Becky Steck
Chrysta Lienczewski
Deborah Hoshizaki
Evren Azeloglu
George Oliver
John F. Bertram
John O'Toole
Jonathan Himmelfarb
Laura Mariani
Matthias Kretzler
Michael Todd Valerius
Ravi Iyengar
Sean Mooney
The KPMP Consortium
Ulysses Balis
Edison Ong
Jennifer Schaub
Ling Wan
Yingtong Liu
Yongqun "Oliver" He
2022-02-16
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: 1.0.102
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 OWL specification label
BFO OWL specification label
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
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
BFO CLIF specification label
editor preferred label
editor preferred label
editor preferred term
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
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
has curation status
definition
definition
textual 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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
DEFINITION
definition
definition
textual definition
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
1
true
editor_note
editor note
editor note
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
definition editor
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
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
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
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.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
1
curator_notes
curator note
curator note
curator notes
term tracker item
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
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.
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
IAO:0000233
external
term_tracker_item
true
true
term_tracker_item
The 'tracker item' can associate a tracker with a specific ontology term.
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
term tracker item
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
imported from
expand expression to
expand expression to
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:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
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
elucidation
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
has associated axiom(fol)
preferred_root
term replaced by
C3829466
NCIT_C106180
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.
A11
Conceptual Entity
Has_NICHD_Parent
Has_NICHD_Parent
Has_NICHD_Parent
true
NHC0
code
code
code
The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
P106
Conceptual Entity
Semantic Type
Semantic_Type
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.
Semantic_Type
Semantic_Type
Provides an alternative Preferred Name for use in some NCI systems.
P107
Conceptual Entity
Display Name
Display_Name
Display Name
Display_Name
Display_Name
The word or phrase that NCI uses by preference to refer to the concept.
P108
Conceptual Entity
Preferred Name
Preferred_Name
Preferred Name
Preferred Term
Preferred_Name
Preferred_Name
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.
P207
Conceptual Entity
UMLS CUI
UMLS_CUI
UMLS_CUI
UMLS_CUI
Contains a Concept Unique Identifier for those concepts that appear in NCI Metathesaurus but not in the NLM UMLS.
P208
Conceptual Entity
NCI Metathesaurus CUI
NCI_META_CUI
NCI_META_CUI
NCI_META_CUI
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.
P310
Conceptual Entity
Concept Status
Concept_Status
Concept_Status
Concept_Status
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.
P322
Conceptual Entity
Contributing Source
Contributing_Source
Contributing_Source
Contributing_Source
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.
P325
Conceptual Entity
[source] Definition
ALT_DEFINITION
ALT_DEFINITION
ALT_DEFINITION
true
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.
P366
Conceptual Entity
Legacy Concept Name
Legacy Concept Name
Legacy_Concept_Name
P371
Conceptual Entity
NICHD_Hierarchy_Term
NICHD
NICHD_Hierarchy_Term
NICHD_Hierarchy_Term
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.
P98
Conceptual Entity
DesignNote
DesignNote
DesignNote
DesignNote
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
Person: Alejandra Gonzalez-Beltran
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
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: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC alternative term
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
the symbol assigned by the nomenclature authority
Oliver He, Yue Liu
symbol from nomenclature authority
the full name assigned by the nomenclature authority
Oliver He, Yue Liu
full name from nomenclature authority
A GeneID in the NCBI Gene database
Oliver He, Yue Liu
NCBI GeneID
the NCBI LocusTag name of a gene
Oliver He, Yue Liu
NCBI LocusTag
the map location of a gene
Oliver He, Yue Liu
gene map location
a date of content modification
Oliver He, Yue Liu
modification date
The NCBITaxon ontology ID of an organism.
Oliver He, Yue Liu
organism NCBITaxon ID
A chromosome ID where a gene is located.
Oliver He
chromosome ID of gene
an annotation property that specifies the type of a gene
Oliver He
type of gene
an annotation property that specifies a nomenclature status
Oliver He
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
Yongqun He
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).
Yongqun He
YH: use the format:
PMID: pmid1, pmid2, ...
where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).
has PubMed association
A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term
Oliver He
term mapping to NCIT ID
A subproperty of seeAlso that represents a UMLS CUI identifier mapped to the specified term
Oliver He
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
temporal interpretation
https://code.google.com/p/obo-relations/wiki/ROAndTime
https://github.com/oborel/obo-relations/wiki/ROAndTime
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.
Chris Mungall
?X DisjointWith RO_0002162 some ?Y
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
RO:0002161
uberon
never_in_taxon
true
true
never_in_taxon
never in taxon
never_in_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.
RO:0002174
uberon
dubious_for_taxon
1
1
dubious_for_taxon
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
dubious_for_taxon
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
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.
https://orcid.org/0000-0002-6601-2165
RO:0002175
applicable for taxon
uberon
present_in_taxon
1
true
1
true
present_in_taxon
present in taxon
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
https://github.com/oborel/obo-relations/wiki/ShortcutRelations
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'
Chris Mungall
is direct form of
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.
UBPROP:0000001
uberon
external_definition
1
true
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
A textual description of an axiom loss in this ontology compared to an external ontology.
UBPROP:0000002
uberon
axiom_lost_from_external_ontology
1
axiom_lost_from_external_ontology
This annotation property may be replaced with an annotation property from an external ontology such as IAO
axiom_lost_from_external_ontology
Notes on the homology status of this class.
UBPROP:0000003
uberon
homology_notes
1
true
homology_notes
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_notes
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'.
UBPROP:0000007
uberon
has_relational_adjective
1
has_relational_adjective
has_relational_adjective
Notes on the how instances of this class vary across species.
UBPROP:0000008
uberon
taxon_notes
1
taxon_notes
taxon_notes
Notes on the structure, composition or histology of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000010
uberon
structure_notes
1
structure_notes
structure_notes
Notes on the ontogenic development of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000011
uberon
development_notes
1
development_notes
development_notes
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000012
uberon
external_ontology_notes
1
external_ontology_notes
external_ontology_notes
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000013
uberon
terminology_notes
1
terminology_notes
terminology_notes
excluded_from_qc_check
true
excluded from QC check
excluded_subClassOf
true
excluded subClassOf
A metadata relation between a class and its taxonomic rank (eg species, family)
ncbi_taxonomy
ncbi_taxonomy
has_rank
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.
http://purl.org/dc/elements/1.1/contributor
uberon
dc-contributor
1
true
dc-contributor
An entity responsible for making contributions to the
content of the resource.
Contributor
Contributor
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.
http://purl.org/dc/elements/1.1/creator
uberon
dc-creator
true
dc-creator
An entity primarily responsible for making the content
of the resource.
Creator
Creator
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
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.
http://purl.org/dc/elements/1.1/description
uberon
dc-description
true
dc-description
An account of the content of the resource.
Description
Description
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
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
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
Subject and Keywords
Typically, a Title will be a name by which the resource is
formally known.
http://purl.org/dc/elements/1.1/title
uberon
dc-title
true
dc-title
A name given to the resource.
Title
Title
title
Mark Miller
2018-05-11T13:47:29Z
http://purl.org/dc/terms/license
uberon
dcterms-license
true
dcterms-license
license
consider
has_alternative_id
has_broad_synonym
database_cross_reference
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.
FULL_SYN
Synonym with Source Data
has exact synonym
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
Concept_In_Subset
in subset
in_subset
shorthand
label
label
label
http://www.w3.org/2000/01/rdf-schema#seeAlso
uberon
seeAlso
true
true
seeAlso
see also
seeAlso
http://xmlns.com/foaf/0.1/depicted_by
uberon
depicted_by
foaf-depicted_by
1
true
depicted_by
foaf-depicted_by
depicted by
depicted_by
C26
CI_ChemClass
C36
CI_with
C24
has_Ingredient
C28
has_MoA
C20
has_PE
C32
has_PK
C40
induces
C38
may_prevent
C34
may_treat
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
BFO:0000050
external
quality
uberon
part_of
part_of
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL: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.
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 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
BFO:0000051
external
protein
quality
uberon
has_part
has_part
has part
has part
has_part
BFO_0000052
BFO_0000052s
BFO_0000052ed
inheres-in_at
inheresInAt
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
http://purl.obolibrary.org/obo/omrse.owl
is 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
http://purl.obolibrary.org/obo/ro.owl
[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])
BFO:0000054
realized_in
realized_in
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
realized in
realized in
BFO_0000055
BFO_0000055s
BFO_0000055ed
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
realizes
concretized-by_st
[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
concretizes_st
concretizesAt
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 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
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
external
uberon
preceded_by
preceded_by
preceded by
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.
BFO:0000063
external
uberon
precedes
precedes
precedes
precedes
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
BFO:0000066
external
occurs_in
occurs_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
occurs in
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
BFO:0000067
uberon
contains_process
contains_process
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
contains process
s-depends-on_at
specificallyDependsOn
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
located-at-r_st
occupiesSpatialRegionAt
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)
BFO2 Reference: independent continuant
BFO2 Reference: spatial region
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
exists-at
existsAt
BFO2 Reference: entity
BFO2 Reference: temporal region
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
BFO_0000117
BFO_0000117s
BFO_0000117ed
o-has-part
hasOccurrentPart
[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
o-has-ppart
hasProperOccurrentPart
[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
r-location-of_st
[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
has-s-dep_st
[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
occupied-by
[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
occupies
occupiesSpatiotemporalRegion
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
BFO_0000132
BFO_0000132s
BFO_0000132ed
o-part-of
occurrentPartOf
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.
BFO2 Reference: 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])
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
o-ppart-of
properOccurrentPartOf
[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
t-part-of
temporalPartOf
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
st-projects-onto-s_st
projects onto spatial region at some time
s-projection-of-st_st
spatial projection of spatiotemporal at some time
st-projects-onto-t
projects onto temporal region
t-projection-of-st
temporal projection of spatiotemporal
spans
occupiesTemporalRegion
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
span-of
spanOf
[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
during-which-exists
[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
bearer-of_at
bearerOfAt
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)'.
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(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
has-d_at
hasDispositionAt
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
BFO_0000167
BFO_0000167s
BFO_0000167ed
has participant at all times
has-s-dep_at
has specific dependent at all times
s-depends-on_st
specificallyDependsOn
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 some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & '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 some time
c-part-of_st
continuantPartOfAt
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])
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.
BFO2 Reference: continuant
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
c-has-part_st
hasContinuantPartAt
[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
c-part-of-object_at
[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
c-has-part-object_at
[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 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.
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior_to
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).
BSPO:0000097
uberon
distal_to
distal_to
distal_to
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).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal_to
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.
caudal_to
posterior_to
x proximal_to y iff x is closer to the point of attachment with the body than y.
proximal_to
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).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral_to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
uberon
deep_to
deep_to
deep_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
in_left_side_of
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
in_right_side_of
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
in_posterior_side_of
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
in_anterior_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
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 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.
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y.
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
immediately_deep_to
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y.
BSPO:0001108
uberon
distalmost_part_of
distalmost_part_of
distalmost_part_of
GOREL:0002004
external
results_in_fission_of
results_in_fission_of
results_in_fission_of
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.
person:Alan Ruttenberg
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.
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
person:Alan Ruttenberg
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
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.
Oliver He, Edison Ong
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.
Oliver He, Edison Ong
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
Oliver He, Edison Ong
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
Oliver He, Edison Ong
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.
Oliver He
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.
Oliver He
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.
Oliver He
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.
Oliver He
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.
Oliver He, Edison Ong
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
Oliver He, Edison Ong
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
Oliver He, Edison Ong
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.
Oliver He
susceptible to be down-regulated in AKI 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 an acute kidney injury (AKI) patient.
Oliver He
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
Oliver He, Yingtong Liu
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
Oliver He, Yingtong Liu
cell has gene marker
Oliver He, Yingtong Liu
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.
Oliver He, Yingtong Liu
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.
Oliver He, Yingtong Liu
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.
Oliver He, Yingtong Liu
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
Yingtong Liu, Oliver He
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.
Yingtong Liu, Oliver He
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.
Yingtong Liu, Oliver He
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.
Yingtong Liu, Oliver He
RNA biomarker of disease
biomarker related
is biomarker of cell
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)
Yongqun He
has participant quality
a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in.
Yongqun He
adverse event occurs in
AE occurs in
a specific 'preceded by' object property that has a domain of an adverse event.
Yongqun He
adverse event preceded by
is_supported_by_data
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
OBI
OBI
Philly 2011 workshop
is_supported_by_data
is_specified_input_of
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
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_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.
Alan Ruttenberg
Liju Fan
has_make
has_manufacturer
is_manufactured_by
is_specified_output_of
is_specified_output_of
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
is_specified_output_of
achieves_planned_objective
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.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
has grain
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
PERSON: Alan Ruttenberg
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
has grain
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
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.
OBI
OBI
objective_achieved_by
has organization member
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
has value specification
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
Yongqun He, Bin Zhao
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.
Oliver He, Yue Liu
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.
is-aggregate-of
true
A kidney biopsy protocol is executed in a kidney biopsy process.
A shortcut relation that is concretized and realized in some process.
Jie Zheng, Oliver He
executed in
A 'has part' object property that has the range of a textual question
Oliver He
has question
form generated by
An object property that indicates a relation between a question and an answer
has answer to question
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.
Fred Dowd, Oliver He
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.
Fred Dowd, Oliver He
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
Anthony Huffman, Oliver He
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
Anthony Huffman, Oliver He
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
Anthony Huffman, Oliver He
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
Anthony Huffman, Oliver He
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.
Oliver He, Long Tran
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.
Long Tran, Oliver He
http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE
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.
http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE
discharged to
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
http://purl.obolibrary.org/obo/ro.owl
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
inheres in
bearer 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.
bearer of
bearer_of
is bearer of
RO:0000053
external
uberon
bearer_of
bearer_of
bearer of
bearer of
bearer_of
has characteristic
is bearer of
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
RO:0000056
external
uberon
participates_in
participates_in
participates in
participates in
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
http://purl.obolibrary.org/obo/ro.owl
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
external
has_participant
has_participant
has participant
has participant
has_participant
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 journal article (a generically dependent continuant) is concretized as the quality (a specifically 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 generically dependent continuant and a specifically 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. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
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.
http://purl.obolibrary.org/obo/obi.owl
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.
concretizes
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
RO:0000086
protein
uberon
has_quality
false
has_quality
has quality
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
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
derives from
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
RO:0001015
uberon
location_of
location_of
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
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
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
file:/Users/michaelashburner/Desktop/gaz/gaz.oboInOwl
uberon
located_in
located_in
located in
located_in
located_in (type level)
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.
David Osumi-Sutherland
has boundary
has_2D_boundary
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has boundary
David Osumi-Sutherland
http://www.ncbi.nlm.nih.gov/pubmed/22402613
RO:0002005
nerve supply
uberon
innervated_by
innervated_by
http://code.google.com/p/obo-relations/issues/detail?id=6
innervated_by
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
David Osumi-Sutherland
RO:0002007
external
uberon
bounding_layer_of
bounding_layer_of
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.
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
bounding layer of
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
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.
dos
2017-05-24T09:49:21Z
has component process
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.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
David Osumi-Sutherland
RO:0002082
coincides_with
is_equal_to
uberon
simultaneous_with
simultaneous_with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
simultaneous_with
David Osumi-Sutherland
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)
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y).
David Osumi-Sutherland
starts_at_end_of
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].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
external
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately_preceded_by
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
external
immediately_precedes
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
immediately_precedes
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
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
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
ends_during
Relation between a neuron and an anatomical structure that its soma is part of.
David Osumi-Sutherland
<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.
Alexander Diehl
Chris Mungall
Lindsay Cowell
<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 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
BFO_0000051 some (BFO_0000050 some ?Y)
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
external
uberon
overlaps
overlaps
overlaps
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.
David Osumi-Sutherland
<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?)))
RO:0002134
uberon
innervates
innervates
http://code.google.com/p/obo-relations/issues/detail?id=6
innervates
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
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)
RO:0002150
uberon
continuous_with
continuous_with
continuous with
continuous_with
FMA:85972
lactation SubClassOf 'only in taxon' some 'Mammalia'
S only_in_taxon T iff: S SubClassOf in_taxon only T.
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
Chris Mungall
RO:0002160
never_outside_taxon
specific_to
specific_to_taxon
protein
uberon
only_in_taxon
false
only_in_taxon
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.
only in taxon
only_in_taxon
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.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
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.
Chris Mungall
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
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
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
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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)
RO:0002176
uberon
connects
connects
connects
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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)
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
attaches_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
RO:0002178
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
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
RO:0002179
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
drains
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.
RO:0002180
external
uberon
has_component
has_component
has component
has component
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
inverse of 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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops from
develops_from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
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
Chris Mungall
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.
Chris Mungall
David Osumi-Sutherland
has developmental precursor
FBbt
RO:0002207
uberon
directly_develops_from
directly_develops_from
TODO - add child relations from DOS
directly develops from
directly_develops_from
inverse of directly develops from
developmental precursor of
directly develops into
process(P1) regulates process(P2) iff:Â 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
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
has_component
regulates
regulates
regulates (processual)
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.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
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.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
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.
Chris Mungall
has function realized in
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)".
RO_0000053 some (RO_0000054 only ?Y)
RO:0002215
external
uberon
capable_of
capable_of
capable of
capable of
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.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
RO:0002216
external
uberon
capable_of_part_of
capable_of_part_of
capable of part of
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
Chris Mungall
has agent
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
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y.
Chris Mungall
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded by
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
x adjacent_to y iff: x and y share a boundary.
This relation acts as a join point with BSPO
Chris Mungall
RO:0002220
external
uberon
adjacent_to
adjacent_to
adjacent to
adjacent to
adjacent_to
inverse of surrounded by
inverse of surrounded_by
inverse of surrounded_by.
Chris Mungall
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
Chris Mungall
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
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.
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
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.
Chris Mungall
started by
RO:0002224
external
uberon
starts_with
starts_with
starts with
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
Chris Mungall
RO:0002225
uberon
develops_from_part_of
develops_from_part_of
develops from part of
develops_from_part_of
Relation between occurrents, shares an end boundary with.
inverse of ends with
Chris Mungall
RO:0002229
finishes
uberon
ends
ends
ends
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.
Chris Mungall
finished by
RO:0002230
external
uberon
ends_with
ends_with
ends with
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
Chris Mungall
starts with process that occurs in
RO:0002231
external
has_start_location
has_start_location
has start location
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
Chris Mungall
ends with process that occurs in
RO:0002232
external
has_end_location
has_end_location
has end location
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.
Chris Mungall
consumes
RO:0002233
external
has_input
has_input
has input
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.
Chris Mungall
produces
RO:0002234
external
has_output
has_output
has output
has output
Any relationship between an exposure event or process and any other entity.
related via exposure to
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
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
induced by
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
GO:0001759
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
developmentally_induced_by
Inverse of developmentally induced by
Chris Mungall
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
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
RO:0002258
uberon
developmentally_preceded_by
developmentally_preceded_by
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
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
Chris Mungall
replaces
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
developmentally_replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
Inverse of 'expressed in'
Chris Mungall
expresses
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.
Chris Mungall
RO:0002295
external
results_in_developmental_progression_of
results_in_developmental_progression_of
results in developmental progression of
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.
Chris Mungall
http://www.geneontology.org/GO.doc.development.shtml
RO:0002296
external
results_in_development_of
results_in_development_of
results in development of
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)
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002297
external
results_in_formation_of
results_in_formation_of
results in formation of
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.
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002298
external
results_in_morphogenesis_of
results_in_morphogenesis_of
results in morphogenesis of
results in morphogenesis of
cjm
RO:0002304
external
causally_upstream_of,_positive_effect
causally_upstream_of,_positive_effect
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
causally upstream of, positive effect
cjm
RO:0002305
external
causally_upstream_of,_negative_effect
causally_upstream_of,_negative_effect
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
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.
has exposure stimulus
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
Chris Mungall
regulates localization of
RO:0002313
external
transports_or_maintains_localization_of
transports_or_maintains_localization_of
transports or maintains localization of
transports or maintains localization of
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 characteristic of part of
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
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
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002315
external
results_in_acquisition_of_features_of
results_in_acquisition_of_features_of
results in acquisition of features of
results in acquisition of features of
A relationship that holds via some environmental process
Chris Mungall
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
Chris Mungall
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)
Chris Mungall
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
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
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.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
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.
Chris Mungall
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
Chris Mungall
regulates levels of (process to entity)
RO:0002332
external
regulates_levels_of
regulates_levels_of
regulates levels of
regulates levels of
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
RO:0002334
external
regulated_by
regulated_by
regulated by
regulated by
inverse of negatively regulates
Chris Mungall
RO:0002335
external
negatively_regulated_by
negatively_regulated_by
negatively regulated by
negatively regulated by
inverse of positively regulates
Chris Mungall
RO:0002336
external
positively_regulated_by
positively_regulated_by
positively regulated by
positively regulated by
A relationship that holds via some process of localization
Chris Mungall
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.
Chris Mungall
RO:0002338
external
has_target_start_location
has_target_start_location
has target start location
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.
Chris Mungall
RO:0002339
external
has_target_end_location
has_target_end_location
has target end location
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
Chris Mungall
RO:0002341
external
results_in_transport_along
results_in_transport_along
results in transport along
results in transport along
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
Chris Mungall
RO:0002344
external
results_in_transport_to_from_or_in
results_in_transport_to_from_or_in
results in transport to from or in
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.
is member of
member part of
SIO
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
has member
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
Chris Mungall
RO:0002353
external
protein
uberon
output_of
false
output_of
output of
output of
output_of
Chris Mungall
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
Chris Mungall
attached to (anatomical structure to anatomical structure)
RO:0002371
uberon
attaches_to
attaches_to
attached to
attaches_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.
Chris Mungall
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
https://github.com/obophenotype/uberon/issues/170
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.
Chris Mungall
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
RO:0002376
uberon
drains into
tributary_of
tributary_of
tributary of
tributary_of
http://en.wikipedia.org/wiki/Tributary
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
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
Chris Mungall
RO:0002380
uberon
branching_part_of
branching_part_of
branching part of
branching_part_of
FMA:85994
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).
Chris Mungall
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
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y.
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
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
Chris Mungall
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
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y.
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
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
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y.
Chris Mungall
RO:0002388
uberon
has_potential_to_directly_develop_into
has_potential_to_directly_develop_into
has potential to directly develop into
has potential to directly develop into
This relation groups causal relations between material entities and causal relations between processes
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.
Chris Mungall
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
Chris Mungall
RO:0002411
external
causally_upstream_of
causally_upstream_of
causally upstream of
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.
Chris Mungall
RO:0002412
external
immediately_causally_upstream_of
immediately_causally_upstream_of
immediately causally upstream of
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.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
RO:0002418
external
affects
causally_upstream_of_or_within
causally_upstream_of_or_within
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
RO:0002427
external
causally_downstream_of_or_within
causally_downstream_of_or_within
causally downstream 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.
Chris Mungall
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between a disease and organism
RO:0002451
transmitted_by
transmitted_by
transmitted by
'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
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y.
Chris Mungall
UBREL:0000002
RO:0002473
uberon
composed_primarily_of
composed_primarily_of
composed primarily of
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.
Chris Mungall
has part that occurs in
Chris Mungall
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).
Chris Mungall
BFO:0000068
RO:0002488
begins_to_exist_during
uberon
existence_starts_during
existence_starts_during
existence starts during
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).
Chris Mungall
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
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))
Chris Mungall
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.
existence overlaps
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)
Chris Mungall
RO:0002491
exists during
uberon
existence_starts_and_ends_during
existence_starts_and_ends_during
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.
existence starts and ends during
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).
Chris Mungall
BFO:0000069
RO:0002492
ceases_to_exist_during
uberon
existence_ends_during
existence_ends_during
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.
existence ends during
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).
Chris Mungall
RO:0002493
uberon
existence_ends_with
existence_ends_with
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.
existence ends with
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
Chris Mungall
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
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
Chris Mungall
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
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).
Chris Mungall
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
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.
existence starts during or after
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.
Chris Mungall
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
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.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in
causal agent in 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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
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
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
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
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
RO:0002507
uberon
has_material_contribution_from
has_material_contribution_from
determined by
has material contribution from
inverse of determined by
Chris Mungall
determines (material entity to system)
determines
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.
Chris Mungall
determined by part of
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.
Chris Mungall
has supporting framework
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).
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
Chris Mungall
causally influenced by (material entity to material entity)
causally influenced by
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
Chris Mungall
RO:0002565
external
results_in_movement_of
results_in_movement_of
results in movement of
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
Chris Mungall
causally influences (material entity to material entity)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
biomechanically related to
inverse of branching part of
Chris Mungall
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
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.
Chris Mungall
GOC:cjm
RO:0002571
uberon
lumen_of
lumen_of
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
Chris Mungall
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
RO:0002573
has_modifier
has_modifier
has modifier
inverse of has skeleton
Chris Mungall
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
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.
Chris Mungall
directly regulates (processual)
directly regulates
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
results in breakdown of
RO:0002588
external
results_in_assembly_of
results_in_assembly_of
results in assembly of
results_in_assembly_of
RO:0002590
external
results_in_disassembly_of
results_in_disassembly_of
results in disassembly of
results_in_disassembly_of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
RO:0002592
external
results_in_organization_of
results_in_organization_of
results in organization of
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
Inverse of 'causal agent in process'
Inverse of 'causal agent in'
RO:0002608
external
process_has_causal_agent
process_has_causal_agent
has causal agent
process has causal agent
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
related via dependence to
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.
Melissa Haendel
RO:0003000
external
uberon
produces
produces
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
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
RO:0003001
external
uberon
produced_by
produced_by
produced by
produced by
produced_by
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
cjm
2018-12-13T11:26:17Z
RO:0004007
external
has_primary_input_or_output
has_primary_input_or_output
has primary input or output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
cjm
2018-12-13T11:26:32Z
RO:0004008
external
has_primary_output
has_primary_output
has primary output
realizable has basis in
is basis for realizable
disease has basis in
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.
RO:0004020
disease_has_basis_in_dysfunction_of
disease_has_basis_in_dysfunction_of
disease has basis in dysfunction of
A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
RO:0004021
disease_has_basis_in_disruption_of
disease_has_basis_in_disruption_of
Editor note: TODO property chain: disease_has_location <- dhbido o occurs_in
disease caused by disruption of
disease has basis in disruption of
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.
RO:0004022
disease_arises_from_feature
disease_arises_from_feature
disease arises from feature
disease has basis in 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.
RO:0004024
disease_disrupts
disease_disrupts
disease causes disruption of
disease disrupts
RO:0004025
disease_causes_dysfunction_of
disease_causes_dysfunction_of
disease causes dysfunction of
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
RO:0004026
disease_has_location
disease_has_location
disease has location
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
RO:0004027
disease_has_inflammation_site
disease_has_inflammation_site
disease has inflammation site
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.
RO:0004028
realized_in_response_to_stimulus
realized_in_response_to_stimulus
realized in response to stimulus
A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
RO:0004029
disease_has_feature
disease_has_feature
disease has feature
A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
RO:0004030
disease_arises_from_structure
disease_arises_from_structure
disease arises from structure
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
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.
RO:0009501
triggered by process
realized_in_response_to
realized_in_response_to
realized in response to
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
pg
2020-06-08T17:21:33Z
RO:0012003
external
acts_on_population_of
acts_on_population_of
acts on population of
acts on population of
pg
2021-02-26T07:28:29Z
RO:0012008
external
results_in_fusion_of
results_in_fusion_of
results in fusion of
results in fusion of
This relation groups relations between diseases and any other kind of entity.
disease relationship
p has anatomical participant c iff p has participant c, and c is an anatomical entity
cjm
2018-09-26T01:08:58Z
results in changes to anatomical or cellular structure
a object property that specifies a relation between a vaccine and a vaccine allergen
YH
has 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.
YL
Yongqun He
vaccine immunization for host
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)
Yongqun He
vaccine immunization against microbe
has parent hydride
is conjugate acid of
is conjugate base of
is substituent group from
has_completed
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).
has_high_plasma_membrane_amount
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).
has_low_plasma_membrane_amount
has_not_completed
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
lacks_part
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)
lacks_plasma_membrane_part
interacts_with
interacts_with_an_exposure_receptor_via
interacts_with_an_exposure stressor_via
disease_causes_feature
disease causes feature
disease_has_basis_in_development_of
disease_has_basis_in_development_of
disease_has_major_feature
disease has major feature
disease_responds_to
disease responds to
disease_shares_features_of
disease shares features of
predisposes_towards
predisposes towards
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.
quality
decreased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
decreased_in_magnitude_relative_to
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.
quality
different_in_magnitude_relative_to
different_in_magnitude_relative_to
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.
quality
has_cross_section
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
has_cross_section
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.
quality
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
protein
has_gene_template
false
has_gene_template
Inverse of part_of.
has_part
has_quality
member_of
X part_of Y if X is a subregion of Y.
part_of
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.
anteriorly connected to
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
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.
distally connected to
uberon
existence_starts_and_ends_during
existence starts and ends during
uberon
extends_fibers_into
extends_fibers_into
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.
uberon
filtered_through
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
filtered through
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.
uberon
in_central_side_of
in_central_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
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.
posteriorly connected to
uberon
protects
protects
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.
uberon
proximally_connected_to
proximally connected to
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
uberon
capable_of_has_part
site_of
site_of
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
.
transitively anteriorly connected to
uberon
transitively_connected_to
transitively_connected to
.
transitively distally connected to
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
http://purl.org/obo/owl/relationship
OBO_REL:0000007
relationship
has_proper_part
has_proper_part
Ingredient
Ingredient Strength
Packaged Product
VA Class
VA Product
Active
Inactive
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.
Oliver He
has digit number
quality measured by year
Chemical Ingredients
N0000000002
991181
C178
Chemical Ingredients [Chemical/Ingredient]
Clinical Kinetics
N0000000003
1030853
C1373163
C180
Clinical Kinetics [PK]
Diseases, Manifestations or Physiologic States
N0000000004
989348
C1373233
C182
Diseases, Manifestations or Physiologic States [Disease/Finding]
Mental Disorders and Manifestations
N0000000006
984721
C2916796
C190
Mental Disorders and Manifestations [Disease/Finding]
Infectious Diseases
N0000000007
1023583
189822004
190563008
191415002
40733004
C0009450
C192
Infectious Diseases [Disease/Finding]
Elimination
N0000000022
986944
C0221102
C222
Elimination [PK]
Metabolism
N0000000023
1023904
C0025519
C224
Metabolism [PK]
Site of Metabolism
N0000000024
988808
C1373176
C226
Site of Metabolism [PK]
Hepatic Metabolism
N0000000026
984512
C1373178
C230
Hepatic Metabolism [PK]
Route of Excretion
N0000000041
987962
C1373186
C260
Route of Excretion [PK]
Renal Excretion
N0000000042
986666
C1373187
C262
Renal Excretion [PK]
Physiochemical Activity
N0000000065
989958
C1372991
C308
Physiochemical Activity [MoA]
Small Ion Transport Pump Interactions
N0000000066
986087
C1373107
C310
Small Ion Transport Pump Interactions [MoA]
Active Transporter Interactions
N0000000072
1031287
C1373104
C322
Active Transporter Interactions [MoA]
Immunologic Factors
D007155
Immunologic Factors
N0000000082
993127
C2757006
C342
Immunologic Factors [MoA]
Receptor Interactions
N0000000085
988560
C1372999
C348
Receptor Interactions [MoA]
Reverse Transcriptase Inhibitors
D018894
Reverse Transcriptase Inhibitors
N0000000103
993157
C2757067
C384
Reverse Transcriptase Inhibitors [MoA]
Dopamine Agonists
D018491
Dopamine Agonists
N0000000117
992714
Dopaminergic Agonist
C2757007
C412
Dopamine Agonists [MoA]
Adrenergic Agonists
D000322
Adrenergic Agonists
N0000000122
1029285
C2757025
C422
Adrenergic Agonists [MoA]
Enzyme Inhibitors
D004791
Enzyme Inhibitors
N0000000133
1032544
C2756995
C444
Enzyme Inhibitors [MoA]
Biological Macromolecular Activity
N0000000142
988641
C2267218
C462
Biological Macromolecular Activity [MoA]
G-Protein-linked Receptor Interactions
N0000000152
984725
G-Protein-linked Receptor-Effector Interactions
C2916797
C482
G-Protein-linked Receptor Interactions [MoA]
Adrenergic Receptor Interactions
N0000000153
987972
C1373072
C484
Adrenergic Receptor Interactions [MoA]
Enzyme Interactions
N0000000163
988200
C1373066
C504
Enzyme Interactions [MoA]
Cytokine Receptor Superfamily Interactions
N0000000175
984937
C1373058
C528
Cytokine Receptor Superfamily Interactions [MoA]
Ion Channel Interactions
N0000000193
988382
C1373047
C564
Ion Channel Interactions [MoA]
Cholinergic Nicotinic Receptor Interactions
N0000000199
985201
C2267220
C576
Cholinergic Nicotinic Receptor Interactions [MoA]
beta Lactamase Inhibitors
N0000000202
989759
beta-Lactamase Inhibitors
C1373040
C582
beta Lactamase Inhibitors [MoA]
Dopamine Receptor Interactions
N0000000203
985948
C1373039
C584
Dopamine Receptor Interactions [MoA]
Electrolyte Activity
N0000000220
984201
C2267221
C618
Electrolyte Activity [MoA]
Cellular or Molecular Interactions
N0000000223
986459
C1373094
C624
Cellular or Molecular Interactions [MoA]
Acid-Base Activity
N0000000226
985379
C2267222
C630
Acid-Base Activity [MoA]
Cholinergic Nicotinic Antagonists
N0000000227
989668
C1373090
C632
Cholinergic Nicotinic Antagonists [MoA]
Structural Macromolecules
N0000000228
984803
C1373089
C634
Structural Macromolecules [MoA]
Nucleic Acid Synthesis Inhibitors
D019384
Nucleic Acid Synthesis Inhibitors
N0000000233
993166
C2757009
C644
Nucleic Acid Synthesis Inhibitors [MoA]
Adrenergic beta-Agonists
D000318
Adrenergic beta-Agonists
N0000000245
992727
Beta-adrenergic Agonist
C2757043
C668
Adrenergic beta-Agonists [MoA]
Polycationic Channel Interactions
N0000000253
990209
C1373076
C684
Polycationic Channel Interactions [MoA]
Immunologic and Biological Factors
D007151
Immunologic and Biological Factors
N0000000254
1032698
C0021048
C686
Immunologic and Biological Factors [MoA]
Congenital Abnormalities
M0000013
D000013
Malformations of organs or body parts during development in utero.
Congenital Abnormalities
N0000000264
1021840
276654001
276655000
276720006
Abnormalities, Congenital
Birth Defects
Congenital Defects
Defects, Congenital
Deformities
C0000768
C706
Congenital Abnormalities [Disease/Finding]
Abnormalities, Drug-Induced
M0000014
D000014
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
N0000000265
989962
Drug-Induced Abnormalities
C0000771
C708
Abnormalities, Drug-Induced [Disease/Finding]
Acid-Base Imbalance
M0000212
D000137
Disturbances in the ACID-BASE EQUILIBRIUM of the body.
Acid-Base Imbalance
N0000000282
1026879
C0001118
C742
Acid-Base Imbalance [Disease/Finding]
Acidosis
M0000213
D000138
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.
Acidosis
N0000000283
1023565
51387008
C0001122
C744
Acidosis [Disease/Finding]
Alcohol Withdrawal Delirium
M0000652
D000430
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 Delirium
N0000000351
1023188
8635005
Alcohol Withdrawal-Induced Delirium Tremens
Delirium Tremens
Delirium Tremens, Alcohol Withdrawal Induced
C0001957
C880
Alcohol Withdrawal Delirium [Disease/Finding]
Alkalosis
M0000714
D000471
A pathological condition that removes acid or adds base to the body fluids.
Alkalosis
N0000000355
1025787
21420006
C0002063
C888
Alkalosis [Disease/Finding]
Anuria
M0001524
D001002
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.
Anuria
N0000000431
1023563
2472002
C0003460
C1040
Anuria [Disease/Finding]
Aortic Stenosis, Subvalvular
M0001552
D001020
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
N0000000442
1025918
Aortic Subvalvular Stenosis
Subvalvular Aortic Stenosis
C0003500
C1062
Aortic Stenosis, Subvalvular [Disease/Finding]
Aortic Valve Stenosis
M0001557
D001024
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.
Aortic Valve Stenosis
N0000000445
1021926
60573004
Aortic Stenosis
C0003507
C1068
Aortic Valve Stenosis [Disease/Finding]
Arrhythmias, Cardiac
M0001715
D001145
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.
Arrhythmias, Cardiac
N0000000469
1023395
195107004
Arrhythmia
Arrythmia
Cardiac Arrhythmia
Cardiac Arrhythmias
Cardiac Dysrhythmia
C0003811
C1116
Arrhythmias, Cardiac [Disease/Finding]
Ascites
M0001791
D001201
Accumulation or retention of free fluid within the peritoneal cavity.
Ascites
N0000000490
1021930
389026000
C0003962
C1158
Ascites [Disease/Finding]
Bacterial Infections and Mycoses
M0002125
D001423
Infections caused by bacteria and fungi, general, specified, or unspecified.
Bacterial Infections and Mycoses
N0000000523
986958
C0004615
C1224
Bacterial Infections and Mycoses [Disease/Finding]
Mental Disorders
M0002289
D001523
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.
Mental Disorders
N0000000538
1022308
74732009
C0004936
C1254
Mental Disorders [Disease/Finding]
Blood Coagulation Disorders
M0002683
D001778
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
N0000000575
1022276
362970003
64779008
Coagulation Disorders, Blood
Disorders, Blood Coagulation
C0005779
C1328
Blood Coagulation Disorders [Disease/Finding]
Bone Diseases
M0002776
D001847
Diseases of BONES.
Bone Diseases
N0000000584
1025929
308147009
76069003
C0005940
C1346
Bone Diseases [Disease/Finding]
Bone Diseases, Metabolic
M0002780
D001851
Bone Diseases, Metabolic
N0000000588
1026469
50279003
Metabolic Bone Diseases
C0005944
C1354
Bone Diseases, Metabolic [Disease/Finding]
Bradycardia
M0002863
D001919
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.
Bradycardia
N0000000600
1025503
48867003
Bradyarrhythmia
Bradyarrhythmias
C0428977
C1378
Bradycardia [Disease/Finding]
Brain Diseases
M0002874
D001927
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.
Brain Diseases
N0000000605
986258
81308009
Brain Disorders
CNS Disorders, Intracranial
Central Nervous System Disorders, Intracranial
Central Nervous System Intracranial Disorders
Encephalon Diseases
Intracranial CNS Disorders
Intracranial Central Nervous System Disorders
C0006111
C1388
Brain Diseases [Disease/Finding]
Calcium Metabolism Disorders
M0003174
D002128
Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization.
Calcium Metabolism Disorders
N0000000646
1024541
71638002
C0006705
C1470
Calcium Metabolism Disorders [Disease/Finding]
Calculi
M0003195
D002137
An abnormal concretion occurring mostly in the urinary and biliary tracts, usually composed of mineral salts. Also called stones.
Calculi
N0000000647
1026851
125243009
56381008
Biliary or Urinary Stones
C0006736
C1472
Calculi [Disease/Finding]
Candidiasis
M0003258
D002177
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)
Candidiasis
N0000000650
1022538
78048006
Moniliasis
C0006840
C1478
Candidiasis [Disease/Finding]
Candidiasis, Chronic Mucocutaneous
M0003259
D002178
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
N0000000651
1023229
234568006
C0006845
C1480
Candidiasis, Chronic Mucocutaneous [Disease/Finding]
Candidiasis, Cutaneous
M0003260
D002179
Candidiasis of the skin manifested as eczema-like lesions of the interdigital spaces, perleche, or chronic paronychia. (Dorland, 27th ed)
Candidiasis, Cutaneous
N0000000652
1025470
49883006
Moniliasis, Cutaneous
C0006846
C1482
Candidiasis, Cutaneous [Disease/Finding]
Candidiasis, Oral
M0003261
D002180
Infection of the mucous membranes of the mouth by a fungus of the genus CANDIDA. (Dorland, 27th ed)
Candidiasis, Oral
N0000000653
1022622
79740000
Moniliasis, Oral
Thrush
C0006849
C1484
Candidiasis, Oral [Disease/Finding]
Candidiasis, Vulvovaginal
M0003262
D002181
Infection of the VULVA and VAGINA with a fungus of the genus CANDIDA.
Candidiasis, Vulvovaginal
N0000000654
1024776
72605008
Moniliasis, Vulvovaginal
C0700345
C1486
Candidiasis, Vulvovaginal [Disease/Finding]
Cardiac Output, Low
M0003453
D002303
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.
Cardiac Output, Low
N0000000683
1024618
86318000
Low Cardiac Output
C0007166
C1544
Cardiac Output, Low [Disease/Finding]
Cardiovascular Diseases
M0003473
D002318
Pathological conditions involving the CARDIOVASCULAR SYSTEM including the HEART; the BLOOD VESSELS; or the PERICARDIUM.
Cardiovascular Diseases
N0000000689
1022075
105980002
49601007
C0007222
C1556
Cardiovascular Diseases [Disease/Finding]
Central Nervous System Diseases
M0003805
D002493
Diseases of any component of the brain (including the cerebral hemispheres, diencephalon, brain stem, and cerebellum) or the spinal cord.
Central Nervous System Diseases
N0000000709
1023588
23853001
CNS Diseases
Central Nervous System Disorders
C0007682
C1596
Central Nervous System Diseases [Disease/Finding]
Cerebrovascular Disorders
M0003914
D002561
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
N0000000730
1022010
62914000
Brain Vascular Disorders
Intracranial Vascular Disorders
Vascular Diseases, Intracranial
C0007820
C1638
Cerebrovascular Disorders [Disease/Finding]
Coma
M0004841
D003128
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.
Coma
N0000000819
988251
371632003
Comatose
C0009421
C1816
Coma [Disease/Finding]
Consciousness Disorders
M0005031
D003244
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
N0000000840
1031236
C0009792
C1858
Consciousness Disorders [Disease/Finding]
Corneal Diseases
M0005177
D003316
Diseases of the cornea.
Corneal Diseases
N0000000851
1024256
15250008
C0010034
C1880
Corneal Diseases [Disease/Finding]
Crohn Disease
M0005335
D003424
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.
Crohn Disease
N0000000875
1024195
34000006
Crohn's Disease
C0010346
C1928
Crohn Disease [Disease/Finding]
Cytomegalovirus Infections
M0005604
D003586
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
N0000000897
1023187
28944009
Cytomegalic Inclusion Disease
Inclusion Disease
Infections, Cytomegalovirus
Salivary Gland Virus Disease
C0010823
C1972
Cytomegalovirus Infections [Disease/Finding]
Deficiency Diseases
M0005753
D003677
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)
Deficiency Diseases
N0000000909
1025258
C0011156
C1996
Deficiency Diseases [Disease/Finding]
Dehydration
M0005757
D003681
The condition that results from excessive loss of water from a living organism.
Dehydration
N0000000911
1023412
34095006
C0011175
C2000
Dehydration [Disease/Finding]
Dermatitis
M0006046
D003872
Any inflammation of the skin.
Dermatitis
N0000000939
1023378
182782007
C0011603
C2056
Dermatitis [Disease/Finding]
Dermatitis, Atopic
M0006050
D003876
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.
Dermatitis, Atopic
N0000000943
1022124
200773006
200775004
24079001
Eczema, Atopic
Neurodermatitis, Atopic
Neurodermatitis, Disseminated
C0011615
C2064
Dermatitis, Atopic [Disease/Finding]
Dermatomycoses
M0006059
D003881
Superficial infections of the skin or its appendages by any of various fungi.
Dermatomycoses
N0000000945
1021749
14560005
276206000
Dermatomycosis
Fungal Skin Diseases
Skin Diseases, Fungal
C0011630
C2068
Dermatomycoses [Disease/Finding]
Digestive System Diseases
M0006374
D004066
Diseases in any part of the GASTROINTESTINAL TRACT or the accessory organs (LIVER; BILIARY TRACT; PANCREAS).
Digestive System Diseases
N0000000973
1023342
53619000
C0012242
C2124
Digestive System Diseases [Disease/Finding]
DNA Virus Infections
M0006675
D004266
DNA Virus Infections
N0000000993
1027612
Infections, DNA Virus
C0012922
C2164
DNA Virus Infections [Disease/Finding]
Drug Hypersensitivity
M0006829
D004342
Immunologically mediated adverse reactions to medicinal substances used legally or illegally.
Drug Hypersensitivity
N0000000999
1024684
416093006
416098002
Allergy, Drug
Drug Allergy
Hypersensitivity, Drug
C0013182
C2176
Drug Hypersensitivity [Disease/Finding]
Drug Toxicity
M0006855
D004362
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.
Drug Toxicity
N0000001000
1022029
7895008
Toxicity, Drug
C0013221
C2178
Drug Toxicity [Disease/Finding]
Edema
M0007051
D004487
Abnormal fluid accumulation in TISSUES or body cavities. Most cases of edema are present under the SKIN in SUBCUTANEOUS TISSUE.
Edema
N0000001057
1022374
20741006
79654002
Dropsy
Hydrops
C0013604
C2292
Edema [Disease/Finding]
Eye Diseases
M0008088
D005128
Eye Diseases
N0000001181
1023594
194183009
C0015397
C2540
Eye Diseases [Disease/Finding]
Female Urogenital Diseases and Pregnancy Complications
M0008309
D005261
Pathological processes of the female URINARY TRACT, the reproductive system (GENITALIA, FEMALE), and disorders related to PREGNANCY.
Female Urogenital Diseases and Pregnancy Complications
N0000001224
985609
C1720765
C2626
Female Urogenital Diseases and Pregnancy Complications [Disease/Finding]
Food Hypersensitivity
M0008686
D005512
Gastrointestinal disturbances, skin eruptions, or shock due to allergic reactions to allergens in food.
Food Hypersensitivity
N0000001270
1025015
414285001
Allergy, Food
Food Allergy
Hypersensitivity, Food
C0016470
C2718
Food Hypersensitivity [Disease/Finding]
Gastroenteritis
M0009018
D005759
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.
Gastroenteritis
N0000001317
1024672
25374005
C0017160
C2812
Gastroenteritis [Disease/Finding]
Gastrointestinal Diseases
M0009033
D005767
Diseases in any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM.
Gastrointestinal Diseases
N0000001320
1022118
119292006
C0017178
C2818
Gastrointestinal Diseases [Disease/Finding]
Genital Diseases, Female
M0009154
D005831
Pathological processes involving the female reproductive tract (GENITALIA, FEMALE).
Genital Diseases, Female
N0000001323
1026095
244938009
310789003
Female Genital Diseases
Gynecologic Diseases
C0017411
C2824
Genital Diseases, Female [Disease/Finding]
Genital Diseases, Male
M0009155
D005832
Pathological processes involving the male reproductive tract (GENITALIA, MALE).
Genital Diseases, Male
N0000001324
1021837
64557000
Male Genital Diseases
C0017412
C2826
Genital Diseases, Male [Disease/Finding]
Graft vs Host Disease
M0009578
D006086
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.
Graft vs Host Disease
N0000001384
1024721
234646005
Graft-Versus-Host Disease
Graft-vs-Host Disease
Homologous Wasting Disease
Runt Disease
C0018133
C2946
Graft vs Host Disease [Disease/Finding]
Heart Arrest
M0009938
D006323
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.
Heart Arrest
N0000001429
1025093
309810002
397829000
410429000
Asystole
Cardiac Arrest
C0018790
C3036
Heart Arrest [Disease/Finding]
Heart Block
M0009945
D006327
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.
Heart Block
N0000001430
1023276
233916004
C0018794
C3038
Heart Block [Disease/Finding]
Heart Diseases
M0009951
D006331
Pathological conditions involving the HEART including its structural and functional abnormalities.
Heart Diseases
N0000001432
1022072
56265001
Cardiac Diseases
C0018799
C3042
Heart Diseases [Disease/Finding]
Heart Failure
M0009953
D006333
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.
Heart Failure
N0000001434
1024953
42343007
Cardiac Failure
C0018802
C3046
Heart Failure [Disease/Finding]
Heart Valve Diseases
M0009972
D006349
Pathological conditions involving any of the various HEART VALVES and the associated structures (PAPILLARY MUSCLES and CHORDAE TENDINEAE).
Heart Valve Diseases
N0000001443
989613
368009
Valvular Heart Diseases
C0018824
C3064
Heart Valve Diseases [Disease/Finding]
Hematologic Diseases
M0010044
D006402
Disorders of the blood and blood forming tissues.
Hematologic Diseases
N0000001459
1021953
191402006
267573000
Blood Diseases
Hematological Diseases
C0018939
C3096
Hematologic Diseases [Disease/Finding]
Hemic and Lymphatic Diseases
M0010072
D006425
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
N0000001466
1026878
C0018981
C3110
Hemic and Lymphatic Diseases [Disease/Finding]
Hemorrhage
M0010152
D006470
Bleeding or escape of blood from a vessel.
Hemorrhage
N0000001481
1023287
195511004
Bleeding
C0019080
C3140
Hemorrhage [Disease/Finding]
Hemorrhagic Disorders
M0010157
D006474
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).
Hemorrhagic Disorders
N0000001485
1023732
191331006
Hemorrhagic Diathesis
C0019087
C3148
Hemorrhagic Disorders [Disease/Finding]
Hepatitis
M0010205
D006505
INFLAMMATION of the LIVER.
Hepatitis
N0000001499
989819
128241005
197351001
C0019158
C3176
Hepatitis [Disease/Finding]
Herpes Genitalis
M0010276
D006558
Infection of the genitals (GENITALIA) with HERPES SIMPLEX VIRUS in either the males or the females.
Herpes Genitalis
N0000001527
1025755
271463009
33839006
Genital Herpes
Herpes Simplex Virus Genital Infection
Herpes Simplex, Genital
C0019342
C3232
Herpes Genitalis [Disease/Finding]
Herpes Simplex
M0010279
D006561
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.)
Herpes Simplex
N0000001530
1023866
88594005
C0019348
C3238
Herpes Simplex [Disease/Finding]
Herpesviridae Infections
M0010285
D006566
Virus diseases caused by the HERPESVIRIDAE.
Herpesviridae Infections
N0000001533
1024733
23513009
Herpesvirus Infections
Infections, Herpesviridae
Infections, Herpesvirus
C0019372
C3244
Herpesviridae Infections [Disease/Finding]
Hypercalcemia
M0010814
D006934
Abnormally high level of calcium in the blood.
Hypercalcemia
N0000001577
1026898
66931009
C0020437
C3332
Hypercalcemia [Disease/Finding]
Hyperglycemia
M0010824
D006943
Abnormally high BLOOD GLUCOSE level.
Hyperglycemia
N0000001586
1021913
80394007
C0020456
C3350
Hyperglycemia [Disease/Finding]
Hyperkalemia
M0010828
D006947
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)
Hyperkalemia
N0000001590
1021945
14140009
238142003
Hyperpotassemia
C0020461
C3358
Hyperkalemia [Disease/Finding]
Hypernatremia
M0010837
D006955
Excessive amount of sodium in the blood. (Dorland, 27th ed)
Hypernatremia
N0000001598
1026718
286926003
39355002
C0020488
C3374
Hypernatremia [Disease/Finding]
Hypersensitivity
M0010851
D006967
Altered reactivity to an antigen, which can result in pathologic reactions upon subsequent exposure to that particular antigen.
Hypersensitivity
N0000001610
1022134
106190000
127072000
269284003
Allergy
C0020517
C3398
Hypersensitivity [Disease/Finding]
Hypersensitivity, Immediate
M0010854
D006969
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
N0000001612
1023968
20671006
Atopic Hypersensitivity
Hypersensitivity, Atopic
Hypersensitivity, Type I
IgE-Mediated Hypersensitivity
Type I Hypersensitivity
C0020523
C3402
Hypersensitivity, Immediate [Disease/Finding]
Hypertension
M0010859
D006973
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.
Hypertension
N0000001616
1023354
38341003
Blood Pressure, High
C0020538
C3410
Hypertension [Disease/Finding]
Hypocalcemia
M0010891
D006996
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)
Hypocalcemia
N0000001632
1022560
5291005
C0020598
C3442
Hypocalcemia [Disease/Finding]
Hypoglycemia
M0010901
D007003
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.
Hypoglycemia
N0000001635
1026036
190433001
237630007
271327008
302866003
C0020615
C3448
Hypoglycemia [Disease/Finding]
Hyponatremia
M0010911
D007010
Deficiency of sodium in the blood; salt depletion. (Dorland, 27th ed)
Hyponatremia
N0000001640
1022083
238115004
89627008
C0020625
C3458
Hyponatremia [Disease/Finding]
Hypoprothrombinemias
M0010925
D007020
Absence or reduced levels of prothrombin in the blood.
Hypoprothrombinemias
N0000001647
1023756
73975000
Deficiency, Factor II
Factor II Deficiency
Prothrombin Deficiency
C0020640
C3472
Hypoprothrombinemias [Disease/Finding]
Immunologic Deficiency Syndromes
M0011155
D007153
Syndromes in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.
Immunologic Deficiency Syndromes
N0000001667
1022772
191005003
234532001
Deficiency Syndrome, Immunologic
Deficiency Syndromes, Immunologic
Immunologic Deficiency Syndrome
Immunological Deficiency Syndromes
C0021051
C3512
Immunologic Deficiency Syndromes [Disease/Finding]
Immune System Diseases
M0011156
D007154
Disorders caused by abnormal or absent immunologic mechanisms, whether humoral, cell-mediated, or both.
Immune System Diseases
N0000001668
1022843
41266007
Diseases of Immune System
Immune Diseases
Immune Disorders
Immunologic Diseases
Immunological Diseases
C0021053
C3514
Immune System Diseases [Disease/Finding]
Infant, Newborn, Diseases
M0011286
D007232
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
N0000001678
1024869
22925008
C0021290
C3534
Infant, Newborn, Diseases [Disease/Finding]
Infant, Premature, Diseases
M0011290
D007235
Infant, Premature, Diseases
N0000001679
990391
C0021295
C3536
Infant, Premature, Diseases [Disease/Finding]
Infection
M0011294
D007239
Invasion of the host organism by microorganisms that can cause pathological conditions or diseases.
Infection
N0000001681
1022093
40733004
C0021311
C3540
Infection [Disease/Finding]
Intestinal Diseases
M0011569
D007410
Pathological processes in any segment of the INTESTINE from DUODENUM to RECTUM.
Intestinal Diseases
N0000001698
1023320
85919009
C0021831
C3574
Intestinal Diseases [Disease/Finding]
Kidney Calculi
M0012008
D007669
Stones in the KIDNEY, usually formed in the urine-collecting area of the kidney (KIDNEY PELVIS). Their sizes vary and most contains CALCIUM OXALATE.
Kidney Calculi
N0000001746
1022167
95570007
Kidney Stones
Renal Calculi
Renal Calculus
C0022650
C3670
Kidney Calculi [Disease/Finding]
Kidney Diseases
M0012014
D007674
Pathological processes of the KIDNEY or its component tissues.
Kidney Diseases
N0000001748
1022215
90708001
C0022658
C3674
Kidney Diseases [Disease/Finding]
Kidney Failure, Acute
M0012015
D058186
Kidney Failure, Acute
N0000001749
1022586
14669001
Acute Kidney Failure
Acute Renal Failure
Renal Failure, Acute
C0022660
C3676
Kidney Failure, Acute [Disease/Finding]
Kidney Failure, Chronic
M0012016
D007676
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
N0000001750
988914
90688005
Chronic Kidney Failure
ESRD
End-Stage Kidney Disease
End-Stage Renal Disease
Renal Disease, End-Stage
Renal Failure, Chronic
Renal Failure, End-Stage
C0022661
C3678
Kidney Failure, Chronic [Disease/Finding]
Lacrimal Apparatus Diseases
M0012135
D007766
Diseases of the lacrimal apparatus.
Lacrimal Apparatus Diseases
N0000001774
1025659
31053003
C0022904
C3726
Lacrimal Apparatus Diseases [Disease/Finding]
Liver Cirrhosis
M0012636
D008103
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.
Liver Cirrhosis
N0000001862
1024193
19943007
Cirrhosis, Liver
Hepatic Cirrhosis
C0023890
C3902
Liver Cirrhosis [Disease/Finding]
Liver Diseases
M0012644
D008107
Pathological processes of the LIVER.
Liver Diseases
N0000001866
1024220
235856003
C0023895
C3910
Liver Diseases [Disease/Finding]
Lung Diseases
M0012744
D008171
Pathological processes involving any part of the LUNG.
Lung Diseases
N0000001879
1021971
19829001
Disease, Pulmonary
Diseases, Pulmonary
Pulmonary Disease
Pulmonary Diseases
C0024115
C3936
Lung Diseases [Disease/Finding]
Lung Neoplasms
M0012749
D008175
Tumors or cancer of the LUNG.
Lung Neoplasms
N0000001883
1023224
126713003
Neoplasms, Lung
Neoplasms, Pulmonary
Pulmonary Neoplasms
C0024121
C3944
Lung Neoplasms [Disease/Finding]
Magnesium Deficiency
M0012886
D008275
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)
Magnesium Deficiency
N0000001921
1024574
238118002
Deficiency, Magnesium
C0024473
C4020
Magnesium Deficiency [Disease/Finding]
Metabolic Diseases
M0013493
D008659
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)
Metabolic Diseases
N0000002004
1022778
30390004
75934005
Diseases, Metabolic
Thesaurismosis
C0025517
C4186
Metabolic Diseases [Disease/Finding]
Stomatognathic Diseases
M0014128
D009057
General or unspecified diseases of the stomatognathic system, comprising the mouth, teeth, jaws, and pharynx.
Stomatognathic Diseases
N0000002034
1027350
Mouth and Tooth Diseases
C0038368
C4246
Stomatognathic Diseases [Disease/Finding]
Mouth Diseases
M0014130
D009059
Mouth Diseases
N0000002036
1027441
118938008
C0026636
C4250
Mouth Diseases [Disease/Finding]
Muscle Hypotonia
M0014238
D009123
A diminution of the skeletal muscle tone marked by a diminished resistance to passive stretching.
Muscle Hypotonia
N0000002059
1024653
398151007
398152000
Decreased Muscle Tone
Hypomyotonia
Hypotonia
Hypotony, Muscle
Muscle Tone Poor
Muscular Hypotonia
C0026827
C4296
Muscle Hypotonia [Disease/Finding]
Musculoskeletal Diseases
M0014259
D009140
Diseases of the muscles and their associated ligaments and other connective tissue and of the bones and cartilage viewed collectively.
Musculoskeletal Diseases
N0000002067
1022076
928000
C0026857
C4312
Musculoskeletal Diseases [Disease/Finding]
Mycoses
M0014313
D009181
Mycoses
N0000002075
1024676
3218000
Fungus Diseases
C0026946
C4328
Mycoses [Disease/Finding]
Congenital, Hereditary, and Neonatal Diseases and Abnormalities
M0014570
D009358
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
N0000002121
989203
C0027612
C4420
Congenital, Hereditary, and Neonatal Diseases and Abnormalities [Disease/Finding]
Neoplasms
M0014585
D009369
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.
Neoplasms
N0000002128
1022284
189525008
189526009
55342001
Tumors
C0027651
C4434
Neoplasms [Disease/Finding]
Neoplasms by Histologic Type
M0014588
D009370
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
N0000002129
986146
Histological Type of Neoplasm
Histological Types of Neoplasms
Neoplasms by Histological Type
C0027652
C4436
Neoplasms by Histologic Type [Disease/Finding]
Neoplasms by Site
M0014589
D009371
A collective term for precoordinated organ/neoplasm headings locating neoplasms by organ, as BRAIN NEOPLASMS; DUODENAL NEOPLASMS; LIVER NEOPLASMS; etc.
Neoplasms by Site
N0000002130
1026659
Neoplasms by Sites
Site, Neoplasm
Sites, Neoplasm
C0027653
C4438
Neoplasms by Site [Disease/Finding]
Neoplasms, Germ Cell and Embryonal
M0014592
D009373
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
N0000002132
1026873
Germ Cell and Embryonal Neoplasms
Germ Cell and Embryonic Neoplasms
Neoplasms, Germ Cell and Embryonic
C0027658
C4442
Neoplasms, Germ Cell and Embryonal [Disease/Finding]
Neoplasms, Nerve Tissue
M0014605
D009380
Neoplasms composed of nerve tissue. This concept does not refer to neoplasms located in the nervous system or its component nerves.
Neoplasms, Nerve Tissue
N0000002139
985772
Neoplasms, Nervous Tissue
Nerve Tissue Neoplasms
Nervous Tissue Neoplasms
C0027665
C4456
Neoplasms, Nerve Tissue [Disease/Finding]
Nephrosis
M0014635
D009401
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.
Nephrosis
N0000002153
1025384
90708001
C0027720
C4484
Nephrosis [Disease/Finding]
Nephrotic Syndrome
M0014639
D009404
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.
Nephrotic Syndrome
N0000002155
1026285
52254009
C0027726
C4488
Nephrotic Syndrome [Disease/Finding]
Nervous System Diseases
M0014667
D009422
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
N0000002159
1026444
118940003
Nervous System Disorders
Neurologic Disorders
Neurological Disorders
C0027765
C4496
Nervous System Diseases [Disease/Finding]
Neurologic Manifestations
M0014716
D009461
Clinical signs and symptoms caused by nervous system injury or dysfunction.
Neurologic Manifestations
N0000002173
1025946
Manifestations, Neurologic
Manifestations, Neurological
Neurologic Manifestation
Neurologic Signs and Symptoms
Neurological Manifestations
C0027854
C4524
Neurologic Manifestations [Disease/Finding]
Nutrition Disorders
M0015120
D009748
Disorders caused by nutritional imbalance, either overnutrition or undernutrition.
Nutrition Disorders
N0000002196
1024039
2492009
Nutritional Disorders
C0028709
C4570
Nutrition Disorders [Disease/Finding]
Nutritional and Metabolic Diseases
M0015124
D009750
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
N0000002197
1026553
C0028715
C4572
Nutritional and Metabolic Diseases [Disease/Finding]
Opportunistic Infections
M0015350
D009894
An infection caused by an organism which becomes pathogenic under certain conditions, e.g., during immunosuppression.
Opportunistic Infections
N0000002225
1025670
61274003
C0029118
C4628
Opportunistic Infections [Disease/Finding]
Osteoporosis
M0015552
D010024
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.
Osteoporosis
N0000002260
1022418
203428004
64859006
C0029456
C4698
Osteoporosis [Disease/Finding]
Paraganglioma
M0015869
D010235
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)
Paraganglioma
N0000002299
1022619
127027008
253029009
302833002
Paraganglioma, Gangliocytic
C0030421
C4776
Paraganglioma [Disease/Finding]
Parasitic Diseases
M0015919
D010272
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.
Parasitic Diseases
N0000002319
987316
17322007
C0030499
C4816
Parasitic Diseases [Disease/Finding]
Pathologic Processes
M0016012
D010335
The abnormal mechanisms and forms involved in the dysfunctions of tissues and organs.
Pathologic Processes
N0000002338
1025320
308489006
370135005
Pathological Processes
Processes, Pathologic
C0030660
C4854
Pathologic Processes [Disease/Finding]
Pheochromocytoma
M0016586
D010673
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)
Pheochromocytoma
N0000002390
1021872
302835009
399343007
C0031511
C4958
Pheochromocytoma [Disease/Finding]
Poisoning
M0017099
D011041
A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
Poisoning
N0000002447
1026915
75478009
C0032343
C5072
Poisoning [Disease/Finding]
Postoperative Complications
M0017367
D011183
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
N0000002467
1022600
385486001
Complication, Postoperative
C0032787
C5112
Postoperative Complications [Disease/Finding]
Psoriasis
M0017975
D011565
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.
Psoriasis
N0000002526
1022582
200961000
9014002
C0033860
C5230
Psoriasis [Disease/Finding]
Pulmonary Edema
M0018125
D011654
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.
Pulmonary Edema
N0000002540
1024136
19242006
Edema, Pulmonary
Edemas, Pulmonary
Pulmonary Edemas
Wet Lung
C0034063
C5258
Pulmonary Edema [Disease/Finding]
Respiratory Tract Diseases
M0018918
D012140
Respiratory Tract Diseases
N0000002602
1024163
C0035242
C5382
Respiratory Tract Diseases [Disease/Finding]
Respiratory Tract Neoplasms
M0018921
D012142
Respiratory Tract Neoplasms
N0000002604
986366
126667002
C0035244
C5386
Respiratory Tract Neoplasms [Disease/Finding]
Retroviridae Infections
M0018986
D012192
Virus diseases caused by the RETROVIRIDAE.
Retroviridae Infections
N0000002623
1025440
105635000
Infections, Retroviridae
Infections, Retrovirus
Retrovirus Infections
C0035369
C5424
Retroviridae Infections [Disease/Finding]
RNA Virus Infections
M0019160
D012327
RNA Virus Infections
N0000002650
1027571
Infections, RNA Virus
C0035690
C5478
RNA Virus Infections [Disease/Finding]
Sexually Transmitted Diseases
M0019758
D012749
Diseases due to or propagated by sexual contact.
Sexually Transmitted Diseases
N0000002724
1023328
8098009
STDs
Venereal Diseases
C0036916
C5626
Sexually Transmitted Diseases [Disease/Finding]
Shock
M0019782
D012769
A pathological condition manifested by failure to perfuse or oxygenate vital organs.
Shock
N0000002728
1023333
274729009
27942005
Circulatory Collapse
Circulatory Failure
C0036974
C5634
Shock [Disease/Finding]
Shock, Hemorrhagic
M0019784
D012771
Acute hemorrhage or excessive fluid loss resulting in HYPOVOLEMIA.
Shock, Hemorrhagic
N0000002730
1026764
355001
Hemorrhagic Shock
C0036982
C5638
Shock, Hemorrhagic [Disease/Finding]
Signs and Symptoms
M0019845
D012816
Clinical manifestations that can be either objective when observed by a physician, or subjective when perceived by the patient.
Signs and Symptoms
N0000002748
1024593
C0037088
C5674
Signs and Symptoms [Disease/Finding]
Skin Diseases
M0019929
D012871
Skin Diseases
N0000002761
1022858
95320005
Dermatoses
Dermatosis
C0037274
C5700
Skin Diseases [Disease/Finding]
Skin Diseases, Genetic
M0019934
D012873
Diseases of the skin with a genetic component, usually the result of various inborn errors of metabolism.
Skin Diseases, Genetic
N0000002763
986094
239001006
Genetic Skin Diseases
C0037277
C5704
Skin Diseases, Genetic [Disease/Finding]
Skin Diseases, Infectious
M0019935
D012874
Skin diseases caused by bacteria, fungi, parasites, or viruses.
Skin Diseases, Infectious
N0000002764
1025346
108365000
Infectious Skin Diseases
C0037278
C5706
Skin Diseases, Infectious [Disease/Finding]
Skin Neoplasms
M0019939
D012878
Tumors or cancer of the SKIN.
Skin Neoplasms
N0000002768
1025991
126488004
Neoplasms, Skin
C0037286
C5714
Skin Neoplasms [Disease/Finding]
Substance Withdrawal Syndrome
M0020676
D013375
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
N0000002855
1027256
C0038587
C5888
Substance Withdrawal Syndrome [Disease/Finding]
Pathological Conditions, Signs and Symptoms
M0020949
D013568
Abnormal anatomical or physiological conditions and objective or subjective manifestations of disease, not classified as disease or syndrome.
Pathological Conditions, Signs and Symptoms
N0000002872
984268
Symptoms and General Pathology
C0039058
C5922
Pathological Conditions, Signs and Symptoms [Disease/Finding]
Tetany
M0021207
D013746
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)
Tetany
N0000002916
1024300
10629009
C0039621
C6010
Tetany [Disease/Finding]
Thoracic Neoplasms
M0021397
D013899
Thoracic Neoplasms
N0000002927
1029082
255058005
C0039981
C6032
Thoracic Neoplasms [Disease/Finding]
Unconsciousness
M0022251
D014474
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)
Unconsciousness
N0000003064
1026031
418107008
419045004
Consciousness, Loss of
Unconscious State
C0041657
C6306
Unconsciousness [Disease/Finding]
Urinary Calculi
M0022362
D014545
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.
Urinary Calculi
N0000003077
1023616
197797001
Urinary Stones
Urinary Tract Stones
C0042018
C6332
Urinary Calculi [Disease/Finding]
Urination Disorders
M0022377
D014555
Abnormalities in the process of URINE voiding, including bladder control, frequency of URINATION, as well as the volume and composition of URINE.
Urination Disorders
N0000003082
1025163
C0042035
C6342
Urination Disorders [Disease/Finding]
Male Urogenital Diseases
M0489510
D052801
Pathological processes of the male URINARY TRACT and the reproductive system (GENITALIA, MALE).
Male Urogenital Diseases
N0000003085
1027597
Male Genitourinary Diseases
C1720894
CMSHM0489510
Male Urogenital Diseases [Disease/Finding]
Urologic Diseases
M0022400
D014570
Pathological processes of the URINARY TRACT in both males and females.
Urologic Diseases
N0000003086
1022769
128606002
197951006
41368006
Urinary Tract Diseases
Urological Diseases
C0042075
C6350
Urologic Diseases [Disease/Finding]
Vaginal Diseases
M0022482
D014623
Pathological processes of the VAGINA.
Vaginal Diseases
N0000003104
1026314
25658005
C0042251
C6386
Vaginal Diseases [Disease/Finding]
Vaginitis
M0022488
D014627
Inflammation of the vagina characterized by pain and a purulent discharge.
Vaginitis
N0000003107
1021851
198213001
30800001
C0042267
C6392
Vaginitis [Disease/Finding]
Vascular Diseases
M0022535
D014652
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.
Vascular Diseases
N0000003111
1024109
27550009
C0042373
C6400
Vascular Diseases [Disease/Finding]
Ventricular Fibrillation
M0022595
D014693
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
N0000003118
1024218
71908006
C0042510
C6414
Ventricular Fibrillation [Disease/Finding]
Ventricular Outflow Obstruction
M0022598
D014694
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
N0000003119
1028258
C0042512
C6416
Ventricular Outflow Obstruction [Disease/Finding]
Virus Diseases
M0022758
D014777
A general term for diseases produced by viruses.
Virus Diseases
N0000003128
1022696
34014006
Viral Diseases
C0042769
C6434
Virus Diseases [Disease/Finding]
Vulvar Diseases
M0022856
D014845
Pathological processes of the VULVA.
Vulvar Diseases
N0000003145
1024723
5089007
C0042994
C6468
Vulvar Diseases [Disease/Finding]
Vulvitis
M0022858
D014847
Inflammation of the VULVA. It is characterized by PRURITUS and painful urination.
Vulvitis
N0000003147
1023099
266586003
63144007
C0042996
C6472
Vulvitis [Disease/Finding]
Vulvovaginitis
M0022859
D014848
Inflammation of the VULVA and the VAGINA, characterized by discharge, burning, and PRURITUS.
Vulvovaginitis
N0000003148
1025805
198215008
53277000
C0042998
C6474
Vulvovaginitis [Disease/Finding]
Water-Electrolyte Imbalance
M0022901
D014883
Disturbances in the body's WATER-ELECTROLYTE BALANCE.
Water-Electrolyte Imbalance
N0000003154
1028873
C0043065
C6486
Water-Electrolyte Imbalance [Disease/Finding]
Wounds and Injuries
M0023019
D014947
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
Wounds and Injuries
N0000003169
1022221
19130008
Injuries and Wounds
Injuries, Wounds
Trauma
Wounds and Injury
Wounds, Injury
C0043251
C6516
Wounds and Injuries [Disease/Finding]
Inflammatory Bowel Diseases
M0023374
D015212
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
N0000003206
1023128
24526004
Bowel Diseases, Inflammatory
C0021390
C6590
Inflammatory Bowel Diseases [Disease/Finding]
Sexually Transmitted Diseases, Viral
M0023402
D015229
Viral diseases which are transmitted or propagated by sexual conduct.
Sexually Transmitted Diseases, Viral
N0000003211
1027279
Sexually Transmitted Disease, Viral
Venereal Diseases, Viral
Viral Sexually Transmitted Disease
Viral Sexually Transmitted Diseases
Viral Venereal Diseases
C0036918
C6600
Sexually Transmitted Diseases, Viral [Disease/Finding]
Dry Eye Syndromes
M0023637
D015352
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.
Dry Eye Syndromes
N0000003223
987360
46152009
C0013238
C6624
Dry Eye Syndromes [Disease/Finding]
Overdose
M0023903
D015537
An accidental or deliberate dose of a medication or street drug that is in excess of what is normally used.
Overdose
N0000003288
1023841
55680006
C0029944
C6754
Overdose [Disease/Finding]
HIV Infections
M0023997
D015658
Includes the spectrum of human immunodeficiency virus infections that range from asymptomatic seropositivity, thru AIDS-related complex (ARC), to acquired immunodeficiency syndrome (AIDS).
HIV Infections
N0000003302
1022756
86406008
HTLV-III Infections
HTLV-III-LAV Infections
T-Lymphotropic Virus Type III Infections, Human
C0019693
C6782
HIV Infections [Disease/Finding]
Corneal Edema
M0024096
D015715
An excessive amount of fluid in the cornea due to damage of the epithelium or endothelium causing decreased visual acuity.
Corneal Edema
N0000003307
1024597
193812004
27194006
C0010037
C6792
Corneal Edema [Disease/Finding]
Lentivirus Infections
M0024697
D016180
Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection.
Lentivirus Infections
N0000003384
1024090
24907000
Infections, Lentivirus
C0079680
C6946
Lentivirus Infections [Disease/Finding]
AIDS-Related Opportunistic Infections
M0025965
D017088
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
N0000003524
1025910
HIV-Related Opportunistic Infections
Opportunistic Infections, AIDS-Related
Opportunistic Infections, HIV-Related
C0162526
C7226
AIDS-Related Opportunistic Infections [Disease/Finding]
Kidney Failure
M0025974
D051437
A severe irreversible decline in the ability of kidneys to remove wastes, concentrate URINE, and maintain ELECTROLYTE BALANCE; BLOOD PRESSURE; and CALCIUM metabolism.
Kidney Failure
N0000003529
1022860
266553002
42399005
Renal Failure
C0035078
C7236
Kidney Failure [Disease/Finding]
Skin Diseases, Viral
M0026098
D017193
Skin diseases caused by viruses.
Skin Diseases, Viral
N0000003547
1029386
128937004
Viral Skin Diseases
C0162628
C7272
Skin Diseases, Viral [Disease/Finding]
Skin and Connective Tissue Diseases
M0026454
D017437
A collective term for diseases of the skin and its appendages and of connective tissue.
Skin and Connective Tissue Diseases
N0000003573
1027511
C0175166
C7324
Skin and Connective Tissue Diseases [Disease/Finding]
Skin Diseases, Eczematous
M0026466
D017443
Any of a variety of eruptive skin disorders characterized by erythema, oozing, vesiculation, and scaling. Etiology is varied.
Skin Diseases, Eczematous
N0000003576
1022475
Eczematous Disorders
Eczematous Skin Diseases
C0162817
C7330
Skin Diseases, Eczematous [Disease/Finding]
Skin Diseases, Papulosquamous
M0026467
D017444
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
N0000003577
1024350
22585003
Papulosquamous Disorders
Papulosquamous Skin Diseases
C0162818
C7332
Skin Diseases, Papulosquamous [Disease/Finding]
Neuroectodermal Tumors
M0026668
D017599
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
N0000003613
1022212
253096008
73676002
C0206093
C7404
Neuroectodermal Tumors [Disease/Finding]
Neuroendocrine Tumors
M0027590
D018358
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.
Neuroendocrine Tumors
N0000003804
1024535
255046005
C0206754
C7786
Neuroendocrine Tumors [Disease/Finding]
Neurobehavioral Manifestations
M0333801
D019954
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
N0000003967
1025867
Cognitive Manifestations
Cognitive Symptoms
Neurobehavioral Signs and Symptoms
Signs and Symptoms, Neurobehavioral
C0525041
C8112
Neurobehavioral Manifestations [Disease/Finding]
Delirium, Dementia, Amnestic, Cognitive Disorders
M0029645
D019965
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
N0000003976
1022574
106014008
111479008
Mental Disorders, Organic
Organic Mental Disorders
C0029227
C8130
Delirium, Dementia, Amnestic, Cognitive Disorders [Disease/Finding]
Substance-Related Disorders
M0029657
D019966
Disorders related to substance abuse, the side effects of a medication, or toxin exposure.
Substance-Related Disorders
N0000003977
1027904
C0236969
C8132
Substance-Related Disorders [Disease/Finding]
Alcohol-Related Disorders
M0029672
D019973
Disorders related to or resulting from abuse or mis-use of alcohol.
Alcohol-Related Disorders
N0000003982
1025655
29212009
C0236664
C8142
Alcohol-Related Disorders [Disease/Finding]
Coagulation Protein Disorders
M0029880
D020147
Hemorrhagic and thrombotic disorders resulting from abnormalities or deficiencies of coagulation proteins.
Coagulation Protein Disorders
N0000004004
1024212
Blood Coagulation Factor Deficiencies
Coagulation Proteins Disorders
C0600503
C8186
Coagulation Protein Disorders [Disease/Finding]
Neurotoxicity Syndromes
M0328313
D020258
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
N0000004080
985040
19466003
Nervous System Poisoning
Neurotoxic Disorders
Neurotoxin Diseases
Neurotoxin Disorders
Poisoning, Nervous System
C0235032
C8338
Neurotoxicity Syndromes [Disease/Finding]
Alcohol-Induced Disorders, Nervous System
M0328091
D020268
Acute and chronic neurologic disorders associated with the various neurologic effects of ETHANOL. Primary sites of injury include the brain and peripheral nerves.
Alcohol-Induced Disorders, Nervous System
N0000004088
1023561
Alcohol Abuse, Nervous System
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
C0751865
C8354
Alcohol-Induced Disorders, Nervous System [Disease/Finding]
Intracranial Hemorrhages
M0328611
D020300
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
N0000004102
1026294
1386000
Hemorrhage, Intracranial
C0151699
C8382
Intracranial Hemorrhages [Disease/Finding]
Alcohol-Induced Disorders
M0328025
D020751
Disorders stemming from the misuse and abuse of alcohol.
Alcohol-Induced Disorders
N0000004170
1025678
C0236970
C8518
Alcohol-Induced Disorders [Disease/Finding]
Pathological Conditions, Anatomical
M0328642
D020763
An abnormal structural condition of the human body, usually macroscopic, that is common to a variety of different diseases.
Pathological Conditions, Anatomical
N0000004178
1026773
C0752135
C8534
Pathological Conditions, Anatomical [Disease/Finding]
Neuromuscular Manifestations
M0328296
D020879
Signs and symptoms associated with diseases of the muscle, neuromuscular junction, or peripheral nerves.
Neuromuscular Manifestations
N0000004213
1027972
Neuromuscular Signs and Symptoms
Signs and Symptoms, Neuromuscular
C0752252
C8604
Neuromuscular Manifestations [Disease/Finding]
Discrete Subaortic Stenosis
M0001558
D021922
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
N0000004248
1031927
Subaortic Stenosis, Discrete
C0012628
C8674
Discrete Subaortic Stenosis [Disease/Finding]
basiliximab
M0292349
C113157
basiliximab
N0000004374
196102
basiliximab
C0676831
C11518
basiliximab [Chemical/Ingredient]
Carbohydrates
M0003360
D002241
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.
Carbohydrates
N0000005723
2028
C0007004
C21790
Carbohydrates [Chemical/Ingredient]
Metolazone
M0013684
D008788
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.
Metolazone
N0000005746
6916
Metolazone
6-Quinazolinesulfonamide, 7-chloro-1,2,3,4-tetrahydro-2-methyl-3-(2-methylphenyl)-4-oxo-
C0025854
C21836
Metolazone [Chemical/Ingredient]
Proteins
M0017890
D011506
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.
Proteins
N0000005817
8859
Proteins
C0033684
C21978
Proteins [Chemical/Ingredient]
torsemide
M0086132
C026116
torsemide
N0000006018
38413
torsemide
1-isopropyl-3-((4-(3-methylphenylamino)pyridine)-3-sulfonyl)urea
1-isopropyl-3-((4-m-toluidino-3-pyridyl)sulfonyl)urea
torasemide
C0076840
C22380
torsemide [Chemical/Ingredient]
Dobutamine
M0006696
D004280
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.
Dobutamine
N0000006055
3616
Dobutamine
1,2-Benzenediol, 4-(2-((3-(4-hydroxyphenyl)-1-methylpropyl)amino)ethyl)-, (+-)-
C0012963
C22454
Dobutamine [Chemical/Ingredient]
Dopamine
M0006756
D004298
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.
Dopamine
N0000006091
3628
Dopamine
1,2-Benzenediol, 4-(2-aminoethyl)-
3,4-Dihydroxyphenethylamine
4-(2-Aminoethyl)-1,2-benzenediol
Hydroxytyramine
C0013030
C22526
Dopamine [Chemical/Ingredient]
Lipids
M0012553
D008055
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)
Lipids
N0000006185
6411
C0023779
C22714
Lipids [Chemical/Ingredient]
Vitamin D
M0022797
D014807
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.
Vitamin D
N0000006277
11253
Vitamin D
C0042866
C22900
Vitamin D [Chemical/Ingredient]
Vitamin K
M0022806
D014812
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.
Vitamin K
N0000006290
11258
Vitamin K
C0042878
C22926
Vitamin K [Chemical/Ingredient]
Magnesium
M0012884
D008274
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.
Magnesium
N0000006335
6574
Magnesium
C0024467
C23018
Magnesium [Chemical/Ingredient]
Glucose
M0009339
D005947
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.
Glucose
N0000006402
4850
Glucose
D-Glucose
Dextrose
C0017725
C23152
Glucose [Chemical/Ingredient]
Hydrochloric Acid
M0010701
D006851
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.
Hydrochloric Acid
N0000006448
5486
Hydrochloric Acid
Hydrochloric acid
Muriatic Acid
C0020259
C23244
Hydrochloric Acid [Chemical/Ingredient]
Calcifediol
M0003141
D002112
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.
Calcifediol
N0000006507
1889
Calcifediol
25-Hydroxycholecalciferol
25-Hydroxyvitamin D 3
25-Hydroxyvitamin D3
9,10-Secocholesta-5,7,10(19)-triene-3,25-diol, (3beta,5Z,7E)-
Calcidiol
C0006657
C23362
Calcifediol [Chemical/Ingredient]
Calcium
M0003153
D002118
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.
Calcium
N0000006512
1895
Calcium
Blood Coagulation Factor IV
Coagulation Factor IV
Factor IV
C0006675
C23372
Calcium [Chemical/Ingredient]
Calcium Chloride
M0003166
D002122
A salt used to replenish calcium levels, as an acid-producing diuretic, and as an antidote for magnesium poisoning.
Calcium Chloride
N0000006545
1901
Calcium Chloride
Calcium Chloride, Anhydrous
Calcium chloride
C0006686
C23438
Calcium Chloride [Chemical/Ingredient]
Sodium Lactate
M0028809
D019354
The sodium salt of racemic or inactive lactic acid. It is a hygroscopic agent used intravenously as a systemic and urinary alkalizer.
Sodium Lactate
N0000006559
56489
Sodium Lactate
C0142874
C23466
Sodium Lactate [Chemical/Ingredient]
Lactates
M0012155
D007773
Salts or esters of LACTIC ACID containing the general formula CH3CHOHCOOR.
Lactates
N0000006568
6201
C0022924
C23484
Lactates [Chemical/Ingredient]
Atracurium
M0001922
D001279
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.
Atracurium
N0000006674
1218
Atracurium
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-
C0004234
C23696
Atracurium [Chemical/Ingredient]
Nystatin
M0015146
D009761
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.
Nystatin
N0000006699
7597
Nystatin
C0028741
C23746
Nystatin [Chemical/Ingredient]
Sulbactam
M0020733
D013407
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.
Sulbactam
N0000006841
10167
Sulbactam
4-Thia-1-azabicyclo(3.2.0)heptane-2-carboxylic acid, 3,3-dimethyl-7-oxo-, 4,4-dioxide, (2S-cis)-
Penicillanic Acid Sulfone
C0038665
C24032
Sulbactam [Chemical/Ingredient]
Fatty Acids
M0008265
D005227
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)
Fatty Acids
N0000006847
4297
C0015684
C24044
Fatty Acids [Chemical/Ingredient]
Chlorothiazide
M0004186
D002740
A thiazide diuretic with actions and uses similar to those of HYDROCHLOROTHIAZIDE. (From Martindale, The Extra Pharmacopoeia, 30th ed, p812)
Chlorothiazide
N0000006932
2396
Chlorothiazide
2H-1,2,4-Benzothiadiazine-7-sulfonamide, 6-chloro-, 1,1-dioxide
C0008273
C24214
Chlorothiazide [Chemical/Ingredient]
Cholecalciferol
M0004229
D002762
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.
Cholecalciferol
N0000006996
2418
Cholecalciferol
(3 beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-trien-3-ol
9,10-Secocholesta-5,7,10(19)-trien-3-ol, (3beta,5Z,7E)-
Calciol
Vitamin D 3
Vitamin D3
C0008318
C24342
Cholecalciferol [Chemical/Ingredient]
Foscarnet
M0026166
D017245
An antiviral agent used in the treatment of cytomegalovirus retinitis. Foscarnet also shows activity against human herpesviruses and HIV.
Foscarnet
N0000007166
33562
Foscarnet
Phosphinecarboxylic acid, dihydroxy-, oxide
Phosphonoformic Acid
C0070895
C24684
Foscarnet [Chemical/Ingredient]
Magnesium Chloride
M0023974
D015636
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
N0000007198
6579
Magnesium Chloride
Magnesium chloride (MgCl2)
MgCl2
C0024472
C24748
Magnesium Chloride [Chemical/Ingredient]
Sodium Chloride
M0020094
D012965
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.
Sodium Chloride
N0000007207
9863
Sodium Chloride
Sodium chloride (NaCl)
C0037494
C24766
Sodium Chloride [Chemical/Ingredient]
Tacrolimus
M0025261
D016559
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.
Tacrolimus
N0000007302
42316
Tacrolimus
15,19-Epoxy-3H-pyrido(2,1-c)(1,4)oxaazacyclotricosine-1,7,20,21(4H,23H)-tetrone, 5,6,8,11,12,13,14,15,16,17,18,19,24,25,26,26a-hexadecahydro-5,19-dihydroxy-3-(2-(4-hydroxy-3-methoxycyclohexyl)-1-methylethenyl)-14,16-dimethoxy-4,10,12,18-tetramethyl-8-(2-p
C0085149
C24956
Tacrolimus [Chemical/Ingredient]
Alkaloids
M0000713
D000470
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)
Alkaloids
N0000007503
496
C0002062
C25362
Alkaloids [Chemical/Ingredient]
Phenethylamines
M0016506
D010627
A group of compounds that are derivatives of beta- aminoethylbenzene which is structurally and pharmacologically related to amphetamine. (From Merck Index, 11th ed)
Phenethylamines
N0000007526
8127
Phenylethylamines
C0031399
C25408
Phenethylamines [Chemical/Ingredient]
Macrolides
M0028311
D018942
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.
Macrolides
N0000007529
586370
C0282563
C25414
Macrolides [Chemical/Ingredient]
Anions
M0001248
D000838
Negatively charged atoms, radicals or groups of atoms which travel to the anode or positive pole during electrolysis.
Anions
N0000007541
853
C0003075
C25438
Anions [Chemical/Ingredient]
Benzothiadiazines
M0002371
D001581
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.
Benzothiadiazines
N0000007554
1414
C0005084
C25464
Benzothiadiazines [Chemical/Ingredient]
Biogenic Monoamines
M0023566
D015306
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
N0000007586
1565
Monoamines, Biogenic
C0005497
C25528
Biogenic Monoamines [Chemical/Ingredient]
Hexoses
M0010338
D006601
Hexoses
N0000007604
5318
C0019494
C25568
Hexoses [Chemical/Ingredient]
Quinazolines
M0018336
D011799
Quinazolines
N0000007605
9064
C0034407
C25570
Quinazolines [Chemical/Ingredient]
Globulins
M0009293
D005916
Globulins
N0000007615
4825
C0017649
C25590
Globulins [Chemical/Ingredient]
Acids
M0000220
D000143
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)
Acids
N0000007626
230
C0001128
C25612
Acids [Chemical/Ingredient]
Acids, Acyclic
M0000221
D000144
Carboxylic acids that have open-chain molecular structures as opposed to ring-shaped structures.
Acids, Acyclic
N0000007627
231
Acyclic Acids
C0001129
C25614
Acids, Acyclic [Chemical/Ingredient]
Acids, Noncarboxylic
M0000225
D000148
Inorganic acids with a non metal, other than carbon, attached to hydrogen, or an acid radical containing no carbon.
Acids, Noncarboxylic
N0000007630
235
Noncarboxylic Acids
C0001133
C25620
Acids, Noncarboxylic [Chemical/Ingredient]
Lactams
M0012143
D007769
Cyclic AMIDES formed from aminocarboxylic acids by the elimination of water. Lactims are the enol forms of lactams.
Lactams
N0000007642
6195
C0022914
C25644
Lactams [Chemical/Ingredient]
Lactones
M0012175
D007783
Cyclic esters of hydroxy carboxylic acids, containing a 1-oxacycloalkan-2-one structure. Large cyclic lactones of over a dozen atoms are MACROLIDES.
Lactones
N0000007646
6209
C0022947
C25652
Lactones [Chemical/Ingredient]
Organic Chemicals
M0015401
D009930
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 Chemicals
N0000007676
7692
C0029224
C25712
Organic Chemicals [Chemical/Ingredient]
Amides
M0000897
D000577
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)
Amides
N0000007681
633
C0002482
C25722
Amides [Chemical/Ingredient]
Organophosphorus Compounds
M0015421
D009943
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
N0000007684
7696
C0029254
C25728
Organophosphorus Compounds [Chemical/Ingredient]
Phosphorus Acids
M0027146
D017976
Inorganic acids that contain phosphorus as an integral part of the molecule.
Phosphorus Acids
N0000007696
67101
C0206451
C25752
Phosphorus Acids [Chemical/Ingredient]
Chlorides
M0004143
D002712
Inorganic compounds derived from hydrochloric acid that contain the Cl- ion.
Chlorides
N0000007711
2364
C0008203
C25782
Chlorides [Chemical/Ingredient]
Catecholamines
M0003647
D002395
A general class of ortho-dihydroxyphenylalkylamines derived from tyrosine.
Catecholamines
N0000007715
2146
Sympathins
C0007412
C25790
Catecholamines [Chemical/Ingredient]
Steroids
M0020527
D013256
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)
Steroids
N0000007720
10072
C0038317
C25800
Steroids [Chemical/Ingredient]
Phosphonoacetic Acid
M0016688
D010746
A simple organophosphorus compound that inhibits DNA polymerase, especially in viruses and is used as an antiviral agent.
Phosphonoacetic Acid
N0000007721
8250
Acetic acid, phosphono-
Phosphonacetic Acid
C0031681
C25802
Phosphonoacetic Acid [Chemical/Ingredient]
Biogenic Amines
M0002518
D001679
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.
Biogenic Amines
N0000007726
1564
Amines, Biogenic
Biogenic Amine
C0005496
C25812
Biogenic Amines [Chemical/Ingredient]
Sterols
M0020532
D013261
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)
Sterols
N0000007730
10077
C0038323
C25820
Sterols [Chemical/Ingredient]
Cholestenes
M0004266
D002782
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.
Cholestenes
N0000007759
2436
C0008375
C25878
Cholestenes [Chemical/Ingredient]
Chlorine Compounds
M0026679
D017606
Inorganic compounds that contain chlorine as an integral part of the molecule.
Chlorine Compounds
N0000007794
67167
Chlorine Compounds, Inorganic
C0206759
C25948
Chlorine Compounds [Chemical/Ingredient]
Calcium Compounds
M0026683
D017610
Inorganic compounds that contain calcium as an integral part of the molecule.
Calcium Compounds
N0000007800
66999
C0206106
C25960
Calcium Compounds [Chemical/Ingredient]
Magnesium Compounds
M0026689
D017616
Inorganic compounds that contain magnesium as an integral part of the molecule.
Magnesium Compounds
N0000007803
67004
C0206112
C25966
Magnesium Compounds [Chemical/Ingredient]
Naphthalenes
M0014459
D009281
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.
Naphthalenes
N0000007809
7251
C0027378
C25978
Naphthalenes [Chemical/Ingredient]
Bicyclo Compounds, Heterocyclic
M0028488
D019086
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
N0000007813
82186
Bicyclic Heterocyclic Compounds
Heterocyclic Bicyclo Compounds
Heterocyclic Cpds, Bicyclic
C0282650
C25986
Bicyclo Compounds, Heterocyclic [Chemical/Ingredient]
Naphthoquinones
M0014463
D009285
Naphthalene rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.
Naphthoquinones
N0000007814
7255
Naphthalenediones
C0027388
C25988
Naphthoquinones [Chemical/Ingredient]
Membrane Lipids
M0013338
D008563
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.
Membrane Lipids
N0000007818
6723
Cell Membrane Lipids
C0025249
C25996
Membrane Lipids [Chemical/Ingredient]
Amino Acids, Peptides, and Proteins
M0000928
D000602
Amino acids and chains of amino acids connected by peptide linkages.
Amino Acids, Peptides, and Proteins
N0000007833
664
C0002526
C26026
Amino Acids, Peptides, and Proteins [Chemical/Ingredient]
Sodium Compounds
M0026726
D017670
Inorganic compounds that contain sodium as an integral part of the molecule.
Sodium Compounds
N0000007844
67017
C0206134
C26048
Sodium Compounds [Chemical/Ingredient]
Peptides
M0016238
D010455
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.
Peptides
N0000007874
8036
C0030956
C26108
Peptides [Chemical/Ingredient]
Glycosides
M0009500
D006027
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)
Glycosides
N0000007897
4958
C0017977
C26154
Glycosides [Chemical/Ingredient]
Elements
M0007227
D004602
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.
Elements
N0000007912
3802
C0013879
C26186
Elements [Chemical/Ingredient]
Blood Coagulation Factors
M0002684
D001779
Endogenous substances, usually proteins, that are involved in the blood coagulation process.
Blood Coagulation Factors
N0000007914
1637
Blood Coagulation Factor
Coagulation Factor
Coagulation Factor, Blood
Coagulation Factors
Coagulation Factors, Blood
Factor, Coagulation
Factors, Coagulation
C0005789
C26190
Blood Coagulation Factors [Chemical/Ingredient]
Secosteroids
M0019588
D012632
Steroids in which fission of one or more ring structures and concomitant addition of a hydrogen atom at each terminal group has occurred.
Secosteroids
N0000007915
9626
C0036532
C26192
Secosteroids [Chemical/Ingredient]
Immunoglobulins
M0011122
D007136
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.
Immunoglobulins
N0000007920
5720
Immunoglobulins
Globulins, Immune
Immune Globulins
Immunoglobulin
C0021027
C26202
Immunoglobulins [Chemical/Ingredient]
Blood Proteins
M0002710
D001798
Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins.
Blood Proteins
N0000007921
1653
C0005832
C26204
Blood Proteins [Chemical/Ingredient]
Terpenes
M0021183
D013729
A class of compounds composed of repeating 5-carbon units of HEMITERPENES.
Terpenes
N0000007940
10372
Terpenoids
C0039561
C26242
Terpenes [Chemical/Ingredient]
Recombinant Proteins
M0018641
D011994
Proteins prepared by recombinant DNA technology.
Recombinant Proteins
N0000007956
9218
Biosynthetic Proteins
Proteins, Biosynthetic
C0034861
C26276
Recombinant Proteins [Chemical/Ingredient]
Isoquinolines
M0011785
D007546
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)
Isoquinolines
N0000007960
6056
C0022248
C26284
Isoquinolines [Chemical/Ingredient]
Hydrocarbons
M0010687
D006838
Hydrocarbons
N0000007973
5476
C0020242
C26310
Hydrocarbons [Chemical/Ingredient]
Hydroxy Acids
M0010745
D006880
Organic compounds containing both the hydroxyl and carboxyl radicals.
Hydroxy Acids
N0000007983
5515
C0020317
C26330
Hydroxy Acids [Chemical/Ingredient]
Hydroxycholecalciferols
M0010754
D006887
Hydroxy analogs of vitamin D 3; (CHOLECALCIFEROL); including CALCIFEDIOL; CALCITRIOL; and 24,25-DIHYDROXYVITAMIN D 3.
Hydroxycholecalciferols
N0000007988
5522
Hydroxycholecalciferol
Hydroxyvitamins D
C0020337
C26340
Hydroxycholecalciferols [Chemical/Ingredient]
Metals, Alkaline Earth
M0013518
D008673
Metals that constitute the group 2 (formerly group IIa) of the periodic table.
Metals, Alkaline Earth
N0000007992
6800
Alkaline Earth Metals
Group 2 Elements
C0025555
C26348
Metals, Alkaline Earth [Chemical/Ingredient]
Metals, Light
M0029055
D019565
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)
Metals, Light
N0000008004
114297
Light Metals
C0376709
C26372
Metals, Light [Chemical/Ingredient]
Ethylamines
M0007897
D005021
Ethylamines
N0000008011
4146
C0015069
C26386
Ethylamines [Chemical/Ingredient]
Sulfites
M0020784
D013447
Inorganic salts of sulfurous acid.
Sulfites
N0000008046
10211
Inorganic Sulfites
Sulfites, Inorganic
C0038750
C26456
Sulfites [Chemical/Ingredient]
Sulfonamides
M0020790
D013449
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)
Sulfonamides
N0000008048
10215
C0038760
C26460
Sulfonamides [Chemical/Ingredient]
Sulfones
M0020791
D013450
Sulfones
N0000008053
10216
C0038761
C26470
Sulfones [Chemical/Ingredient]
Heterocyclic Compounds
M0010290
D006571
Ring compounds having atoms other than carbon in their nuclei. (Grant & Hackh's Chemical Dictionary, 5th ed)
Heterocyclic Compounds
N0000008095
5283
C0019398
C26554
Heterocyclic Compounds [Chemical/Ingredient]
Acetic Acids
M0000132
D000088
Acetic acid and its derivatives which may be formed by substitution reactions. Mono- and di-substituted, as well as halogenated compounds have been synthesized.
Acetic Acids
N0000008114
169
C0000985
C26592
Acetic Acids [Chemical/Ingredient]
Carboxylic Acids
M0003405
D002264
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.
Carboxylic Acids
N0000008137
2060
C0007066
C26638
Carboxylic Acids [Chemical/Ingredient]
Bridged Compounds
M0002922
D001952
Cyclic hydrocarbons that contain multiple rings and share one or more atoms.
Bridged Compounds
N0000008149
1740
C0006174
C26662
Bridged Compounds [Chemical/Ingredient]
Phosphorus Compounds
M0026614
D017553
Inorganic compounds that contain phosphorus as an integral part of the molecule.
Phosphorus Compounds
N0000008156
67164
C0206756
C26676
Phosphorus Compounds [Chemical/Ingredient]
Polycyclic Hydrocarbons, Aromatic
M0017164
D011084
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
N0000008164
8504
Polycyclic Aromatic Hydrocarbons
Polynuclear Aromatic Hydrocarbons
C0032458
C26692
Polycyclic Hydrocarbons, Aromatic [Chemical/Ingredient]
Amines
M0000913
D000588
A group of compounds derived from ammonia by substituting organic radicals for the hydrogens. (From Grant & Hackh's Chemical Dictionary, 5th ed)
Amines
N0000008168
823705
C0002508
C26700
Amines [Chemical/Ingredient]
Bicyclo Compounds
M0002469
D001643
Bicyclo Compounds
N0000008171
1530
C0005378
C26706
Bicyclo Compounds [Chemical/Ingredient]
Fatty Acids, Volatile
M0008273
D005232
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
N0000008176
4303
Fatty Acids, Short-Chain
C0015691
C26716
Fatty Acids, Volatile [Chemical/Ingredient]
Phosphonic Acids
M0016684
D010745
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.
Phosphonic Acids
N0000008178
8248
C0031679
C26720
Phosphonic Acids [Chemical/Ingredient]
Quinones
M0018356
D011809
Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.
Quinones
N0000008181
9083
C0034435
C26726
Quinones [Chemical/Ingredient]
Cholestanes
M0004254
D002776
Derivatives of the saturated steroid cholestane with methyl groups at C-18 and C-19 and an iso-octyl side chain at C-17.
Cholestanes
N0000008187
2432
C0008366
C26738
Cholestanes [Chemical/Ingredient]
Ions
M0011678
D007477
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.
Ions
N0000008197
5964
C0022023
C26758
Ions [Chemical/Ingredient]
Diterpenes
M0006609
D004224
Twenty-carbon compounds derived from MEVALONIC ACID or deoxyxylulose phosphate.
Diterpenes
N0000008216
3557
Diterpenoids
C0012780
C26796
Diterpenes [Chemical/Ingredient]
Immunoglobulin Fragments
M0011106
D007128
Partial immunoglobulin molecules resulting from selective cleavage by proteolytic enzymes or generated through PROTEIN ENGINEERING techniques.
Immunoglobulin Fragments
N0000008221
5710
C0021009
C26806
Immunoglobulin Fragments [Chemical/Ingredient]
Immunoproteins
M0011167
D007162
Blood proteins whose activities affect or play a role in the functioning of the immune system.
Immunoproteins
N0000008223
5744
C0021072
C26810
Immunoproteins [Chemical/Ingredient]
Hydrocarbons, Aromatic
M0010690
D006841
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
N0000008229
5479
Aromatic Hydrocarbons
C0020245
C26822
Hydrocarbons, Aromatic [Chemical/Ingredient]
Metals
M0013515
D008670
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)
Metals
N0000008237
6797
C0025552
C26838
Metals [Chemical/Ingredient]
Serum Globulins
M0019698
D012712
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)
Serum Globulins
N0000008244
9701
C0036800
C26852
Serum Globulins [Chemical/Ingredient]
Sulfur Compounds
M0020800
D013457
Inorganic or organic compounds that contain sulfur as an integral part of the molecule.
Sulfur Compounds
N0000008249
10225
C0038776
C26862
Sulfur Compounds [Chemical/Ingredient]
Monosaccharides
M0014043
D009005
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)
Monosaccharides
N0000008250
7044
C0026492
C26864
Monosaccharides [Chemical/Ingredient]
Inorganic Chemicals
M0011365
D007287
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
N0000008257
5824
C0021521
C26878
Inorganic Chemicals [Chemical/Ingredient]
Heterocyclic Compounds, Bridged-Ring
M0010291
D006572
A class of organic compounds which contain two rings that share a pair of bridgehead carbon atoms.
Heterocyclic Compounds, Bridged-Ring
N0000008258
5288
Bridged-Ring Heterocyclic Compounds
C0019403
C26880
Heterocyclic Compounds, Bridged-Ring [Chemical/Ingredient]
Heterocyclic Compounds, 1-Ring
M0010292
D006573
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
N0000008259
5284
Heterocyclic Cpds, 1-Ring
C0019399
C26882
Heterocyclic Compounds, 1-Ring [Chemical/Ingredient]
Heterocyclic Compounds, 2-Ring
M0010293
D006574
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
N0000008260
5285
C0019400
C26884
Heterocyclic Compounds, 2-Ring [Chemical/Ingredient]
Electrolytes
M0007189
D004573
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)
Electrolytes
N0000008272
3793
C0013832
C26910
Electrolytes [Chemical/Ingredient]
Hydrocarbons, Cyclic
M0010694
D006844
Organic compounds composed exclusively of carbon and hydrogen forming a closed ring that may be either alicyclic or aromatic.
Hydrocarbons, Cyclic
N0000008280
5482
Cyclic Hydrocarbons
C0020248
C26926
Hydrocarbons, Cyclic [Chemical/Ingredient]
Alveolar Surface Tension Alteration
N0000008293
989276
C1371276
C26952
Alveolar Surface Tension Alteration [PE]
Alveolar Surface Tension Reduction
N0000008294
988631
C1371492
C26954
Alveolar Surface Tension Reduction [PE]
Arterial Vasoconstriction
N0000008298
986283
C1371490
C26962
Arterial Vasoconstriction [PE]
Arterial Vasodilation
N0000008299
984618
C1371278
C26964
Arterial Vasodilation [PE]
Blood & Lymphatic Fluid Function Alteration
N0000008307
988284
C1371289
C26980
Blood & Lymphatic Fluid Function Alteration [PE]
Carbohydrate Metabolism Alteration
N0000008327
1033881
C1371294
C27020
Carbohydrate Metabolism Alteration [PE]
Cardiac Contractility Alteration
N0000008328
986415
C1371293
C27022
Cardiac Contractility Alteration [PE]
Cardiac Rate Alteration
N0000008329
985479
C2825066
C27024
Cardiac Rate Alteration [PE]