biological interactions including development, tissue repair, angiogenesis, inflammation and hemostasis. [PMID:10402956, PMID:11988479, PMID:9676575].
A protein that is primarily known as an irreversible serine protease inhibitor active against S1, S8 and C14 peptidases. There are both extra- and intra-cellular serpins, which are found in all groups of organisms with the notable exception of fungi. Serpin contains a copy of the Serpin (Pfam:PF00079) domain.
A protein that is encoded in the genome of Mus musculus.
A protein that is encoded in the genome of Homo sapiens.
A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit.
A protein that is a translation product of the Escherichia coli K-12 ggt gene or a 1:1 ortholog thereof.
A protein that is encoded in the genome of some Eukaryota.
A T-cell surface glycoprotein CD1 that is encoded in the genome of human.
Category=organism-family. Requested by=IEDB. Requested by=ImmPort.
A protein that includes at least one glycosylated residue.
A protein that is a translation product of some metazoan gene that encodes a signal peptide followed by a single Cathepsin propeptide inhibitor domain (Pfam:PF08246) followed by a single Papain family cysteine protease (Pfam:PF00112) domain at the C terminus.
An ion channel protein that has voltage-gated ion channel activity. A voltage-gated ion channel enables the transmembrane transfer of a solute by a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
A voltage-gated ion channel protein that has potassium channel activity. A potassium channel enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
A voltage-gated ion channel protein that has voltage-gated sodium channel activity. A voltage-gated sodium channel enables the transmembrane transfer of a sodium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
voltage-dependent sodium channel protein
voltage-gated sodium ion channel protein
voltage-sensitive sodium channel protein
A protein that has channel activity. Channel proteins enable energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel.
A channel protein that has ion channel activity. An ion channel enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
A protein that is a translation product of the mouse Ren1 or Ren2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof.
An amino acid chain that is produced as an outcome of a planned process with the intent to create an amino acid sequence different from native proteins known at the time.
A receptor-type tyrosine-protein phosphatase C that is a translation product of a transcript that minimally includes the region encoded by the variable exon 4(A).
receptor-type tyrosine-protein phosphatase C isoform CD45R
A material entity that minimally consists of a protein.
Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).
A TLD domain-containing protein 2 that is encoded in the genome of human.
TBC/LysM-associated domain-containing protein 2 (human)
An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of human.
phosphodiesterase I/nucleotide pyrophosphatase 3 (human)
ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (human)
A forkhead box protein N1 that is encoded in the genome of human.
winged-helix transcription factor nude (human)
A proline dehydrogenase 1, mitochondrial that is encoded in the genome of human.
proline dehydrogenase 1, mitochondrial (human)
A prominin-1 that is encoded in the genome of human.
An adenylate cyclase type 3 that is encoded in the genome of human.
adenylate cyclase, olfactive type (human)
A nephrin that is encoded in the genome of human.
renal glomerulus-specific cell adhesion receptor (human)
A receptor activity-modifying protein 3 that is encoded in the genome of human.
CRLR activity-modifying protein 3 (human)
calcitonin-receptor-like receptor activity-modifying protein 3 (human)
receptor activity-modifying protein 3 (human)
A LIM domain-binding protein 3 that is encoded in the genome of human.
Z-band alternatively spliced PDZ-motif protein (human)
A retinal dehydrogenase 2 that is encoded in the genome of human.
aldehyde dehydrogenase family 1 member A2 (human)
retinaldehyde-specific dehydrogenase type 2 (human)
A potassium channel subfamily K member 2 that is encoded in the genome of human.
outward rectifying potassium channel protein TREK-1 (human)
two pore domain potassium channel TREK-1 (human)
two pore potassium channel TPKC1 (human)
potassium channel subfamily K member 2 (human)
A neurexophilin-2 that is encoded in the genome of human.
A haptoglobin that is encoded in the genome of human.
A renin that is encoded in the genome of human.
An angiotensinogen that is encoded in the genome of human.
A cystatin-C that is encoded in the genome of human.
neuroendocrine basic polypeptide (human)
A protein c-Fos that is encoded in the genome of human.
Fos proto-oncogene, AP-1 transcription factor subunit (human)
G0/G1 switch regulatory protein 7 (human)
transcription factor AP-1 subunit c-Fos (human)
A pro-epidermal growth factor that is encoded in the genome of human.
A somatotropin that is encoded in the genome of human.
A tumor necrosis factor that is encoded in the genome of human.
tumor necrosis factor ligand superfamily member 2 (human)
Category=organism-gene. Requested by=PubChem.
An interferon gamma that is encoded in the genome of human.
An interleukin-2 receptor subunit alpha that is encoded in the genome of human.
interleukin-2 receptor subunit alpha (human)
An immunoglobulin J chain that is encoded in the genome of human.
joining chain of multimeric IgA and IgM (human)
A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human.
T-lymphocyte differentiation antigen T8/Leu-2 (human)
T-cell surface glycoprotein CD8 alpha chain (human)
A T-cell surface glycoprotein CD8 alpha chain isoform 1 that is encoded in the genome of human.
T-cell surface glycoprotein CD8 alpha chain isoform mCD8alpha (human)
T-cell surface glycoprotein CD8 alpha chain isoform membrane (human)
T-cell surface glycoprotein CD8 alpha chain isoform 1 (human)
An MHC class II histocompatibility antigen beta chain DRB1 that is encoded in the genome of human.
MHC class II histocompatibility antigen (human)
Category=organism-gene. Requested by=IEDB. Requested by=ImmPort.
HLA class II histocompatibility antigen, DRB1 beta chain (human)
A collagen alpha-1(IV) chain that is encoded in the genome of human.
A retinol-binding protein 4 that is encoded in the genome of human.
A protein AMBP that is encoded in the genome of human.
A C-X-C motif chemokine 10 that is encoded in the genome of human.
10 kDa interferon gamma-induced protein (human)
A transferrin receptor protein 1 that is encoded in the genome of human.
A serotransferrin that is encoded in the genome of human.
A lactotransferrin that is encoded in the genome of human.
A DNA nucleotidylexotransferase that is encoded in the genome of human.
terminal deoxynucleotidyltransferase (human)
A Thy-1 membrane glycoprotein that is encoded in the genome of human.
A von Willebrand factor that is encoded in the genome of human.
An insulin-like growth factor I that is encoded in the genome of human.
An arginase-1 that is encoded in the genome of human.
A myeloperoxidase that is encoded in the genome of human.
An interleukin-6 that is encoded in the genome of human.
A T-cell surface glycoprotein CD1a that is encoded in the genome of human.
T-cell surface glycoprotein CD1a (human)
A T-cell surface glycoprotein CD5 that is encoded in the genome of human.
A fatty acid-binding protein, liver that is encoded in the genome of human.
liver-type fatty acid-binding protein (human)
fatty acid-binding protein, liver (human)
A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of human.
macrophage colony-stimulating factor 1 receptor (human)
A uromodulin that is encoded in the genome of human.
Tamm-Horsfall urinary glycoprotein (human)
A 72 kDa type IV collagenase that is encoded in the genome of human.
A neprilysin that is encoded in the genome of human.
common acute lymphocytic leukemia antigen (human)
A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of human.
receptor-type tyrosine-protein phosphatase C (human)
A receptor-type tyrosine-protein phosphatase C isoform CD45RA that is encoded in the genome of human.
Category=organism-sequence. Requested by=CL.
receptor-type tyrosine-protein phosphatase C isoform CD45RA (human)
A vimentin that is encoded in the genome of human.
A matrilysin that is encoded in the genome of human.
An interleukin-8 that is encoded in the genome of human.
chemokine (C-X-C motif) ligand 8 (human)
granulocyte chemotactic protein 1 (human)
monocyte-derived neutrophil chemotactic factor (human)
monocyte-derived neutrophil-activating peptide (human)
Category=organism-gene. Salivary oral cancer biomarker.
A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of human.
T-cell surface glycoprotein CD8 beta chain (human)
An integrin alpha-M that is encoded in the genome of human.
CD11 antigen-like family member B (human)
cell surface glycoprotein MAC-1 subunit alpha (human)
A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of human.
high affinity immunoglobulin epsilon receptor subunit alpha (human)
A C-C motif chemokine 2 that is encoded in the genome of human.
monocyte chemoattractant protein 1 (human)
monocyte chemotactic and activating factor (human)
A neural cell adhesion molecule 1 that is encoded in the genome of human.
A keratin, type II cytoskeletal 5 that is encoded in the genome of human.
A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of human.
tartrate-resistant acid phosphatase type 5 (human)
An interleukin-2 receptor subunit beta that is encoded in the genome of human.
high affinity IL-2 receptor subunit beta (human)
interleukin-15 receptor subunit beta (human)
interleukin-2 receptor subunit beta (human)
A granulocyte-macrophage colony-stimulating factor receptor subunit alpha that is encoded in the genome of human.
granulocyte-macrophage colony-stimulating factor receptor subunit alpha (human)
A vascular endothelial growth factor A that is encoded in the genome of human.
vascular endothelial growth factor A (human)
A V(D)J recombination-activating protein 1 that is encoded in the genome of human.
V(D)J recombination-activating protein 1 (human)
An erythroid transcription factor that is encoded in the genome of human.
A leukosialin that is encoded in the genome of human.
A platelet glycoprotein 4 that is encoded in the genome of human.
leukocyte differentiation antigen CD36 (human)
A natriuretic peptides B that is encoded in the genome of human.
brain natriuretic factor prohormone (human)
A carboxypeptidase E that is encoded in the genome of human.
prohormone-processing carboxypeptidase (human)
An interleukin-7 receptor subunit alpha that is encoded in the genome of human.
interleukin-7 receptor subunit alpha (human)
An integrin alpha-2 that is encoded in the genome of human.
CD49 antigen-like family member B (human)
platelet membrane glycoprotein Ia (human)
A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human.
T-cell leukemia/lymphoma protein 5 (human)
class A basic helix-loop-helix protein 17 (human)
T-cell acute lymphocytic leukemia protein 1 (human)
A transcription factor PU.1 that is encoded in the genome of human.
A glutathione peroxidase 2 that is encoded in the genome of human.
gastrointestinal glutathione peroxidase (human)
glutathione peroxidase-gastrointestinal (human)
glutathione peroxidase-related protein 2 (human)
A syndecan-1 that is encoded in the genome of human.
A vascular cell adhesion protein 1 that is encoded in the genome of human.
vascular cell adhesion protein 1 (human)
A tumor necrosis factor receptor superfamily member 1A that is encoded in the genome of human.
tumor necrosis factor receptor 1 (human)
tumor necrosis factor receptor type I (human)
tumor necrosis factor receptor superfamily member 1A (human)
A tumor necrosis factor receptor superfamily member 1B that is encoded in the genome of human.
tumor necrosis factor receptor 2 (human)
tumor necrosis factor receptor type II (human)
tumor necrosis factor receptor superfamily member 1B (human)
An integrin alpha-X that is encoded in the genome of human.
CD11 antigen-like family member C (human)
leukocyte adhesion glycoprotein p150,95 alpha chain (human)
leukocyte adhesion receptor p150,95 (human)
A collagen alpha-1(V) chain that is encoded in the genome of human.
A synaptotagmin-1 that is encoded in the genome of human.
A macrophage scavenger receptor types I and II that is encoded in the genome of human.
macrophage acetylated LDL receptor I and II (human)
scavenger receptor class A member 1 (human)
macrophage scavenger receptor types I and II (human)
An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of human.
galactoside 3-L-fucosyltransferase (human)
ELAM-1 ligand fucosyltransferase (human)
4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase (human)
alpha-(1,3)-fucosyltransferase 4 (human)
An interleukin-10 that is encoded in the genome of human.
cytokine synthesis inhibitory factor (human)
A macrophage mannose receptor 1 that is encoded in the genome of human.
C-type lectin domain family 13 member D (human)
C-type lectin domain family 13 member D-like (human)
macrophage mannose receptor 1-like protein 1 (human)
An endothelial transcription factor GATA-2 that is encoded in the genome of human.
endothelial transcription factor GATA-2 (human)
A COUP transcription factor 2 that is encoded in the genome of human.
apolipoprotein A-I regulatory protein 1 (human)
nuclear receptor subfamily 2 group F member 2 (human)
A tenascin that is encoded in the genome of human.
glioma-associated-extracellular matrix antigen (human)
A C-X-C chemokine receptor type 1 that is encoded in the genome of human.
high affinity interleukin-8 receptor A (human)
A C-X-C chemokine receptor type 2 that is encoded in the genome of human.
high affinity interleukin-8 receptor B (human)
A signal transducer CD24 that is encoded in the genome of human.
small cell lung carcinoma cluster 4 antigen (human)
An integrin beta-7 that is encoded in the genome of human.
Gut homing receptor beta subunit (human)
A progranulin that is encoded in the genome of human.
An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of human.
2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (human)
2'-phospho-cyclic-ADP-ribose transferase (human)
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (human)
A CCN family member 2 that is encoded in the genome of human.
cellular communication network factor 2 (human)
hypertrophic chondrocyte-specific protein 24 (human)
insulin-like growth factor-binding protein 8 (human)
A carcinoembryonic antigen-related cell adhesion molecule 8 that is encoded in the genome of human.
non-specific cross-reacting antigen NCA-95 (human)
carcinoembryonic antigen-related cell adhesion molecule 8 (human)
A cadherin-5 that is encoded in the genome of human.
A macrosialin that is encoded in the genome of human.
An alpha-1A adrenergic receptor that is encoded in the genome of human.
A vascular endothelial growth factor receptor 2 that is encoded in the genome of human.
protein-tyrosine kinase receptor flk-1 (human)
vascular endothelial growth factor receptor 2 (human)
A DNA-binding protein inhibitor ID-1 that is encoded in the genome of human.
class B basic helix-loop-helix protein 24 (human)
DNA-binding protein inhibitor ID-1 (human)
An extracellular calcium-sensing receptor that is encoded in the genome of human.
parathyroid cell calcium-sensing receptor 1 (human)
extracellular calcium-sensing receptor (human)
A C-C chemokine receptor type 2 that is encoded in the genome of human.
monocyte chemoattractant protein 1 receptor (human)
A cathepsin K that is encoded in the genome of human.
A Rap1 GTPase-activating protein 1 that is encoded in the genome of human.
Rap1 GTPase-activating protein 1 (human)
A CCAAT/enhancer-binding protein alpha that is encoded in the genome of human.
CCAAT/enhancer-binding protein alpha (human)
A regulator of G-protein signaling 6 that is encoded in the genome of human.
regulator of G-protein signaling 6 (human)
A neuronal membrane glycoprotein M6-a that is encoded in the genome of human.
neuronal membrane glycoprotein M6-a (human)
A C-C chemokine receptor type 3 that is encoded in the genome of human.
An alpha-N-acetylglucosaminidase that is encoded in the genome of human.
A V(D)J recombination-activating protein 2 that is encoded in the genome of human.
V(D)J recombination-activating protein 2 (human)
A visual system homeobox 2 that is encoded in the genome of human.
Ceh-10 homeodomain-containing homolog (human)
A neutrophil gelatinase-associated lipocalin that is encoded in the genome of human.
25 kDa alpha-2-microglobulin-related subunit of MMP-9 (human)
neutrophil gelatinase-associated lipocalin (human)
A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of human.
lymphocyte translocation chromosome 10 protein (human)
nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (human)
nuclear factor NF-kappa-B p100 subunit (human)
An interleukin-5 receptor subunit alpha that is encoded in the genome of human.
interleukin-5 receptor subunit alpha (human)
A paired box protein PAX-5 that is encoded in the genome of human.
B-cell-specific transcription factor (human)
A urokinase plasminogen activator surface receptor that is encoded in the genome of human.
urokinase plasminogen activator surface receptor (human)
A collagen alpha-1(XVI) chain that is encoded in the genome of human.
A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of human.
interleukin-1 receptor-like 1 ligand (human)
putative T1/ST2 receptor-binding protein (human)
transmembrane emp24 domain-containing protein 1 (human)
An adhesion G protein-coupled receptor E1 that is encoded in the genome of human.
EGF-like module-containing mucin-like hormone receptor-like 1 (human)
adhesion G protein-coupled receptor E1 (human)
A sonic hedgehog protein that is encoded in the genome of human.
Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (human)
An adiponectin that is encoded in the genome of human.
30 kDa adipocyte complement-related protein (human)
adipocyte complement-related 30 kDa protein (human)
adipocyte, C1q and collagen domain-containing protein (human)
adipose most abundant gene transcript 1 protein (human)
A hypoxia-inducible factor 1-alpha that is encoded in the genome of human.
basic-helix-loop-helix-PAS protein MOP1 (human)
class E basic helix-loop-helix protein 78 (human)
hypoxia-inducible factor 1-alpha (human)
A coiled-coil domain-containing protein 102B that is encoded in the genome of human.
coiled-coil domain-containing protein 102B (human)
A multiple C2 and transmembrane domain-containing protein 1 that is encoded in the genome of human.
multiple C2 and transmembrane domain-containing protein 1 (human)
An extracellular sulfatase Sulf-1 that is encoded in the genome of human.
A putative thiamine transporter SLC35F3 that is encoded in the genome of human.
solute carrier family 35 member F3 (human)
putative thiamine transporter SLC35F3 (human)
A solute carrier family 4 member 11 that is encoded in the genome of human.
solute carrier family 4 member 11 (human)
A choline transporter-like protein 5 that is encoded in the genome of human.
solute carrier family 44 member 5 (human)
choline transporter-like protein 5 (human)
A prospero homeobox protein 1 that is encoded in the genome of human.
homeoboInOwlx prospero-like protein PROX1 (human)
A hepatitis A virus cellular receptor 1 that is encoded in the genome of human.
T-cell immunoglobulin and mucin domain-containing protein 1 (human)
T-cell immunoglobulin mucin receptor 1 (human)
hepatitis A virus cellular receptor 1 (human)
A 2-acylglycerol O-acyltransferase 1 that is encoded in the genome of human.
acyl-CoA:monoacylglycerol acyltransferase 1 (human)
diacylglycerol O-acyltransferase candidate 2 (human)
diacylglycerol acyltransferase 2-like protein 1 (human)
monoacylglycerol O-acyltransferase 1 (human)
2-acylglycerol O-acyltransferase 1 (human)
A sodium channel protein type 2 subunit alpha that is encoded in the genome of human.
sodium channel protein brain II subunit alpha (human)
sodium channel protein type II subunit alpha (human)
voltage-gated sodium channel subunit alpha Nav1.2 (human)
sodium channel protein type 2 subunit alpha (human)
A protein FEV that is encoded in the genome of human.
PC12 ETS domain-containing transcription factor 1 (human)
A fibroblast growth factor 23 that is encoded in the genome of human.
tumor-derived hypophosphatemia-inducing factor (human)
An adipocyte adhesion molecule that is encoded in the genome of human.
coxsackie- and adenovirus receptor-like membrane protein (human)
A transcription factor SOX-17 that is encoded in the genome of human.
A roundabout homolog 2 that is encoded in the genome of human.
A klotho that is encoded in the genome of human.
A netrin-G1 that is encoded in the genome of human.
A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of human.
osteoclast differentiation factor receptor (human)
tumor necrosis factor receptor superfamily member 11A (human)
A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
Any extent of continuous biological sequence.
The point at which one or more contiguous nucleotides were excised.
A deviation in chromosome structure or number.
An attribute describes a quality of sequence.
The signal peptide can be cleaved either co- or post-translationally. For this reason, we do not use the derives_from relation when defining protein forms lacking the signal peptide (because the precursor form might not yet exist at the time of removal).
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
An attribute describing a located_sequence_feature.
A genome is the sum of genetic material within a cell or virion.
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
partially characterised change in DNA sequence
A region containing at least one unique origin of replication and a unique termination site.
A collection of discontinuous sequences.
A region defined by its disposition to be involved in a biological process.
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
A collection of sequences (often chromosomes) of an individual.
A collection of one or more sequences of an individual.
An attribute of alteration of one or more chromosomes.
An attribute of a change in the structure or number of a chromosomes.
A change in chromosomes that occurs between two separate chromosomes.
When a genome contains an abnormal amount of chromosomes.
A position or feature where two sequences have been compared.
A sequence alteration where the length of the change in the variant is the same as that of the reference.
A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
A chromosomal structure variation within a single chromosome.
An alteration of the genome that leads to a change in the structure or number of one or more chromosomes.
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
the clusters of hormone-producing cells that are scattered throughout the pancreas
The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin.
The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO].
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
camera-type eye plus associated structures
An organ that is capable of transducing sensory stimulus to the nervous system.
Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
Dense regular connective tissue that connects muscle to bone[VSAO].
A biological tissue mass, most commonly a mass of nerve cell bodies.
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
in humans, consists of adventitial, muscular and mucoa layers
The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A stage that is part of the embryo stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
proximo-distal subdivision of respiratory tract
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO].
ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
An anatomical structure that develops from the endoderm and the mesoderm.
mixed endoderm/mesoderm-derived structure
The organs associated with producing offspring in the gender that produces spermatozoa.
The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney
By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]
A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum.
A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes.
A mass of cells that develop into the body of the embryo and some extraembryonic tissues
embryoblastus; massa cellularis interna; pluriblastus senior
the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta
A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
Stage succeeding embryo, including mature structure.
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The stage of being a sexually mature adult animal.
Structure derived from foregut that becomes a lung[GO].
Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO)
A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
hindgut endoderm and proctodeal ectoderm.
Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females.
The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
The orifice that connects the mouth to the exterior of the body.
The pair of anatomical structures comprised of a left lung and right lung.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
The upper ventral region of the torso of an organism.
A mucosa that is part of a duodenum [Automatically generated definition].
An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.
Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin
the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated
The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO].
The inner portion of the kidney consisting of the renal pyramids.
The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water
Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different.
An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra.
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A gland in which the principal secretory cells are mucus secreting cells.
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
organism substance
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Multi-tissue structure that is part of a compound organ.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
The organs and associated structures associated with bearing offspring in a female animal.
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Anatomical group whose component anatomical structures lie in close proximity to each other.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Compound organ that contains one or more macroscopic anatomical spaces.
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA].
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
A membranous fold of the heart that prevents reflux of fluid
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
Middle part of an organ, surrounded by the cortex.
this class is used in a very general sense
A decussation of the diencephalon where the fibers of the optic nerve cross
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
the gonad of a female organism which contains germ cells
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
tubular parts of female reproductive system
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
An airway through which respiratory air passes in organisms.
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.
In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed).
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
A filament, mostly protein, that grows from follicles found in the dermis[WP].
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Consider generalizing to deuterostome pharynx
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
in FMA this represents an embryonic region.
The caudalmost subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
the caudal portion of the primitive digestive tube of the embryo
in FMA this class has no children. In MA it has a single child hindgut epithelium
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla.
A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food.
Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe.
The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted].
The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted].
The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism.
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.
The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].
in EHDAA2, the renal vein is part of the kidney
the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct
The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO].
the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells
the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum
the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between
An anatomical wall that is part of a small intestine [Automatically generated definition].
The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel.
The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids.
A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder.
the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct
Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP].
The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct.
The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct.
One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates.
The mucosal layer that lines the stomach.
A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP].
A mucosa that is part of a small intestine [Automatically generated definition].
A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP].
In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter
Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]
Tip of renal pyramid projecting into a minor calyx.
The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron.
A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]
A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]
The part of the nephron that filters blood.[TAO]
Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron
A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus
Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]
Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP].
One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]
An epithelial tube that is part of the nephron, the functional part of the kidney.
note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA
The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient
Renal duct that collects the output from renal tubules.[TAO]
in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron
the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
opening of terminal part of digestive tract
The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad.
Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
An anatomical wall that lines the insider of a urinary bladder.
the mucous membrane lining the urinary bladder
An anatomical wall that is part of a intestine [Automatically generated definition].
The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct.
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions.
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel
The functional units of the liver including the lobules.
the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule
The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]
kidney terms require review for cross-vertebrate compatibility and developmental relationships.
Functional unit of the kidney that filters waste.[TAO]
In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)
A narrow chalice-shaped cavity between the glomerular and capsular epithelium of the glomerular capsule of the kidney[TFD]. Between the visceral and parietal layers, into which the filtrate enters after passing through the podocytes' filtration slits[WP]. luminal region between the glomerular capsule visceral and parietal layers, into which filtrate enters after passing through the filtration barrier from the glomerular capillaries[MP].
Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO]
The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule.
Renal tubule that connects to the renal corpuscle.[TAO]
The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine.
the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review.
A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]
The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva .
The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids.
The portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure.
The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule.
TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)
Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]
thick descending limb of proximal tubule
The distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule.
TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions
loop of Henle ascending limb thick segment
straight portion of distal convoluted renal tubule
straight portion of distal convoluted tubule
The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa.
a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule].
in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter.
The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO].
Innermost region of the mammalian kidney.
The anus and surrounding regions. Encompasses both internal and external regions, where present
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]
Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA].
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia].
The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery.
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries.
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
Subdivision of urinary system which consists of the urinary bladder and the urethra.
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
Skeletal muscle derived from cranial mesoderm and controls eye movements.
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system.
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
Cranial nerve which connects the midbrain to the extra-ocular and intra-ocular muscles.
A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
Subdivision of skeleton which includes upper and lower jaw skeletons.
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane
the groups of nerve cell bodies associated with the twelve cranial nerves
cranial ganglion part of peripheral nervous system
Nuclear complex containing subnuclei that give rise to the axons of the occulomotor nerve, both motor and parasympathetic fibers, situated at the midline at the level of the superior colliculus in the midbrain tegmentum (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 533-534).
Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP].
A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta.
Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular.
A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ.
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
the smooth stratified squamous epithelium that covers the outer surface of the cornea
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]
Any of the layers that make up the retina[MP].
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina
Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified]
The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified].
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP].
this class is used more generically than in FMA, and includes e.g. cortex of hair
Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP].
The most anterior region the brain including both the telencephalon and diencephalon.
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
The division of the forebrain that develops from the foremost primary cerebral vesicle.
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF].
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
The liquid component of blood, in which erythrocytes are suspended.
vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO].
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
A tiny smooth muscle that connects the hair follicle with the dermis.
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Respiration organ that develops as an outpocketing of the esophagus.
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO].
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.
Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]
The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]
Cardiac chamber in which blood enters the heart.
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
Cardiac chamber through which blood leaves the heart.
A cardiac ventricle that is in the left side of the heart.
The post-cranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
The sensory system subserving the sense of vision.
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
An organ that aids digestion and stores bile produced by the liver[WP].
A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.
A paired organ of the urinary tract which has the production of urine as its primary function.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].
A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]
Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]
The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]
In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
Cardiac valve which has as its parts the anterior, right posterior and left posterior cusps, attached to the fibrous ring of aortic valve.[FMA]
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lung which consists of the left upper lobe and left lower lobe.[FMA]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA].
The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Vasculature that is part of a head [Automatically generated definition].
A vasculature that is part of a trunk [Automatically generated definition].
Vasculature that is part of the eye region.
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree).
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP].
Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.
The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries.
WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here.
A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (muscle, smooth, vascular), phagocytes and the mesangial extracellular matrix.
The tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus.
EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus?
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO].
not part of a nephron or distal tubule in MA and FMA
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest.
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
Membrane organ that surrounds the brain and the spinal cord.
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop.
check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland.
Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]
A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]
The soft tissue that fills the cavities of bones.
TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs
consider placement of NCIT:C53466 medullary bone
The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]
In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine.
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A gland that is part of a skin of body [Automatically generated definition].
The part of the digestive system that contains the liver and the biliary system
A bone that is part of a limb [Automatically generated definition].
The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP].
Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]
Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]
The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]
The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]
We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments.
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot
The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).
The proximal free limb segment. Includes as parts the stylopod skeleton.
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd].
Replacement bone that forms within cartilage.
Connective tissue composed of elastic fibers.
The middle layer of an artery or vein. [WP,unvetted].
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
An organ that functions as a secretory or excretory organ.
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
digit (phalangeal portion) plus soft tissue
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]
The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]
all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').
The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements.
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].
Consider adding subclasses for male and female specific variants
TODO - mesonephric portion of the nephric duct
Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]
In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus.
the narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Gonochoristic organism that can produce female gametes.
Gonochoristic organism that can produce male gametes.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus.
Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus.
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles
The vessels formed within the fourth pair of branchial arches in embryogenesis.
The vessels formed within the sixth pair of branchial arches in embryogenesis
Upper portion of the skull that excludes the mandible (when present in the organism).
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
GO uses genitalia for the singular organ
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].
A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]
When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.
An endoderm that is part of a foregut [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
A gland that is part of a foregut [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis.
A gland that is part of a integumental system [Automatically generated definition].
Mesenchyme that is part of a developing camera-type eye.
A layer of epithelial cells on the surface of the mucosa.
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
A extraembryonic structure that develops_from a ectoderm and is part of a chorion.
any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi
A gland that is part of a digestive tract [Automatically generated definition].
A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition].
An artery that is part of a respiratory system [Automatically generated definition].
A vein that is part of a thoracic cavity [Automatically generated definition].
A portion of lymphoid tissue that is part of a thymus [Automatically generated definition].
A blood vessel that is part of a head [Automatically generated definition].
A blood vessel that is part of an abdomen [Automatically generated definition].
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a trunk [Automatically generated definition].
A blood vessel that is part of a kidney [Automatically generated definition].
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
A capillary that is part of a kidney [Automatically generated definition].
A gray matter that is part of a brain [Automatically generated definition].
The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.
A portion of connective tissue that is part of a head [Automatically generated definition].
portion of connective tissue of adult head
A long bone that is part of a limb [Automatically generated definition].
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
An arterial blood vessel that is part of a kidney [Automatically generated definition].
Any joint that is part of a (free) limb.
A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl.
The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).
Anatomical space in the abdominal cavity behind (retro) the peritoneum. It has no specific delineating anatomical structures. Organs are retroperitoneal if they only have peritoneum on their anterior side.
Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct.
Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct.
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
A blood vessel that is part of a thorax [Automatically generated definition].
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
blood vessel of abdominal segment of trunk
A limb joint that is part of an autopod [Automatically generated definition].
joint of limb of distal free limb segment
An anatomical space that surrounded_by a neural tube.
An epithelium that is part of a thymus, forming a supporting framework[MP,modified].
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a diencephalon.
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla.
A presumptive structure that has the potential to develop into a ganglion.
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
Initial section of the oviduct through which the ova pass from the ovary to the uterus
paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.
A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum.
The part of the retina that contains neurons and photoreceptor cells[GO].
hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food.
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].
A blood vessel that carries blood from the capillaries toward the heart
embryonic structure that develops into pancreatic bud.
The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID].
pancreatic bud that gives rise to the accessory pancreatic duct.
pancreatic bud that gives rise to the major pancreatic duct.
A duct that is part of a digestive system [Automatically generated definition].
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
White matter that is part of a diencephalon [Automatically generated definition].
predominantly white regional part of diencephalon
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
internal genitalia of female reproductive system
The funnel-like expansion of the abdominal extremity of the uterine tube[MP]
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present
The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone.
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches.
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].
TODO - ensure definition works across species.
The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments
The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules
TODO - check for applicability across species
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
The outflow tract is the portion of the heart through which blood flows into the arteries
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
The external genitalia are the outer sex organs, such as the penis or vulva in mammals
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
A portions of the gut that is derived from endoderm.
The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.
TODO - check - GO says outer, BTO says inner. Make this a superclass
The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus.
The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.
A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water.
ascending limb thin segment of loop of Henle
loop of Henle ascending limb thin segment
The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron
The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron
Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.
not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)
The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules.
The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules
The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex.
The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla.
The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla.
Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron
The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]
The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.
note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap
The nephron epithelium is a tissue that covers the surface of a nephron
The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus.
Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]
The smooth muscle tissue surrounding the urothelium of the kidney pelvis.
smooth muscle found within, and composing the majority of the wall of blood vessels.
A muscle that is part of the eye region.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
An endothelium that is part of a glomerular capillary.
A phalanx located between proximal and distal phalanges.
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]
(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]
VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826
primitive streak - blastopore - germ ring
outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The embryonic structure that gives rise to the corneal ectoderm
multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
The collection of all skeletal elements in an individual limb.
Sum of all sensory systems in an organism.
A projection or outgrowth of tissue from a larger body or organ.
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
A vascular network consisting of blood vessels.
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all arteries.
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning.
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
The blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism.
The blood vessels that convey blood from the glomerulocapillary network to the capillary bed of the proximal convoluted tubule.
arteriola glomerularis efferens capsulae renalis
The epithelial lining of the luminal space of the urinary bladder.
transitional epithelium of urinary bladder
the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein
An endothelium that is part of an arterial system [Automatically generated definition].
A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities.
An appendage that is part of an appendage girdle complex.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
Any of the veins that parallel the arcuate arteries, receive blood from the interlobular veins and straight venules, and terminate in the interlobar veins.
The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule.
In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle.
TODO - is this a vein or set of veins? in MA it is a venous blood vessel
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
An organ subunit that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Anatomical system that consists of all the joints of the body.
A vasa recta that is part of a outer medulla of kidney [Automatically generated definition].
outer zone of medulla of kidney vasa recta
vasa recta of outer zone of medulla of kidney
vasa recta of outer zone of renal medulla
A vasa recta that is part of a inner medulla of kidney [Automatically generated definition].
inner zone of medulla of kidney vasa recta
set of inner region of renal pyramids vasa recta
vasa recta of inner zone of medulla of kidney
vasa recta of inner zone of renal medulla
vasa recta of set of inner region of renal pyramids
A mucosa that is part of a gastrointestinal system.
The epithelial lining of the luminal space of the kidney pelvis.
transitional epithelium of kidney pelvis
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
An epithelium that is part of a uterine cervix [Automatically generated definition].
An epithelium that is part of a oviduct [Automatically generated definition].
columnar epithelium of the fallopian tube
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
The cellular avascular layer of the renal tubule luminar surfaces.
See https://github.com/obophenotype/uberon/issues/1305
The cellular avascular layer of the kidney luminar surfaces.
An endothelium that is part of the cardiovascular system.
A vasculature that is part of a retina [Automatically generated definition].
Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP].
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
A portion of the urogenital ridge which is the source of much of the urinary system[WP].
part_of or develops_from urogenital ridge?
One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].
Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct.
One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A part of a wall of an organ that forms a layer.
A mucosa that is part of a pylorus [Automatically generated definition].
mucosa of organ of pyloric part of stomach
mucosa of organ of stomach pyloric region
mucous membrane of pyloric part of stomach
mucous membrane of stomach pyloric region
An organ that is part of a immune system [Automatically generated definition].
A gland that is part of a hemolymphoid system [Automatically generated definition].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].
The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate.
An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO].
A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
Missing definition for term UBERON:0005095. Please replace it using linked reference.
class added for consistency with GO - consider merging with kidney mesenchyme.
The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO].
thin descending limb of the loop of Henle
The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO].
The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology[GO].
The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla[GO].
The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive[GO].
The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO].
An epithelium that is part of a mesonephros [Automatically generated definition].
A metanephric tubule is an epithelial tube that is part of the metanephros[GO].
An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO].
A metanephric nephron is the functional unit of the metanephros[GO].
The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]
The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO].
A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO].
A bud is a protrusion that forms from an epithelial sheet by localized folding.
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP].
TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule
The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx.
Any of the veins that parallel the interlobular arteries, receiving blood from the peritubular capillary plexus and empty into the arcuate veins.
Connective tissue between the cellular elements of a structure.
Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion).
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
The portion of the collecting duct that resides in the renal medulla.
Tissue surrounding the loop of Henle in the renal medulla.
It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct.
A portion of interstitial tissue that is part of a outer medulla of kidney [Automatically generated definition].
A portion of interstitial tissue that is part of a inner medulla of kidney [Automatically generated definition].
The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.
See https://sourceforge.net/p/geneontology/ontology-requests/10941/
The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment.
The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue.
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesenchyme that is part of a developing trunk.
An artery that supplies the renal cortex.
Artery that receives blood from the renal cortex[MP, modified].
A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells.
In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c.
The part of the renal cortex nearest to the medulla.
The tiny blood vessels that receive blood from the efferent arterioles of the glomerulus, and interact with superficial cortical nephrons allowing reabsorption and secretion between blood and the inner lumen of the nephron; peritubular capillaries are situated around the tubule and are at low pressure.
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
A portion of tissue that is part of an embryo.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
A pronephric nephron is the functional unit of the pronephros[GO].
The structure that is the basic functional unit of the pronephros.[AAO]
The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO].
Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]
The endothelial lining of the endocardium.
A nephron that is part of a mesonephros.
The structure that is the basic functional unit of the kidney.[AAO]
Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO].
A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros[GO].
The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO].
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
An outflow tract that is part of a aorta.
An array of photoreceptors and any supporting cells found in an eye.
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
The adipose capsule of kidney (or perinephric fat or perirenal fat) is a structure between the renal fascia and renal capsule, and may be regarded as a part of the latter. A different structure, the pararenal fat, is the adipose tissue superficial to the renal fascia.
Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow.
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
alimentary part of gastrointestinal system
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
Portion of tissue that gives rise to the lens.
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID].
we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution.
A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]
variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
the valves that gate the flow of blood from the ventricles into the aorta and pulmonary trunk
Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo.
A mesoderm that has the potential to develop into a pronephros.
Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
limb/fin field of lateral plate mesoderm
A ring of cells capable of forming a limb.
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
The capillary loops of the kidney that normally function as a filtration unit[MP].
...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus
A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP].
TODO - check this. BTO has podocytes under here
Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO]
The inner (visceral) layer of the renal glomerular capsule, overlying the capillaries, composed of podocytes, and separated from the outer (parietal) layer by the capsular (Bowman's) space[BTO]. This epithelial layer is superficially adjacent to the thickened glomerular basement membrane and is made of podocytes. Beneath the visceral layer lie the glomerular capillaries[WP]. This inner epithelial layer of the glomerular capsule surrounds the capillary endothelial cells and is composed of highly specialized epithelial cells (podocytes) that are separated by filtration slits; the inner visceral layer is separated from the outer parietal layer by the urinary space (also known as the Bowman's or capsular space)[MP].
TODO - check - the BTO class 'glomerular epithelium' is the visceral layer. But GO uses 'glomerular epithelium' as the mereological sum of P+V layers
inner epithelial layer of Bowman's capsule
Formerly had rdfs:label 'visceral layer of glomerular capsule'. The current label 'glomerular visceral epithelium' was copied from UBERON:0006852, which is now obsolete since it represented the same entity as this IRI.
The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.
The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.
A acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter.
Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]
Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.
TODO - check ridge vs cord vs nephrogenic cord vs blastema
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP].
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system.
Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH)
the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system
dorsal part of alar plate of metencephalon
The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.
A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]
In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]
The foremost region of the future forebrain that develops into the diencephalon.
An anatomical junctions that overlaps the foregut and midgut.
A presumptive structure that has the potential to develop into a forebrain.
A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops.
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
presumptive cardiac ventricle heart tube
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
A segment of the eyeball that is filled with refractive media
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
fluid
A peritubular capillary that is part of a outer medulla of kidney.
kidney outer medulla peritubular capillary
outer renal medulla peritubular capillary
Missing definition for term UBERON:0006376. Please replace it using linked reference.
distal straight tubule premacula segment
kidney medulla loop of Henle ascending limb thick segment
medullary thick ascending limb of Henle's loop
renal medulla loop of Henle ascending limb thick segment
premacula segment of distal straight tubule
Recesses of the kidney pelvis which divides into two wide, cup-shaped major renal calices, with each major calix subdivided into 7 to 14 minor calices. Urine empties into a minor calix from collecting tubules, then passes through the major calix, renal pelvis, and ureter to enter the urinary bladder. (From Moore, Clinically Oriented Anatomy, 3d ed, p211).
Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble.
A loop of Henle that is part of a kidney outer medulla inner stripe.
outer medulla inner stripe loop of Henle
A loop of Henle that is part of a kidney outer medulla outer stripe.
outer medulla outer stripe loop of Henle
A tube in the kidney that collect and transport urine.
in ZFA this is defined as part of mesonephros
A tube that is part of a excretory system.
An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
A joint that connects one phalanx to another along a proximodistal axis.
The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)
The collection of all skeletal elements in an autopodium region.
A canthus is a corner of the eye where the upper and lower eyelids meet. The bicanthal plane is the transversal plane linking both canthi and defines the upper boundary of the midface.
An epithelium that is composed primarily of secretory cells.
Structural framework that provides support to the nasal sacs and ducts.
A peritubular capillary that is part of a cortex of kidney.
A region of nephron tubule that is part of a cortex of kidney.
cortical thick ascending limb of Henle's loop
kidney cortex loop of Henle ascending limb thick segment
renal cortex loop of Henle ascending limb thick segment
distal straight tubule postmacula segment
This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
A head mesenchyme that develops_from a mesoderm.
An anatomical space that surrounded_by a digestive tract.
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
Any gland that is part of the digestive system.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
stomach glandular region glandular mucous membrane
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
A pharyngeal puch that is between the pharyngeal arches 2 and 3.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
mesenchyme derived from head neural crest
An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching.
Of or pertaining to the period of time immediately following birth, or to the newborn.
Gray matter of the central nervous system which is a collection of clustered nuclei.
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
A presumptive structure that has the potential to develop into a endocardium.
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
A presumptive structure that has the potential to develop into a paraxial mesoderm.
The part of the blastula that has the potential to develop into a paraxial mesoderm.
A presumptive structure that has the potential to develop into a pronephric mesoderm.
A vasculature that is part of a chordate pharynx.
A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans.
A duct that collects and carries secretions of the exocrine pancreas to the intestine.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO]
connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)
A neural decussation that is part of a diencephalon.
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
Mesenchyme with little extracellular matrix.
Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix.
this class will be an important part of the NC reorganization
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx.
An anatomical structure that connects two structures
Functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule.
consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts
Region of the embryo into the area in which the kidney rudiment will develop.
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP].
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
characteristically low in protein and cellular content (unless there has been secondary concentration)
the FMA def is Transudate contained in a serous sac
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.
Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]
Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]
The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
Musculature system of the pharyngeal and head regions.
A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them.
An endothelium that is part of a heart [Automatically generated definition].
The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions.
epithelium of proximal convoluted tubule
An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter
The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP].
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of endoskeleton derived from pharyngeal arches
The functional tissue of the kidney, consisting of the nephrons.
Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb
inner medulla vasa recta descending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb
outer medulla vasa recta descending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb
An organism containing a developing embryo, fetus, or unborn offspring within the body.
A gonad prior to differentiating into a definitive testis or ovary.
The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
A nephric duct is a tube that drains a primitive kidney[GO].
This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb
An epithelium that is part of a foregut-midgut junction.
An endoderm that is part of a foregut-midgut junction.
A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium).
midbrain-hindbrain boundary neural plate
midbrain hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx.
A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.
this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
Branch or outpocketing of the digestive tract.
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
Outer portion of the renal cortex. Site of formation of medullary and cortical elements.
see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish.
Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton
The interlobar veins are veins of the renal circulation which drain the renal lobes.
Mesenchyme that is part of a developing face.
A portion of an organ, such as the liver, lung, breast, or brain.
The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP].
human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
An anatomical structure that has more than one cell as a part.
A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function.
An organ of the digestive tract that is capable of retaining and storing food
Organ system subdivision that consists primarily of chromaffin cells and their supporting structures.
An extrahepatic bile duct that has the potential to develop into a common hepatic duct.
Mesenchyme that has the potential to develop into a dermis.
A developing anatomical structure that has the potential to develop into a metencephalon.
A developing anatomical structure that has the potential to develop into a myelencephalon.
The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw)
any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli
A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid.
An anatomical cavity that surrounded_by a blood vessel.
An anatomical boundary that corresponds to some physical discontinuity.
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
The core globe-shaped component of the camera-type eye.
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
Developing anatomical structure that develops into the eyeball and associated structures.
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
Mesenchyme that is part of a extraembryonic membrane.
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla.
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
Mesenchyme that develops_from a somatopleure.
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic.
nephrogenic interstitium of nephrogenic zone
cap mesenchyme of metanephros of urinary system
An epithelial tube that is fated to become a nephron.
EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells
A primitive nephron that is part of a metanephros.
An appendage segment that is part of a limb/fin.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified].
Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.
An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.
Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)
pectoral girdle plus anterior limb or fin
pectoral girdle plus pectoral limb or fin
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here
pelvic girdle plus posterior limb or fin
Skeletal subdivision that is a segment of the limb skeleton.
The subdivision of the skeleton of either the pectoral or pelvic girdle.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
The collection of all meningeal layers that line a central nervous system.
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
subdivision of organism along appendicular axis
A skeletal element that is part of a limb and composed of cartilage tissue.
A skeletal element that is part of a limb and composed of pre-cartilage tissue.
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Any muscle organ that is part of either the head or the neck.
A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints.
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
Any synovial joint that is part of a (free) limb.
Subdivision of urinary system which consists of the kidney and the ureters.
Subdivision of skull that consists of the facial bones.
The skull can be divided into two: the neurocranium and the facial skeleton
primary subdivision of cranial skeletal system
A sphincter muscle that is part of the gastrointestinal system
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
A blood vasculature that is part of a head.
The collection of all skeletal elements in an individual limb or fin.
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
Section of the forelimb skeleton located between the stylopodium and the autopodium.
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix.
An axon tract that is part of a diencephalon.
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A cardiovascular system that is part of a conceptus.
Ectodermal placode that does not develop into a component of the nervous system.
An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales).
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle
A region of the stomach that is lined with glandular epithelium.
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.
A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.
An artery that originates from the abdominal aorta
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]
Epithelium that derives from the mesoderm. [Automatically generated definition].
One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly
We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts
One of five swellings formed during the development of the face
any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen.
The segment of the autopod that is distal to the metapodial region and consists of the digits.
A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.
Blood-forming tissue, consisting of reticular fibers and cells.
Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
An endothelium that is part of a peritubular capillary.
An anatomical space with no opening to another space or to the exterior.
The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle.
skeleton of anterior limb/fin and girdle
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
skeleton of posterior limb/fin and girdle
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
Anatomical projection that is part of the integumentl system.
A organ component layer that is part of a integumental system.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
Mesenchyme that develops_from the neural crest[Automatically generated definition].
Any member of the network of tubes that return blood from the renal tissues to the systemic circulation.
we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory.
A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A portion of tissue that will develop into vasculature.
A phalanx bone or its cartilage or pre-cartilage precursor.
A limb bone or its cartilage or pre-cartilage precursor.
A endochondral element that is part of a autopod region.
A autopod endochondral element that is composed primarily of cartilage tissue.
An anatomical group whose component structures share a common function.
A non-connected functional system that is composed primarily of a gland.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
A epithelium that is part of a camera-type eye.
An epithelium that is part of a foregut.
is the sensory system for the sense of hearing.
An roughly circular indentation in a surface.
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
A mammalian developmental stage that covers the period from birth until weaning.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
The part of the eye that consists of both the retina and the optic choroid
A white matter that is part of the forebrain.
An exocrine gland that is part of a integumental system.
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
Any substance in the body or expelled from the body that is in a gaseous state.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
the area of axial mesoderm that develops into the prechordal plate
Nursing stage that follows the neonate stage in mammals and ends at weaning.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts.
organ region with floating fiat boundary
Any portion of gas located in a part of the respiratory system.
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
Any chamber of the left side of the heart
Any chamber of the right side of the heart.
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
The primordial mouth region of the developing head.
The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity.
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
An organ subunit in the skin that gives rise to cutaneous appendage.
Material anatomical entity that forms the outermost boundary of an anatomical structure.
Any gland that is part os the respiratory system.
The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra.
vasculature of central nervous system plus retina
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit ( phalanges plus metapodial) plus soft tissue
A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element.
individual digit of digitopodial skeleton
Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.
An anatomical system that eliminates waste products that arise as a result of metabolic activity.
A muscle tissue that is associated with soft internal organs (viscera).
It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated.
A unit which is a standard measure of the dimension in which events occur in sequence.
phenotype
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
Many vaccines are developed to protect against infectious pathogens that causes infectious diseases. Many vaccines are also being developed against other diseases such as cancer, allergy, and autoimmune diseases.
a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo.
a medical intervention that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intent to invoke an adaptive immune response.
a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response.
a vaccine adjuvant that is formed as a mineral salt.
an adjuvant role that inheres in a vaccine component which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen.
The Latin "adjuvans" means to help, particularly to reach a goal. Adjuvant therapy for cancer is surgery followed by chemotherapy or radiation to help decrease the risk of the cancer recurring (coming back). An adjuvant is a substance that helps and enhances the pharmacological effect of a drug or increases the ability of an antigen to stimulate the immune system.
A vaccine that targets against a bacterial disease.
a processed material that is output of the vaccine preparation and part of a vaccine.
vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host.
PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term.
A legal organization that represents an association of people with a specific objective.
a route of administration that inject the material(such as vaccines, allergens) directly into a muscle.
Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008
a role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity.
preventive vaccine function is a vaccine function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which protects against a specific disorder.
immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens.
WEB: http://en.wikipedia.org/wiki/Immunization
Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target.
Active immunization entails the introduction of a foreign molecule into the body, which causes the body itself to generate immunity against the target. This immunity comes from the T cells and the B cells with their antibodies. Active immunization can occur naturally when a person comes in contact with, for example, a microbe. If the person has not yet come into contact with the microbe and has no pre-made antibodies for defense (like in passive immunization), the person becomes immunized. The immune system will eventually create antibodies and other defenses against the microbe. The next time, the immune response against this microbe can be very efficient; this is the case in many of the childhood infections that a person only contracts once, but then is immune. Artificial active immunization is where the microbe, or parts of it, are injected into the person before they are able to take it in naturally. If whole microbes are used, they are pre-treated, Attenuated vaccine. (Wikipedia)
artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.
induction of adaptive immune response to antigen is an active immunization process that results in induction of adaptive immune response to some antigens, for example, in a vaccine.
induction of adaptive immune response to antigen
disorder prevention is a processual entity that prevents a disorder that is the physical basis of a disease.
disorder treatment is a processual entity that leads to treat a disorder that is the physical basis of a disease.
modification of adaptive immune response to antigen is an active immunization process that results in modification of an adaptive immune response to some antigens, for example, in a therapeutic vaccine.
modification of adaptive immune response to antigen
The therapeutic vaccine function is a function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which ameliorates a specific disorder.
a path that is located in gross anatomical part of an organism (e.g., human) and is used for administering a vaccine, a drug, fluid, poison, or other substance into the body.
CDISC has a codelist: Rout of Administration. Desription from CDISC: The course by which a substance was administered in order to reach the site of action in the body. CDISC_SDTM_Route_of_Administration_Terminology
a vaccine component that is chemical substance added to vaccine and enhance and direct immune response to protective antigen. Many of vaccine adjuvants cause a range of serious side-effects.
immunization objective is the specification of an objective to achieve immunization.
vaccine preparation is a manufacturing process to produce a vaccine.
A vaccine that targets against a viral disease.
a role that inheres in a prepared material entity that is designed to induce protection or treatment for a disease or infection.
vaccine role
a role that inheres in a material entity that becomes an ingredient of a vaccine.
vaccine component role
licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market.
A bacterial vaccine that protects against infection with Clostridium spp.
a Clostridium vaccine that protects against infection with Clostridium tetani that causes tenanus.
A viral vaccine that protects against infection with Hepatitis B virus.
a vaccine role that indicates the vaccine being a toxoid vaccine.
toxoid vaccine role
a licensed vaccine role that indicates the vaccine occurs in USA.
a vaccine component that remains from the vaccine manufacturing process.
Although no all manufacturing residuals may be identified and quantified, their presence and quantity is assumed to be constant because of the constancy of the manufacturing process.
Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 73.
a vaccine residual that is generatead from cell culture for vaccine preparation. Examples include: antibiotics, sensitizing substances, bacterial and cellular residuals, and adventitious agents.
Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 78-81.
a licensed status that occurs in Canada.
a mineral salt vaccine adjuvant that is composed of aluminum salt.
Aluminum vaccine adjuvant is a vaccine adjuvant that is composed of some aluminum compound.
vaccine allergen is a material entity that is capable of stimulating a type-I hypersensitivity reaction in atopic individuals who has been vaccinated with a vaccine.
WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
a cell culture residual in vaccine that is yeast protein.
yeast protein cell culture residual in vaccine
a vaccination that occurs in the intramuscular route.
a role of host that contains vaccine. It is a role that inheres in an organism that is the target of a vaccine administration (vaccination process).
The objective that intends to produce vaccine via the vaccine preparation process.
RECOMBIVAX HB is indicated for vaccination against infection caused by all known subtypes of hepatitis B virus.
A protein coding gene TNFRSF1A in human.
A protein coding gene TNFRSF1B in human.
A protein coding gene CCDC102B in human.
A protein coding gene HLA-DRB1 in human.
Part of the landmass of Eurasia, with the western portion of the latter occupied by Europe, lying east of the Suez Canal, east of the Ural Mountains, and south of the Caucasus Mountains and the Caspian and Black Seas. It is bounded on the east by the Pacific Ocean, on the south by the Indian Ocean, and on the north by the Arctic Ocean.
A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.
United Kingdom of Great Britain and Northern Ireland
An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.
A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.
A group of islands off the northwest coast of continental Europe that include the islands of Great Britain and Ireland, and over six thousand smaller islands. There are two sovereign states located on the islands: the United Kingdom and the Republic of Ireland. The British Isles also include two dependencies of the United Kingdom: the Isle of Man and, by tradition, the Channel Islands, although the latter are not physically a part of the island group.
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
KPMP organization
participant candidate 1
participant candidate 2
participant candidate 3
filled CRF by candidate 1
filled CRF by candidate 2
filled CRF by candidate 3
European Union Drug Regulating Authorities Clinical Trials
EudraCT
ClinicalTrials.gov is a resource provided by the U.S. National Library of Medicine.
Clinicaltrials.gov
SDY269 study
SDY269
human subject SUB112829
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
Adam Goldstein
Albert Goldfain
Barry Smith
Carlo Torniai
Chris Stoeckert
Christian A. Boelling
Darren Natale
David Osumi-Sutherland
Gwen Frishkoff
Holger Stenzhorn
James A. Overton
James Malone
Jie Zheng
Jonathan Rees
Larisa Soldatova
Lawrence Hunter
Matt Brush
Melanie Courtot
Michel Dumontier
Paolo Ciccarese
Pat Hayes
Philippe Rocca-Serra
Randy Dipert
Ron Rudnicki
Satya Sahoo
Sivaram Arabandi
Werner Ceusters
William Duncan
Yongqun (Oliver) He
An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html
This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
Bill Bug
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Jay Greenbaum
Jeffrey Grethe
Jessica Turner
Joe White
John Westbrook
Kevin Clancy
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philip Lord
Phillip Lord
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
An ontology for the annotation of biomedical and functional genomics experiments.
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
NYSTATIN 100000UNT/ML SUSP,ORAL [VA Product]
<Product_Component>MAGNESIUM CHLORIDE</Product_Component> 5.08 MG/100ML <VA.IEN>810</VA.IEN>
<Product_Component>CALCIUM CHLORIDE</Product_Component> 25.7 MG/100ML <VA.IEN>682</VA.IEN>
Calcium Chloride 0.00014 MEQ/ML / Glucose 1 MG/ML / Magnesium Chloride 0.0000245 MEQ/ML / Sodium Chloride 0.00368 MEQ/ML / Sodium Lactate 0.0016 MEQ/ML Intraperitoneal Solution [Dianeal PD-2/2.5]
<Product_Component>SODIUM CHLORIDE</Product_Component> 538 MG/100ML <VA.IEN>35</VA.IEN>
DEXTROSE/PERITONEAL DIALYSIS SOLUTION SOLN
<Product_Component>SODIUM LACTATE</Product_Component> 448 MG/100ML <VA.IEN>1292</VA.IEN>
DIANEAL PD-2/DEXTROSE 2.5% SOLN [VA Product]
One of the large, unbroken masses of land into which the Earth's surface is divided.
A reference to a place on the Earth, by its name or by its geographical location.
The convention used in gaz.obo is that the Europe-Asia boundary follows the watershed of the Ural Mountains from near Kara, Russia on the Kara Sea to the source of the Ural River, then follows that river to the Caspian Sea. The border then follows the watershed of the Caucasus Mountains from the Caspian Sea to the Black Sea.
A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.
See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.
DrOn contains content developed by the National Library of Medicine in RxNorm. In creating DrOn, we have used RxNorm content only with SAB = RXNORM.
When citing DrOn, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/dron.owl. When referencing a specific component of the DrOn, such as a class, object property, annotation property, or individual, use the Uniform Resource Identifier (URI) of that component.
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 186 Logical Axioms: 30]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 132 Logical Axioms: 23]
ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ Please see www.environmentontology.org for more information and citations.
Phenotypic abnormalities encountered in human disease
Peter Robinson, Sebastian Koehler, The Human Phenotype Ontology Consortium, and The Monarch Initiative
The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.
Please see license of HPO at http://www.human-phenotype-ontology.org
Includes Ontology(OntologyID(Anonymous-35)) [Axioms: 88199 Logical Axioms: 0]
Includes Ontology(OntologyID(Anonymous-33)) [Axioms: 7236 Logical Axioms: 0]
Desikan Jagannathan
An ontology for the annotation of the adverse event domain.
Vision Release; 1.2.19
Product version
Shelley Zhang
Meiu Wong
The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
OAE: Ontology of Adverse Events
Bingjian Yang
MIABIS_v2_accepted and UPenn Biobank ontology
The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.
development version
Ontology for BIoBanking (OBIB)
Vision Release: 1.0.59
OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl The OGMS developer site is https://github.com/OGMS/ogms If you are interested in participating in the development of OGMS, please send email to baeverma
This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
Swetha Garimalla
The Ontology of Medically Related Social Entities
Shariq Tariq
Use reasoner in Protege to see the correct hierarchy.
The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details.
Philip Huang
Yu Lin (YL)
Shunzhou Deng
Ronak Sutariya
Anthony Huffman
October 5, 2022
Ningxian Fan
Zuoshuang "Allen" Xiang
Yongqun "Oliver" He (YH)
Randi Vita
The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
Rohit Goru
Anna Maria Masci
An ontology in the domain of vaccine and vaccination
Vaccine Ontology