Becky Steck
Christopher Park
John F. O’Toole
Sean Mooney
Anthony Huffman
Fred Dowd
Hong Yu
Jennifer Schaub
Jie Zheng
Yongqun "Oliver" He (YH)
OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles.
OWL-DL
OPMI subject: Precision medicine and related investigations
OPMI: Ontology of Precision Medicine and Investigation
Vision Release: 1.0.166
BFO OWL specification label
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
ontology term requester
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
expand assertion to
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
term_mapping_to_UMLS
term_mapping_to_NCIT
A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source.
The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
Provides an alternative Preferred Name for use in some NCI systems.
The word or phrase that NCI uses by preference to refer to the concept.
Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
Contains a Concept Unique Identifier for those concepts that appear in NCI Metathesaurus but not in the NLM UMLS.
An NCI Thesaurus property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used.
This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software.
A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
has_MedDRA_id
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA tools project (http://isa-tools.org)
NIAID GSCID-BRC alternative term
An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term
term mapping to NCIT ID
A subproperty of seeAlso that represents a UMLS CUI identifier mapped to the specified term
term mapping to UMLS CUI
An annotation property that refers to a code defined by NCIT
NCIT code
alternative term in Chinese
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
tooth SubClassOf 'never in taxon' value 'Aves'
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
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
taxonomic class assertion
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL
logical macro assertion on a class
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
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'
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
Notes on the how instances of this class vary across species.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
A metadata relation between a class and its taxonomic rank (eg species, family)
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
An entity responsible for making contributions to the content of the resource.
Contributor
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
An entity primarily responsible for making the content of the resource.
Creator
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
A date associated with an event in the life cycle of the resource.
Date
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
An account of the content of the resource.
Description
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
The physical or digital manifestation of the resource.
Format
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a resource from which the present resource is derived.
Source
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
The topic of the content of the resource.
Subject and Keywords
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.
Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
label
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
bearer of
bearer_of
is bearer of
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
[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
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 dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
is_about is a (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased.
an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality.
This is a shortcut relation of the following full version: 'has participant' some (participant 'has quality' ) in: process 'has participant' some (participant 'has quality' some quality)
has participant quality
a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in.
AE occurs in
a specific 'preceded by' object property that has a domain of an adverse event.
adverse event preceded by
The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client.
A relation between a service and the primary processual part of the service that is performed by the provider for the consumer.
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
has_specified_input
see is_input_of example_of_usage
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
Alan Ruttenberg
is_specified_input_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
The inverse property of is_specified_output_of
is_specified_output_of
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
has organization member
A relation between an information content entity and a value specification that specifies its value.
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
true
A kidney biopsy protocol is executed in a kidney biopsy process.
A shortcut relation that is concretized and realized in some process.
executed in
A 'has part' object property that has the range of a textual question
has question
form generated by
An object property that indicates a relation between a question and an answer
has answer
An object property that represents a relation between a form and a question where the question sets up an exclusion criterion. Specifically, when the answer to the question is Yes, the candidate becomes ineligible for the participation of a study.
has exclusion question
An object property that represents a relation between a form and a question where the question sets up an inclusion criterion. Specifically, when the answer to the question is Yes, then the candidate fulfills a criterion for being eligible for participating in a study. Note that there might be other criteria that the candidate also need to meet in order to be fully eligible. Meanwhile, if the answer is No, the candidate may still be eligible depending on the other restriction.
has inclusion question
has process quality
An object property that represents a relation between a person with a biological sex and a process where the person has a specific susceptbility to a process
has sex-specific susceptibility to
An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding male population
has increased susceptibility compared to male to
Male has increased susceptibility to death due to COVID-19 infection compared to female. Note that in this case, the male can mean one single male individual. however, the female here means the whole female population. It is reported that the ratio of deaths in COVID-19 infected males to females is 1·21:1 in high-income countries, but 2·8:1 in low-income countries (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023692/).
An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding female population
has increased susceptibility compared to female to
An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to the whole population with all sexes included
has increased sex-specific susceptibility compared to sex baseline to
A care_site has a care_site_id (OMOP: http://ohdsi.github.io/CommonDataModel/cdm54.html#CARE_SITE)
An object property that represents a relation between an entity and its corresponding identifier that is owned by the entity.
has identifier
A patient was admitted to the hospital from home or a long-term care facility.
An object property that represents a relation between a patient and a site from which the patient was admitted.
admitted from
After a visit, a person was discharged to home or a long-term care site. Typically this applies only to visits that have a length of stay of a day or more.
An object property that represents a relation between a patient and a site to which the patient was discharged after a visit.
discharged to
An admission diagnosis status has the content of adimission diagnosis (as an information content entity).
An object property that represents a relation between a status and an information content entity where the status has its content information defined by the information content entity.
has status content
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
'inheres in at all times'
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
concretizes
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
function of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
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.
Primitive instance level timing relation between events
before or simultaneous with
Relation between occurrents, shares start and end boundaries.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
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.
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)
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
has active participant
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
adjacent to
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
Relation between occurrents, shares an end boundary with.
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
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.
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.
has output
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.
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
inheres in part of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
enabled by
regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
formed as result of
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
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.
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
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.
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
inverse of causally upstream of or within
'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
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
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.
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
causal relation between material entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
determined by (system to material entity)
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
causally influenced by (material entity to material entity)
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
causally influences (material entity to material entity)
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.
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
x is a conduit for y iff y passes through the lumen of x.
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.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
has_proper_part
has measurement value
The data type "last 4 digits of social security number" has digit number of 4.
A data property that represents a relation between a data type and a number of integer digits that the data type has.
has digit number
quality measured by year
entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
fiat object
fiat object part
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
A cardiovascular drug that tends to raise reduced blood pressure.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6.
A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring.
A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring.
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
Any p-block molecular entity containing a chalcogen.
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
An oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
Any molecule that consists of a series of atoms joined together to form a ring.
A molecule that features two fused rings.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
A p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
Any organic molecule that consists of atoms connected in the form of a ring.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
polymer
Any heteroorganic entity containing at least one carbon-nitrogen bond.
A beta-lactam is a lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon.
Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified.
Any molecular entity consisting of more than one atom.
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
A cyclic compound in which a carbonyl group in a ring is bonded to one or two skeletal heteroatoms.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
Any molecular entity that contains carbon.
A cyclic compound having as ring members atoms of at least two different elements.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
The number of contractions of the cardiac ventricles per unit of time.
Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
The maximum arterial pressure within the cardiac cycle, i.e. at the point at which the heart is in its maximal state of contraction. This is the time when the blood is forced from the ventricles of the heart into the pulmonary artery and the aorta.
The minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
The minimum pressure in the heart left ventricle, usually at the point at which the heart is in a state of relaxation and expansion and the ventricles fill with blood.
left ventricular diastolic blood pressure
Measurement of the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta.
left ventricular systolic blood pressure
A blood pressure measurement which has been normalized or adjusted by a mathematical process or computation. Blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
The average blood pressure within an artery over a specified period of time. It is often calculated using the formula of one third systolic pressure plus two thirds diastolic pressure, or alternatively, using the formula diastolic pressure plus 1/3 of the difference between systolic pressure and diastolic pressure (i.e. 1/3 pulse pressure).
A calculated value for the difference between the systolic blood pressure and the diastolic blood pressure at a given point in time when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
A measurement of the physical form or structure of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system.
This is the term which was just "heart measurement". Since it was under body morphological measurement it seemed to clearly refer to a morphological measurement. I made this term more specific so that another term for "heart measurement" could be added to the ontology above it which would also be a parent to other non-morphological heart-related terms. JRS 2-15-2012.
The heaviness of the heart (the central cardiac muscle which maintains the circulation of the blood) or the degree to which it is drawn to the earth by gravity.
A calculated measurement of the difference between the systolic pressure and the diastolic pressure in the heart left ventricle at a given point in time in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
Measurement of the structure or forms of the entire body or parts of the body of an organism.
A quantification of a parameter of the chemical composition of blood.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of one or more of the various, specific types of leukocytes present in a sample of blood for which a total white blood cell count was taken, usually 1 cubic mm of peripheral venous blood.
calculated blood differential leukocyte count
calculated differential white blood cell count
The amount of hemoglobin in a specific volume of blood, expressed as grams per deciliter of whole blood in humans.
The number of white blood cells in a specified volume of blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in blood.
The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood.
A measurement of the blood, it's contents, cells or other factors contained within the blood.
A value resulting from the quantification of a morphological or physiological parameter of blood cells, i.e. cells native to the circulation, including those of erythroid, lymphoid, myeloid and monocytic lineages. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
The level of urea in the blood in terms of nitrogen content; converted to urea concentration by multiplying by 60/28 or 2.14. Urea is the chief nitrogenous end product of protein metabolism in whole blood. Urea is formed in the liver from amino acids and from ammonia compounds and can be found in urine, blood, and lymph.
Any value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipid, any of a structurally diverse group of organic compounds found in blood that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure.
Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them.
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in high-density lipoprotein (HDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. HDL is the smallest of the major lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The HDL class of lipoproteins, specifically the subtypes of HDL2 and HDL3, have densities between 1.063 and 1.210 g/ml.
Values for density ranges of the lipoprotein classes are approximate. The classes may be defined differently by different researchers, in part because class definitions depend on the number of subclasses into which the lipoprotein fractions are divided.
blood high density lipoprotein cholesterol level
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in low-density lipoprotein (LDL) molecules in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. LDL constitute a class of relatively large, heterogeneous lipoprotein particles, complex molecules that consist of a protein membrane surrounding a core of lipids. The LDL class of lipoproteins has a density between 1.019 and 1.063 g/ml. In some animal species, such as canine and rodents, this may overlap with the HDL1 class and be designated LDL/HDL1.
blood low density lipoprotein cholesterol level
Measurement of the total amount of all proteins, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, found in a specific volume of plasma, the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended.
A quantification of one or more mineral salts found in the blood in the form of electrically charged ions.
Any quantitation of the catalytic effect exerted by an enzyme in a specified sample of blood. An enzyme is a protein that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reaction(s).
A measurement of the physical form and structure of an organ.
This is the term which used to be just "organ measurement". Since it was under body morphological measurement, it clearly referred to a morphological measurement. Because a term for organ measurement was needed that was not morphological, and since this one already had annotations, I changed the term while keeping the ID and location in the ontology the same. JRS 2-15-2012.
The weight of the heart after removal from the body but without desiccation.
The weight of the heart after desiccation.
The weight of the lower left chamber of the heart, which pumps oxygenated blood through the aorta into the systemic arteries, after removal from the body and separation from the rest of the heart but without desiccation.
The weight of the lower right chamber of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, after removal from the body and separation from the rest of the heart but without desiccation.
A calculated value in which the weight of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system, is divided by the total weight of the body, and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
A calculated value in which the weight of the heart, the chambered, muscular organ in vertebrates that pumps blood received from the veins into the arteries, thereby maintaining the flow of blood through the entire circulatory system, is presented as percentage of the total weight of the body, thus normalizing it to body weight.
heart weight as percentage of body weight
The weight of the aorta, the main trunk from which the arterial system proceeds. Weight is the heaviness or degree to which a body is drawn to the earth by gravity.
Any quantification of a morphological or physiological parameter of one or more blood vessels, the network of muscular tubes that carry blood through the body.
The weight of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The weight of the right kidney, the organ which lies on the right side of the body from the perspective of the subject and functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight of the left kidney, the organ which lies on the left side of the body from the perspective of the subject and functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight of a single kidney, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight of both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
Measurement of the physical form or structure of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated value which compares the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, with the weight of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body, and presents it as a ratio.
heart right ventricle weight to left ventricle weight ratio
The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter.
The amount of lipoproteins, any of a group of conjugated proteins that have at least one lipid component, in a specific volume of blood.
Measurement of the amount of creatinine in a specified sample of urine, the fluid waste product excreted by the kidneys. Creatinine is a nitrogenous compound formed in muscle as the end product of creatine metabolism. Blood and urine tests for creatinine are used as diagnostic indicators of kidney function and muscle mass.
Any measurement of the physical form or structure of the skeletal, smooth and/or heart muscles of the body.
The amount of albumin in a specified volume of urine. Urine albumin levels which are above normal but not detectable with routine protein testing are referred to as microalbuminuria.
A calculated measurement in which the weight after removal from the body but without desiccation of both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a percentage, thus normalizing it to body weight.
both kidneys wet weight as percentage of body weight
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of one or both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The weight of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, after removal from the body but without desiccation.
The weight after desiccation of one or both kidneys, the organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at either the inner surface or outer surface of the blood vessel wall.
Percentage of blood pumped out of the left ventricle with each heart beat.
Volume of blood left in a ventricle at end of contraction.
Any measurement of the movement of blood through the heart and blood vessels.
The volume of blood flowing through a vessel or organ per unit of time.
The volume of blood pumped from the right or left ventricle per minute, also used to calculate - stroke volume X heart rate.
The volume of blood flowing through an artery per unit time.
The volume of blood passing through a vein per unit time.
Movement of blood along the solid wall of a vessel, often represented by the Hagen-Poiseuille equation.
The time needed for plasma to form a fibrin clot after the addition of calcium and a phospholipid reagent. It is used to evaluate the intrinsic clotting system.
lumen diameter at maximum dilation expressed as percent of baseline
lumen diameter at maximum constriction expressed as percent of baseline
Resistance to blood flow by blood vessels throughout the body, the degree to which the blood vessels impede the flow of blood, often calculated as SVR equal to the difference between mean arterial blood pressure(MAP) and central venous pressure(CVP) divided by cardiac output(CO).
Volume of blood in ventricle immediately before a contraction.
Volume of blood pumped from one ventricle of the heart with each beat, calculated by subtracting the volume of blood in the ventricle at the end of a beat (end-systolic volume) from the volume of blood just prior to the beat (end-diastolic volume).
Any quantification of a morphological or physiological parameter of one or more cells. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
Number of cells of muscular tissue in the heart in a specified sample size.
The enumeration, i.e. measurement of the total number, of the specialized liner cells that form an interface between the circulating blood and the rest of the vessel wall in a specified sample of blood vessel, any one of the network of muscular tubes that carry blood through the body.
Any measurement of components of the Electrical conduction system of the heart.The electrical conduction system of the heart transmits signals generated usually by the sinoatrial node to cause contraction of the heart muscle.
Interval between an R wave and the next R wave of successive heart beats, inverse of the heart rate.
Time between the beginning of the P wave to the beginning of the QRS complex, reflects the time the electrical impulse takes to travel from the sinus node through the AVE node and entering the ventricles, used as an estimate of AV node function.
The time between the J point ( the point at which the QRS complex finishes and the ST segment begins) to the end of the T wave.
An interval measured from the onset of the QRS wave complex to the offset of the T wave.
The depth of the wall of the aorta, the main trunk from which the arterial system proceeds.
The thickness or depth of the dorsal/posterior wall of the heart. The dorsal wall is the portion of the heart muscle which is closest to the spine and farthest from the chest wall of the organism.
The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
heart left ventricle dorsal wall thickness
Note that "left" in this context refers to the perspective of the organism, not that of the observer.
heart left ventricle posterior wall thickness
The thickness or depth of the dorsal/posterior wall of the right ventricle of the heart. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism.
heart right ventricle dorsal wall thickness
heart right ventricle posterior wall thickness
Any measurement of urine, the fluid waste product excreted by the kidneys, or its components.
Measure of the concentration of particles in the urine.
The magnitude of the P wave, the initial deflection of the cardiac cycle representing excitation of the atria as presented in an electrocardiogram.
The time from start to finish of the P wave , in the electrocardiograph illustrating the initial deflection of the cardiac cycle, representing the excitation of the atria.
The distance to the lowest part of the Q wave which shows the initial downward deflection related to the initial phase of depolarization of the ventricular myocardium and the depolarization of the interventricular septum as measured by electrocardiograph.
The time from start to finish of the Q wave which illustrates the initial downward deflection related to the initial phase of depolarization of the ventricular myocardium and the depolarization of the interventricular septum as measured by an electrocardiograph.
The time from start to finish of the QRS interval as calculated from a set of measurements taken from the beginning of the QRS complex to the end of the QRS complex representing the time it takes for ventricles to depolarize.
The magnitude of the portion of the electrocardiograph comprising the Q, R, and S waves which together represent ventricular depolarization.
QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds.
The magnitude of the R wave, which is the initial upward deflection of the QRS complex following the Q wave representing early depolarization of the ventricles as illustrated by an electrocardiograph.
The time from start to finish of the R wave, the initial upward deflection of the QRS complex following the Q wave which represents early depolarization of the ventricles as illustrated in and electrocardiograph.
The magnitude of the S wave, the downward deflection of the QRS complex following the R wave representing late depolarization of the ventricles as illustrated in an electrocardiograph.
The time from start to finish of the S wave which is the downward deflection of the QRS complex following the R wave representing late depolarization as illustrated by an electrocardiograph.
The magnitude of the T wave, the deflection following the QRS complex representing repolarization of the ventricles as illustrated by and electrocardiograph.
An interval measured from the onset of the P wave in one PQRST wave complex to the onset of the P wave in the following PQRST wave complex.
The difference between systolic and diastolic blood pressures, i.e. the difference between the maximal arterial pressure and minimal arterial pressure during the cardiac cycle.
The count of the rhythmic contractions and expansions of an artery due to the surge of blood from the beat of the heart.
Measurement of the physical form or structure of either the right or the left upper chamber of the heart that receives blood from the veins and forces it into a ventricle.
The weight of the left atrium of the heart, the upper chamber on the left which empties into the lower chamber. Weight is the heaviness or degree to which a body is drawn toward the earth by gravity.
The weight of the right atrium, the upper right chamber of the heart which empties into the lower right chamber, i.e. the right ventricle. Weight is the heaviness or degree to which a body is drawn to the earth by gravity.
A measure of the capacity of the left heart atrium, the upper left chamber which empties into the lower heart chamber.
A measure of the three dimensional capacity of the right atrium of the heart, the upper right chamber which empties into the lower right chamber, i.e. the right ventricle.
Any measurement of the physical form or structure of one or both ventricles of the heart, that is, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body.
heart ventricle morphological measurement
A calculated measurement in which the weight after removal from the body but without desiccation of both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a ratio, fraction or quotient, thus normalizing it to body weight.
both kidneys wet weight to body weight ratio
The amount of triglycerides in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Triglycerides are any of a group of lipids that are esters formed from one molecule of glycerol and three molecules of one or more fatty acids, are widespread in adipose tissue, and commonly circulate in the blood in the form of lipoproteins.
Measurement of the entire amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, without taking into account any association with other molecules such as lipoproteins, in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter.
blood differential white blood cell count
A calculated measurement in which the number of all granulocytes (regardless of type) in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
granulocyte count as percentage of total white blood cells
granulocyte count to total WBC count ratio
granulocyte count to total white blood cell count ratio
blood granulocyte count to total leukocyte count ratio
A calculated measurement in which the number of eosinophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. An eosinophil is a granular leukocyte having a nucleus with two lobes connected by a thread of chromatin, and cytoplasm containing coarse, round granules of uniform size that stain readily with eosin and other acid dyes.
eosinophil count as percentage of total white blood cells
eosinophil count to total WBC count ratio
blood eosinophil count to total leukocyte count ratio
A calculated measurement in which the number of neutrophil granulocytes is divided by the number of all white blood cells in a specified sample of peripheral venous blood, and the result presented as a ratio, fraction, quotient or percentage. A neutrophil is, or is in the process of becoming, a granular leucocyte having a nucleus with three to five lobes connected by threads of chromatin, cytoplasm containing very fine granules, and which is readily stainable with neutral dyes.
neutrophil count as percentage of total white blood cells
neutrophil count to total WBC count ratio
blood neutrophil count to total leukocyte count ratio
A calculated measurement in which the number of lymphocytes in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
lymphocyte count as percentage of total white blood cells
lymphocyte count to total WBC count ratio
blood lymphocyte count to total leukocyte count ratio
The complete or entire amount of bilirubin in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Bilirubin is the bile pigment produced by breakdown of heme and reduction of biliverdin.
The amount of carbonic acid dissolved in carbon dioxide and carbonate ion found in a specified volume of serum.
The amount of chloride ions found in a specified volume of serum.
An estimation of the volume of blood filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time based on serum creatinine level, wieght and age of organism and other factors.
blood glomerular filtration rate, Diet in Renal Disease Formula (MDRD)
A calculated measurement which estimates the glomerular filtration rate (GFR), that is, the volume of fluid filtered from the renal capillaries per unit time, based on the serum creatinine level and adjusted for gender.
blood glomerular filtration rate, Chronic Kidney Disease Epidemiology Collaboration formula (CKE-EPI)
blood glomerular filtration rate, May Quadratic formula
blood glomerular filtration rate, Schwartz formula
Amount of potassium ions in a specified volume of serum.
The amount of sodium ions in a specified volume of serum.
The amount of calcium ions in a specified volume of serum.
Blood pressure measured in the pulmonary artery during diastole, that is, during dilation or relaxation of the heart ventricles.
pulmonary arterial diastolic blood pressure
Blood pressure measured in the pulmonary artery during systole, that is, during contraction of the heart ventricles.
pulmonary arterial systolic blood pressure
A calculated value in which the weight of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and by extension to the size of the organism.
heart left ventricle weight as a percentage of body weight
heart left ventricle weight to body weight ratio
The difference in mean arterial blood pressure between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
The term "absolute change" refers to the subtraction of one value from another, as opposed to a dissimilarity of two values expressed as a ratio or as a percentage. In this context it is not intended to necessarily imply the difference expressed as an absolute value |n|, that is, the numeric value of the difference without regard to its sign.
absolute change in mean arterial blood pressure
Absolute difference in heart rate between two points in time or two conditions.
The number of glomeruli in all or part of a kidney. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
The amount of phosphorus, measured as inorganic phosphate, in a specified sample of serum.
Measurement of the amount of glucose, the monosaccharide sugar, C6H12O6, occurring widely in plant and animal tissues which is one of the three dietary monosaccharides that are absorbed directly into the bloodstream during digestion, is the end product of carbohydrate metabolism, and is the chief source of energy for living organisms, in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
The amount of albumin in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
The amount of ezymatic activity of glutamic-pyruvate transaminase enzyme, commonly known as alanine transaminase or alanine aminotransferase (ALT), enzyme in a specified sample of serum. ALT catalyzes the reversible transamination between alanine and 2-oxoglutarate to generate pyruvate and glutamate. Serum ALT level is used as an enzymatic marker for liver disease or damage.
serum alanine transaminase activity level
serum glutamic-pyruvate transaminase activity level
serum alanine aminotransferase activity level
Quantitation of the catalytic effect exerted by alkaline phosphatase (AP) in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. AP is an enzyme that catalyzes the cleavage of orthophosphate from orthophosphoric monoesters under alkaline conditions.
serum alkaline phosphatase activity level
The amount of enzymatic activity of glutamic-oxaloacetic transaminase enzyme, commonly known as aspartate transaminase or aspartate aminotransferase (AST), in a specified sample of serum. AST catalyzes the reversible transfer of an amine group from l-glutamic acid to oxaloacetic acid, forming alpha-ketoglutaric acid and l-aspartic acid. Serum AST level is used as an enzymatic marker for liver disease or damage.
serum aspartate transaminase activity level
serum glutamic-oxaloacetic transaminase activity level
serum aspartate aminotransferase activity level
Measurement of the pressure within the heart left ventricle at the end of systole, the period of contraction of the heart when the blood is forced from the ventricles into the pulmonary artery (right ventricle) and the aorta (left ventricle).
left ventricular end-systolic blood pressure
The pressure in the heart left ventricle at the end of diastole, the period when the heart is in a state of relaxation and expansion and the ventricles fill with blood.
left ventricular end-diastolic blood pressure
Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity.
absolute change in systolic blood pressure
Calculated measurement of a difference in diastolic blood pressure between two points or two conditions expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
absolute change in diastolic blood pressure
A calculated measurement in which the weight after removal from the body but without desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a ratio, fraction or quotient, thus normalizing it to body weight.
individual kidney wet weight to body weight ratio
single kidney wet weight to body weight ratio
A calculated measurement in which the weight after removal from the body but without desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, is divided by the total weight of the body and presented as a percentage, thus normalizing it to body weight.
individual kidney wet weight as percentage of body weight
single kidney wet weight as percentage of body weight
Any measurement of components of the periodic tightening and loosening of the heart muscle.
Measure of the time from the relaxation of the heart muscle to the beginning of the tightening of the heart muscle during contraction.
Measurement of the time from the beginning of heart muscle contraction to the maximum contracted state.
Pressure exerted by the heart muscle in its maximally contracted state.
Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function.
This is not the same term as the original "heart measurement". That term is now "heart morphological measurement".
A measurement made on a fluid flowing out of the heart.
The volume of a fluid flowing out of the heart.
The volume of a fluid flowing out of the heart during a specified amount of time.
The amount of an enzyme in a specified volume of fluid flowing out of the heart.
The amount of lactate dehydrogenase activity measured in a specified volume of fluid flowing out of the heart.
heart effluent lactate dehydrogenase activity level
Measurement of a lesion in an organ. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
A measurement of any lesion of the heart. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
Measurement of an area of necrotic tissue resulting from a reduction or obstruction of the oxygen supplied to that tissue.
Measurement of an area of necrotic tissue in the heart resulting from a reduction or obstruction of the oxygen supply.
Measurement of an area of necrotic tissue in the left ventricle of the heart resulting from a reduction or obstruction of the oxygen supply to the heart.
heart left ventricle infarction measurement
Measurement of the area, volume or weight of necrotic tissue resulting from a reduction or obstruction of the oxygen supplied to that tissue.
Measurement of the area, volume or weight of necrotic tissue in the heart resulting from a reduction or obstruction of the oxygen supply to the heart.
Measurement of the area, volume or weight of necrotic tissue in the heart left ventricle resulting from a reduction or obstruction of the oxygen supply to the heart.
calculated heart left ventricle infarction size
heart left ventricle infarction size as percentage of total heart left ventricle size
The heaviness of one or both ventricles of the heart, that is, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body, or the degree to which one or both ventricles of the heart are drawn toward the earth by gravity.
calculated heart left ventricle infarction area
calculated heart left ventricle infarction weight
heart left ventricle infarction weight as percentage of total heart left ventricle weight
The difference in body temperature between two different points in time or between two different conditions.
Measurement of the amount of resistance in a blood vessel to the flow of blood or other fluid through it.
Resistance to blood flow by blood vessels in the lung.
Measurement of vascular resistance in lung blood vessels calculated from other indirect measurements.
calculated pulmonary vascular resistance
calculated pulmonary vascular resistance normalized to body weight
Measurement made on the endothelial tissue or endothelial cells lining a blood vessel.
calculated blood vessel endothelium measurement
methylene blue metabolism-surface area product without auto-oxidation
methylene blue metabolism-surface area product after auto-oxidation
Ratio of the methylene blue metabolism-surface area product without auto-oxidation to the FAPGG metabolism-surface area product.
methylene blue to FAPGG metabolism-surface area product ratio
Any measurement of the energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
blood vessel contractile force measurement
Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
blood vessel maximum contractility measurement
maximum contractile force per wet weight of vessel
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to a drug or other chemical stimulus.
chemical response/sensitivity measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
calculated blood vessel contractile force measurement
A calculated value for the concentration of phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of PE is halfway between the baseline value and the highest achievable value of such PE-induced contractile energy.
phenylephrine half maximal effective concentration (EC50)
concentration of phenylephrine at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of PE is halfway between the baseline value and the highest achievable value of such PE-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
phenylephrine Log half maximal effective concentration (Log EC50)
logarithm of the concentration of phenylephrine at which the force of blood vessel contraction is half the maximum value (Log EC50)
Measurement of the reduction in force during dilation of a blood vessel via calculations from direct measurements rather than expressing the direct measurements themselves.
calculated blood vessel dilation force reduction measurement
A calculated value for the concentration of acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of ACh is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during ACh-induced relaxation of the vessel wall (i.e. the maximum effect of Ach which is the minimum contractile energy).
acetylcholine half maximal effective concentration (EC50)
concentration of acetylcholine at which the reduction in force during dilation of a blood vessel is half the maximum value (EC50)
A calculated value for logarithm of the concentration of acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of ACh is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during ACh-induced relaxation of the vessel wall (i.e. the maximum effect of Ach which is the minimum contractile energy). The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
acetylcholine Log half maximal effective concentration (Log EC50)
logarithm of the concentration of acetylcholine at which the reduction in force during dilation of a blood vessel is half the maximum value (Log EC50)
A calculated value for the concentration of sodium nitroprusside (SNP), the red-colored inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of SNP is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during SNP-induced relaxation of the vessel wall (i.e. the maximum effect of SNP which is the minimum contractile energy).
sodium nitroprusside half maximal effective concentration (EC50)
concentration of sodium nitroprusside at which the reduction in force during dilation of a blood vessel is half the maximum value (EC50)
A calculated value for logarithm of the concentration of sodium nitroprusside (SNP), the red-coloured inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator, at which the energy exerted during the active expansion in the diameter of a blood vessel in response to the application of SNP is halfway between the highest value, that is the force at greatest constriction (often measured in a pre-constricted blood vessel), and the lowest achievable value of such contractile energy during SNP-induced relaxation of the vessel wall (i.e. the maximum effect of SNP which is the minimum contractile energy).
sodium nitroprusside Log half maximal effective concentration (Log EC50)
logarithm of the concentration of sodium nitroprusside at which the reduction in force during dilation of a blood vessel is half the maximum value (Log EC50)
maximum contractile force per wet weight of aorta
Measurement of the reduction in force during blood vessel dilation.
blood vessel dilation force reduction measurement
blood vessel dilation expressed as percent of force at maximum constriction
acetylcholine-induced blood vessel dilation expressed as percent of phenylephrine-induced vasoconstriction
acetylcholine-induced blood vessel dilation expressed as percent of force at maximum constriction
sodium nitroprusside-induced blood vessel dilation expressed as percent of phenylephrine-induced vasoconstriction
sodium nitroprusside-induced blood vessel dilation expressed as percent of force at maximum constriction
hypoxia-induced blood vessel dilation expressed as percent of force at maximum constriction
slope measurement of phenylephrine-induced contraction
slope measurement of drug-induced contraction
slope measurement of chemical-induced contraction
fast-slope measurement of phenylephrine-induced contraction
fast-slope measurement of drug-induced contraction
fast-slope measurement of chemical-induced contraction
slow-slope measurement of phenylephrine-induced contraction
slow-slope measurement of drug-induced contraction
slow-slope measurement of chemical-induced contraction
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to acetylcholine (ACh), the ester of acetic acid and choline with chemical formula CH3C=OO(CH2)2-N(+)-(CH3)3 and IUPAC name 2-acetoxy-N,N,N-trimethylethanaminium, which acts as a neurotransmitter.
acetylcholine response/sensitivity measurement
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to phenylephrine (PE), the phenylethanolamine with IUPAC name (R)-3-[-1-hydroxy-2-(methylamino)ethyl]phenol and formula C9H13NO2 that acts as a selective alpha1-adrenergic receptor agonist, decongestant and vasoconstrictor.
phenylephrine response/sensitivity measurement
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to sodium nitroprusside (SNP), the red-colored inorganic salt with the formula Na2[Fe(CN)5NO]-2H2O used as a potent vasodilator.
sodium nitroprusside response/sensitivity measurement
Calculation of a difference between representations of blood pressure in a treated versus untreated state or over time, after the original values have been normalized or adjusted by a mathematical process or computation. Blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood.
A calculated measurement of the difference in developed blood pressure between a treated state and a control state. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
A calculated measurement of the difference in developed blood pressure between a treated state and a control state, expressed as a percentage. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
percent change in developed blood pressure
Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions.
The relative difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time or two conditions expressed as a percentage.
percent change in systolic blood pressure
percent change in arterial blood flow rate
absolute change in arterial blood flow rate
A calculated measurement of the difference in developed pressure measured in the heart left ventricle between a treated state and a control state, expressed as a percentage. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
percent change in left ventricular developed pressure
A calculated measurement of the difference in developed pressure measured in the heart left ventricle between a treated state and a control state. Developed pressure is systolic minus diastolic pressure when measured in an isolated organ or vessel under conditions where perfusion pressure or flow can be controlled.
change in left ventricular developed pressure
Difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions.
change in left ventricular systolic blood pressure
The relative difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions expressed as a percentage.
percent change in left ventricular systolic blood pressure
The activity level of LDH in effluent expressed relative to the weight of the heart; calculated as LDH activity divided by heart wet weight.
heart effluent lactate dehydrogenase activity level normalized to heart weight
The average blood pressure within the pulmonary artery over a specified period of time, or technically over a complete cycle of one heartbeat.
Measurement of blood pressure in the pulmonary artery.
pulmonary artery (PA) blood pressure measurement
pulmonary arterial blood pressure measurement
Measurement of an organ lesion which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells.
Measurement of an organ lesion which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc.
Measurement of a heart lesion which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc.
Measurement of a lesion of the heart which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells.
Any measurement, morphological or physiological, involving the kidney or any part thereof.
Renal blood flow (RBF) is the volume of blood delivered to or exiting from the kidneys per unit time.
Arterial renal blood flow (RBFa) is the volume of blood delivered to the kidneys per unit time via the renal arteries.
Venous renal blood flow (RBFv) is the volume of blood exiting from the kidneys per unit time via the renal veins.
A calculated value in which the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is divided by the total weight of the body and presented as a ratio thus normalizing it to body weight.
heart right ventricle weight to body weight ratio
A calculated value in which the weight of the right ventricle, the lower chamber of the right side of the heart, which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is presented as percentage of the total weight of the body thus normalizing it to body weight.
heart right ventricle weight as a percentage of body weight
Any measurement of the physical form or structure of the left ventricle of the heart. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
Note, "left" in this context refers to the perspective of the organism, not that of the nobserver.
heart left ventricle morphological measurement
Any measurement of the physical form or structure of the right ventricle of the heart. The right ventricle is the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
heart right ventricle morphological measurement
Measurement of a localized pathological change in structure of a blood vessel due to injury or disease; especially one that is circumscribed and well defined.
A measurement of blood vessel diameter which has been normalized or adjusted by a mathematical process or computation.
calculated blood vessel diameter measurement
A measurement of the depth of the wall of a blood vessel which has been normalized or adjusted by a mathematical process or computation.
calculated blood vessel wall thickness measurement
A measurement of the depth of the wall of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
A measurement of the depth of the wall of an artery which has been normalized or adjusted by a mathematical process or computation. An artery is one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
calculated artery wall thickness measurement
The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at the inner surface of the blood vessel wall.
The length of a line which crosses a transverse view of a blood vessel, passing through its center and ending on either side at the outer surface of the blood vessel wall.
The length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall.
The length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall.
Measurement of the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at either the inner surface or outer surface of the blood vessel wall, which has been normalized or adjusted by a mathematical process or computation.
Any measurement of one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
Measurement of any localized pathological change in structure of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues, due to injury or disease; especially one that is circumscribed and well defined.
Measurement which has been normalized or adjusted by a mathematical process or computation of any localized pathological change in structure of an artery due to injury or disease; especially one that is circumscribed and well defined.
Measurement which has been normalized or adjusted by a mathematical process or computation of any localized pathological change in structure of a blood vessel due to injury or disease; especially one that is circumscribed and well defined.
calculated blood vessel lesion measurement
A calculated measurement in which the ratio of the wall thickness (WT) of a blood vessel is divided by the inner diameter (ID) of that vessel at that location, and the result presented as a ratio, fraction, quotient or percentage, for example, WT/ID x 100. This measurement is often used to assess stenosis, a pathological narrowing of a blood vessel.
blood vessel wall thickness as percentage of blood vessel lumen diameter
blood vessel wall thickness as percentage of blood vessel inner diameter
blood vessel wall thickness to blood vessel inner diameter ratio
Ratio of the wall thickness (WT) of an artery to inner diameter (ID) of that artery at that location, usually expressed as a percentage, i.e. WT/ID x 100, but could also be expressed as a ratio, fraction or quotient. This measurement can be used to assess stenosis, a pathological narrowing of a blood vessel.
artery wall thickness as percentage of artery inner diameter
artery wall thickness as percentage of artery lumen diameter
artery wall thickness to artery inner diameter ratio
A measurement of the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. An artery is a blood vessel that carries blood away from the heart.
calculated artery inner diameter measurement
Any measurement of components of the periodic tightening and loosening of the muscles of a ventricle of the heart.
The diameter across the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed, and usually corresponds to its largest diameter.
left ventricular end-diastolic dimension
heart left ventricular end-diastolic diameter
The diameter across the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted, and usually corresponds to its smallest diameter.
heart left ventricle end-systolic diameter
A measurement of the physical form or structure of the left ventricle of the heart which has been normalized or adjusted by a mathematical process or computation. The heart left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated heart left ventricle morphological measurement
A calculated measurement corresponding to the ratio or percent reduction in left ventricular diameter between end-diastole and end-systole. Can be calculated as the left ventricle end-diastolic diameter (LVDd) minus the left ventricle end-systolic diameter (LVSd) divided by the left ventricle end-diastolic diameter (LVDd) with the quotient multiplied by 100, i.e. FS = [(LVDd-LVSd)/LVDd] x 100.
heart left ventricle fractional shortening
The thickness or depth of the ventral/anterior wall of the left ventricle of the heart. The ventral/anterior wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism.
heart left ventricle ventral wall thickness
heart left ventricle anterior wall thickness
The thickness or depth of the septal wall of the heart ventricles. The septal wall is the portion of the heart left ventricle ventral/anterior wall and right ventricle dorsal/posterior wall which is shared between the ventricles.
A calculated measurement of left ventricular geometry and is calculated by dividing the end-diastolic diameter into 2x the posterior wall thickness, 2x the septal wall thickness or the sum of the posterior and septal wall thicknesses. It represents a measure of the wall thickness normalized to the size of the ventricle lumen.
heart left ventricle relative wall thickness
A calculated measurement of left ventricular geometry and is calculated by dividing the end-diastolic diameter into 2x the posterior wall thickness at end-diastole, 2x the septal wall thickness at end-diastole or the sum of the posterior and septal wall thicknesses at end-diastole. It represents a measure of the wall thickness normalized to the size of the ventricle lumen.
heart left ventricle end-diastolic relative wall thickness
The thickness or depth of the ventral/anterior wall of the heart. The ventral wall is the portion of the heart muscle which is farthest from the spine and closest to the chest wall of the organism.
calculated heart wall thickness measurement
The extent of shortening of the minor internal circumference (at the midpoint of the long axis) between end-diastole and end-systole, divided by the time required for shortening.
mean circumferential fiber shortening rate
mean velocity of circumferential fiber shortening
The thickness or depth of the ventral/anterior wall of the right ventricle of the heart. The ventral wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism.
heart right ventricle ventral wall thickness
heart right ventricle anterior wall thickness
Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis, and directly in contact with the surface of the kidney, i.e. the renal capsule. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
count of superficial glomeruli directly contacting the kidney surface
Count of the number of glomeruli located in the superficial layer of the renal cortex, the cortex corticis but without any direct contact with the surface of the kidney, i.e. the renal capsule. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
count of superficial glomeruli not directly contacting the kidney surface
Measurement of any change or difference in the diastolic blood pressure between two points or two conditions. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
The relative difference in the diastolic blood pressure between two points or two conditions, expressed as a percentage. The diastolic pressure is the minimum arterial pressure within the cardiac cycle, usually at the point at which the heart is in a state of relaxation and expansion. This is the time when the ventricles fill with blood.
percent change in diastolic blood pressure
Calculated measurement of a difference in the pressure within the heart left ventricle at the point of maximal contraction, when the blood is forced from the left ventricle into the aorta, between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in left ventricular systolic blood pressure
Temperature measured at the surface of or within the head of an experimental subject. Because the temperature of the head/brain can influence neurological measurements, head temperature is or can be considered to be distinct from core body temperature.
The temperature of the internal tissues and organs of the body.
A measurement which has been normalized or adjusted by a mathematical process or computation of the weight of the left ventricle of the heart, that is, its the heaviness or degree to which it is drawn toward the earth by gravity. The heart left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated heart right ventricle morphological measurement
The length of a line which crosses a transverse view of a cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The cerebral arteries are those which supply blood to the brain, more specifically, to the cerebrum.
The length of a line which crosses a transverse view of an anterior cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The anterior cerebral artery (ACA) is one of a pair of arteries that supply oxygenated blood to the most medial portions of the frontal lobes and superior medial parietal lobes of the brain.
The length of a line which crosses a transverse view of a middle cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The middle cerebral arteries are the largest of the cerebral arteries and supply blood to the lateral cerebral cortex, anterior temporal lobes and insular cortices of the brain.
The length of a line which crosses a transverse view of a posterior cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall. The posterior cerebral artery (PCA) is one of a pair of blood vessels that supply blood to the posterior aspect, i.e. the occipital lobe, of the brain.
posterior cerebral artery lumen diameter
posterior cerebral artery inner diameter
Measurement of a lesion in kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
Measurement of a lesion in the kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, which is not neoplastic in origin. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. Examples of non-tumorous lesions would include wounds, sores, ulcers, infarctions, etc.
Measurement of a lesion in the kidney, he organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes, which is or has the potential to become a tumor, that is, a neoplasm or new growth of tissue in which cell multiplication is more or less uncontrolled and progressive. Tumorous lesions include tumors, preneoplastic lesions, and hyperplastic lesions composed of histologically normal cells.
Any measurement of lesions resulting from fibrosis, scarring or hyaline deposits within a kidney glomerulus, a tuft of capillaries situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney, that filters waste products from the blood and thus initiates urine formation.
renal glomerulosclerotic lesion measurement
kidney glomerulosclerotic lesion measurement
A measurement of lesions resulting from fibrosis, scarring or hyaline deposits within one or more kidney glomeruli which has been normalized, adjusted or derived by a mathematical process or computation.
calculated kidney glomerulosclerosis measurement
calculated renal glomerulosclerosis measurement
calculated renal glomerulosclerotic lesion measurement
calculated kidney glomerulosclerotic lesion measurement
A measurement of lesions resulting from fibrosis, scarring or hyaline deposits within kidney glomeruli which is derived from a combination of multiple measurements and/or objective or subjective severity scores according to a specified formula or set of criteria.
Any measurement, morphological or physiological of a muscle or a group of muscles. Muscles are organs or tissues composed of bundles of fibers that have the power to contract and hence to produce movement.
Measurement of the physical form or structure of one or more glomeruli in the kidney. Glomeruli are the tufts of capillaries each situated within a Bowman's capsule at the end of a renal tubule in the vertebrate kidney that filter waste products from the blood and thus initiate urine formation.
kidney glomerulus morphological measurement
The length of a straight line passing through the center of a kidney glomerulus and connecting opposite points on its circumference.
A measurement of the volume of blood delivered to or exiting from the kidneys per unit time, which has been normalized, adjusted or derived by a mathematical process or computation.
The difference in the volume of blood delivered to or exiting from the kidneys per unit time between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in renal blood flow rate
The number of kidney glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits, or the number of such lesions in a specified sample.
Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins (complex high molecular weight organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) or peptides (low molecular weight compounds composed of at least two amino acids joined by peptide linkages) in kidney.
kidney tissue protein/peptide composition measurement
kidney protein/peptide composition measurement
Any measurement, morphological or physiological of the outer part of the kidney, composed mainly of glomeruli and convoluted tubules.
Any measurement, morphological or physiological, of the renal medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in kidney medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood.
Any measurement involving the amount, composition or type of protein, the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages, in renal cortex, the outer part of the kidney, composed mainly of glomeruli and convoluted tubules.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the composition, that is, the absolute amount, relative amount or type, of protein (the complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) in kidney.
calculated renal protein composition measurement
calculated kidney protein composition measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation involving the amount, composition or type of protein in the kidney cortex, the outer part of the kidney, composed mainly of glomeruli and convoluted tubules.
calculated kidney cortex protein composition measurement
calculated renal cortex protein composition measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation involving the amount, composition or type of protein in the renal medulla, the innermost part of the kidney which contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood.
calculated kidney medulla protein composition measurement
calculated renal medulla protein composition measurement
A calculated value in which the amount of TRPV4 protein in a specified sample of kidney is divided by the amount of beta-actin protein in the same or a corresponding sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level.
renal TRPV4 protein level to beta-actin protein level ratio
kidney TRPV4 protein level to beta-actin protein level ratio
A calculated value in which the amount of TRPV4 protein in a specified sample of renal cortex is divided by the amount of beta-actin protein in the same or a corresponding sample of renal cortex and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level.
kidney cortex TRPV4 protein level to beta-actin protein level ratio
renal cortex TRPV4 protein level to beta-actin protein level ratio
A calculated value in which the amount of TRPV4 protein in a specified sample of renal medulla is divided by the amount of beta-actin protein in the same or a corresponding sample of renal medulla and presented as a ratio, fraction or quotient, thus normalizing it to the beta-actin protein level.
kidney medulla TRPV4 protein level to beta-actin protein level ratio
renal medulla TRPV4 protein level to beta-actin protein level ratio
The length of a line which crosses a transverse view of a cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. The cerebral arteries are those which supply blood to the brain, more specifically, to the cerebrum.
calculated cerebral artery inner diameter measurement
The length of a line which crosses a transverse view of a middle cerebral artery, passing through its center and ending on either side at the inner surface of the blood vessel wall, after that measurement has been normalized or adjusted by a mathematical process or computation. The middle cerebral arteries are the largest of the cerebral arteries and supply blood to the lateral cerebral cortex, anterior temporal lobes and insular cortices of the brain.
calculated middle cerebral artery inner diameter measurement
A calculated measurement of the relative difference in the middle cerebral artery inner diameter between a treated state and a control state or between two points in time, expressed as a percentage.
percent change in middle cerebral artery inner diameter
A measurement of the extent of a two-dimensional plane through the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed, and usually corresponds to its largest diameter.
A measurement of the extent of a two-dimensional plane through the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted, and usually corresponds to its smallest diameter.
A calculated value in which the weight of the heart, the chambered, muscular organ that maintains the circulation of the blood, is divided by the length of the tibia, the inner and larger bone of the lower leg or hindlimb, and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the length of the leg and, by extension, to the length of the body.
A calculated value in which the total weight after removal from the body but without desiccation of both kidneys is divided by the length of the tibia, the inner and larger bone of the lower leg or hindlimb, and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the length of the leg and, by extension, to the length of the body.
both kidneys wet weight to tibia length ratio
A calculated measurement of the ratio between the change in mean arterial blood pressure and the concentration of sodium infused directly into the ventricle(s) of the brain; calculated as the slope of the curve of mean arterial blood pressure versus intracerebroventricular-infused sodium concentration.
change in mean arterial blood pressure to change in intracerebroventricular sodium concentration ratio
A calculated measurement of the ratio between the change in heart rate and the concentration of sodium infused directly into the ventricle(s) of the brain; calculated as the slope of the curve of heart rate versus intracerebroventricular-infused sodium concentration.
change in heart rate to change in intracerebroventricular sodium concentration ratio
A value calculated by dividing the proportionate change in renal blood flow (RBF) by the proportionate change in renal perfusion pressure (RPP), i.e. (RBF2 - RBF1)/RBF1 divided by (RPP2 - RPP1)/RPP1.
ratio of renal blood flow change to renal perfusion pressure change
ratio of change in renal blood flow to change in renal perfusion pressure
Any measurement of a lesion in the kidney characterized by an abnormal proliferation of fibrous connective tissue. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
Any measurement of the physical dimensions, proportions, magnitude, or extent of a lesion in the kidney characterized by an abnormal proliferation of fibrous connective tissue. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined.
A measurement of the extent of a two-dimensional surface of or plane through a single kidney fibrotic lesion, or a measurement of the total area occupied by fibrotic lesions in a cross-section of the kidney.
A measurement of the extent of a two-dimensional surface of or plane through a single kidney fibrotic lesion, or a measurement of the total area occupied by fibrotic lesions in a cross-section of the kidney, when that value has been normalized, adjusted or derived by a mathematical process or computation.
calculated kidney fibrotic lesion area measurement
A calculated value in which the extent of the two-dimensional surface occupied by fibrotic lesions is divided by the total extent of the two-dimensional surface of the kidney and presented as a ratio, fraction, quotient or percentage, thus normalizing it to the size of the kidney.
kidney fibrotic lesion area to total kidney area ratio
A calculated value in which the number of glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits is divided by the total number of glomeruli in a specified sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli.
sclerotic glomeruli to total glomeruli ratio
kidney glomerulosclerotic lesion count to total glomeruli count ratio
kidney sclerotic glomeruli count to total glomeruli count ratio
The combined weight of both ventricles of the heart, that is, their heaviness or the degree to which they are drawn toward the earth by gravity. The ventricles are the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body.
A measurement of the combined weight of both heart ventricles that has been normalized, adjusted or derived by a mathematical process or computation.
A calculated value in which the combined weight of both the left and right ventricles, the lower chambers of the heart that pump blood away from the heart either to the lungs to be oxygenated or, once oxygenated, to the rest of the body, is presented as percentage of the total weight of the body thus normalizing it to body weight.
total heart ventricle weight as a percentage of body weight
Any measurement of the cavity or channel within an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
A measurement of the two-dimensional extent of the enclosed cavity or channel in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
Any measurement of the fibrous and muscular structure of one of the large blood vessels carrying blood in a direction away from the heart to the tissues. The wall of an artery is composed of three layers: the tunica intima, the inner coat; the tunica media, the middle coat; and the tunica adventitia, the outer coat.
Any measurement of the tunica media, or middle coat, of the wall of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues.
A direct measurement of two dimensional extent of the tunica media, the middle coat of the arterial wall, in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. The total area of the tunica media gives an indication of the thickness of the arterial wall.
A calculated measurement of the average width of the tunica media, the middle coat of the arterial wall. Can be calculated using the media area and the length of the internal elastic lamina.
A measurement of the extent of a two-dimensional surface of or plane through a single hyperplastic lesion of the tunica intima, that is, the inner coat of the arterial wall, or a measurement of the total area occupied by hyperplastic lesions of the tunica intima in a cross-section of an artery, one of the large blood vessels carrying blood in a direction away from the heart to the tissues. A hyperplastic lesion is a localized pathological increase in the number of cells of an organ or tissue resulting from an increased rate of cellular division due to injury or disease; especially one that is circumscribed and well defined.
artery neointimal hyperplastic lesion area
Any measurement of one or more hyperplastic lesions of the arterial tunica intima which has been normalized, adjusted or derived by a mathematical process.
calculated arterial intima hyperplasia area
calculated artery neointimal hyperplastic lesion area
A calculated measurement in which the area of the arterial tunica intima occupied by one or more hyperplastic lesions is divided by the total cross-sectional area of the artery wall and presented as a ratio, fraction, quotient or percentage.
ratio of neointimal hyperplasia area to total wall area of artery
artery neointimal hyperplastic lesion area to total wall area ratio
The area of the arterial lumen remaining when the luminal space is restricted by a pathological process, e.g. hyperplasia.
The weight after desiccation of both kidneys, the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The weight after desiccation of a single kidney, one of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
Any measurement of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
Any quantification of the physical form or structure of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
The speed at which the blood flows through the circulatory system or through a specific segment of a vein or artery, expressed as distance per unit of time.
The speed at which the blood flows through an artery, expressed as distance per unit of time.
The speed at which the blood flows through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds, expressed as distance per unit of time.
Any measurement of the movement of blood through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds.
The volume of blood flowing through the aorta, the great artery arising from the left ventricle from which the systemic arterial system proceeds, per unit of time.
The maximum speed at which the blood flows through the aorta during the cardiac cycle, expressed as distance per unit of time.
The length of time in the cardiac cycle between the closing of the aortic and pulmonic/pulmonary semilunar valves and opening of the atrioventricular (AV) valves marking the beginning of ventricular filling. Used as an indicator of diastolic dysfunction.
Measurement of the physical form or structure of the left upper chamber of the heart that receives blood from the veins and forces it into the left ventricle.
heart left atrium morphological measurement
Measurement of the physical form or structure of the right upper chamber of the heart that receives blood from the veins and forces it into the right ventricle.
heart right atrium morphological measurement
The distance between two specified opposite points on the periphery of the left atrium of the heart at the end of systole, that is, when the left ventricle is maximally contracted, and usually corresponds to the left atrium's largest diameter.
The distance between two specified opposite points on the periphery of the left atrium of the heart at the end of diastole, that is, when the left ventricle is maximally dilated, and usually corresponds to the left atrium's smallest diameter.
heart left atrium end-diastolic diameter
A measurement of the physical form or structure of the left atrium, the left upper chamber of the heart that receives blood from the veins and forces it into the left ventricle, which has been normalized, adjusted or derived by a mathematical process or computation.
calculated heart left atrium morphological measurement
A calculated measurement corresponding to the ratio or percent reduction in left atrial diameter between end-systole and end-diastole. It is calculated as the left atrium end-systolic diameter (LADs) minus the left atrium end-diastolic diameter (LADd) divided by the left atrium end-systolic diameter (LADs).
Measurement of the number of white blood cells, including lymphocytes and monocytes, with a single round or oval nucleus in a specified volume of blood.
A measurement of the movement of blood through one or more vessels or organs in the body which has been normalized, adjusted or derived by a mathematical process or computation.
Any measurement of the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall.
The volume of fluid flowing into, out of or through the blood vessels and microvasculature of the myocardium, the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall, per unit time.
Measurement of the amount of radioactive or other tracer is lost from the myocardium, the thick contractile middle layer of uniquely constructed and arranged muscle cells that forms the bulk of the heart wall, per unit time.
A value resulting from the quantification of a morphological or physiological parameter of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body.
Any quantification of the physical form or structure of the layered tissue which encloses and constitutes the structural component of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
Measurement of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
Measurement of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of vascular smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of blood vessels, the network of muscular tubes that carry blood through the body.
calculated vascular smooth muscle cell count
calculated blood vessel smooth muscle cell count
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds.
calculated aortic smooth muscle cell count
calculated aorta smooth muscle cell count
A calculated value in which the total number of cells, membrane-enclosed protoplasmic masses constituting the smallest structural unit of an organism that is capable of independent functioning, in a specified sample of the aorta smooth muscle, the contractile soft tissue having fine myofibrils but lacking transverse striations composing the majority of the wall of the great artery arising from the left ventricle from which the systemic arterial system proceeds, is divided by the length of the smooth muscle section in which that number is determined.
aortic smooth muscle cell count per unit vessel length
aorta smooth muscle cell count per unit vessel length
The amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body.
heart left ventricle deoxyribonucleic acid content
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated heart left ventricle DNA content
calculated heart left ventricle deoxyribonucleic acid content
A calculated measurement in which amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart left ventricle, the lower chamber of the left side of the heart (from the perspective of the organism rather than the observer), which pumps oxygenated blood out through the aorta to all the tissues of the body, is divided by the total weight or heaviness of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
heart LV DNA content to body weight ratio
heart left ventricle DNA content to BW ratio
heart left ventricle DNA content to body weight ratio
heart left ventricle deoxyribonucleic acid content to body weight ratio
The amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
heart right ventricle deoxyribonucleic acid content
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
calculated heart right ventricle DNA content
calculated heart right ventricle deoxyribonucleic acid content
A calculated measurement in which amount of deoxyribonucleic acid (DNA), the molecule composed of the sugar deoxyribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or thymine, extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung, is divided by the total weight or heaviness of the body and presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
heart RV DNA content to body weight ratio
heart right ventricle DNA content to BW ratio
heart right ventricle DNA content to body weight ratio
heart right ventricle deoxyribonucleic acid content to body weight ratio
Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel which does not involve the action of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect.
blood vessel receptor-independent maximum contractility
receptor-independent blood vessel maximum contractile force
Measurement of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel which is instigated by the activation of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect.
blood vessel receptor-dependent maximum contractility
receptor-dependent blood vessel maximum contractile force
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from contraction of the muscular wall of the vessel.
calculated blood vessel maximum contractile force measurement
A calculated measurement in which the receptor-dependent maximum contractile force of a blood vessel is divided by the receptor-independent maximum contractile force of a blood vessel and presented as a ratio, fraction, quotient or percentage. The maximum contractile force of a blood vessel is the highest achievable amount of energy produced by the active reduction in the diameter of a blood vessel, any one of the network of muscular tubes that carry blood through the body, resulting from a contraction of the muscular wall of the vessel. Receptor-dependent refers to such a contraction which is instigated by the activation of a receptor, a molecule on the surface or within a cell that recognizes and binds with specific molecules, producing a specific effect. Receptor-independent denotes such a contraction that does not involve the action of a receptor.
blood vessel receptor-dependent contractility to receptor-independent contractility ratio
receptor-dependent blood vessel maximum contractile force exoressed as a percentage of receptor-independent blood vessel maximum contractile force
receptor-dependent blood vessel maximum contractile force to receptor-independent blood vessel maximum contractile force ratio
A calculated value for the concentration of angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of AngII is halfway between the baseline value and the highest achievable value of such AngII-induced contractile energy.
Ang2 half maximal effective concentration
AngII half maximal effective concentration
angiotensin 2 half maximal effective concentration
angiotensin II half maximal effective concentration (EC50)
concentration of angiotensin II at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion, at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of AngII is halfway between the baseline value and the highest achievable value of such AngII-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
Ang2 Log half maximal effective concentration
AngII Log half maximal effective concentration
angiotensin 2 Log half maximal effective concentration
angiotensin II Log half maximal effective concentration (EC50)
logarithm of the concentration of angiotensin II at which the force of blood vessel contraction is half the maximum value (Log EC50)
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to angiotensin II (AngII), the octapeptide, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, that is derived from angiotensinogen and acts as a powerful vasopressor and stimulator of aldosterone secretion.
angiotensin II response/sensitivity measurement
The difference in left ventricular diastolic blood pressure between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in left ventricular diastolic blood pressure
Any measurement of the blood pressure in the left ventricle of the heart which has been normalized or adjusted by a mathematical process or computation. Left ventricular blood pressure is the pressure, or force per area, exerted by circulating blood against the walls of the left ventricle, the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
calculated left ventricular blood pressure
A calculated measurement that is used as an index to characterize the contractile ability of the heart. It is believed that maximum dP/dt is a reasonable index of the initial velocity of myocardial contraction.
rate of maximum positive change in left ventricular blood pressure
maximum rate of positive change in left ventricular blood pressure
A calculated hemodynamic measurement related to the ability of the heart left ventricle to relax. The point at which the negative pressure fall velocity reaches its peak is taken to be the onset of isovolumic relaxation of the left ventricle.
rate of maximum negative change in left ventricular blood pressure
maximum rate of negative change in left ventricular blood pressure
A calculated hemodynamic value related to the ability of the heart left ventricle to relax. Tau is calculated as an exponential function of the change in intraventricular pressure during the diastolic isovolumic left ventricular pressure decrease.
time constant of left ventricular relaxation
time constant of left ventricular pressure decay
The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart at the end of systole, that is, when the heart muscle is maximally contracted. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism. The left ventricle is the lower chamber of the left side of the heart, which pumps oxygenated blood out through the aorta to all the tissues of the body.
end-systolic heart left ventricle posterior wall thickness
heart left ventricle end-systolic posterior wall thickness
Any quantification of the amounts or proportions of proteins, lipids, minerals, nutrients, gases, or other substances ina specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
kidney molecular composition measurement
Quanitification of one or more lipids in a specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes. A lipid is any of a structurally diverse group of organic compounds that are insoluble in water but soluble innonpolar solvents that, among other biological functions, serve as a source of fuel and are an important constituent of cell structure.
The amount of 20-hydroxyeicosatetraenoic acid, a vasoconstrictor that consists of arachidonic acid (a C20, polyunsaturated fatty acid having four (Z)-double bonds at positions 5, 8, 11 and 14) bearing a hydroxy substituent at position 20, in a specified sample of kidney tissue, that is, tissue from one or both of the paired organs which function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
kidney 20-hydroxyeicosatetraenoic acid level
The number of immune cells in a specified sample. An immune cell is any cell involved in the immune system, a complex set of interconnected and interdependent cellular and molecular components having the primary functions of distinguishing self from not self and of defense against foreign organisms or substances. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning.
The difference in the pulse pressure of an individual between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. Pulse pressure is the difference between systolic and diastolic blood pressures, i.e. the difference between the maximal arterial pressure and minimal arterial pressure during the cardiac cycle.
A calculated measurement of the degree to which a change in the size of the remaining kidney after surgical removal of the other kidney can be attributed to compensatory growth, calculated as the ratio of the normalized weight of a single kidney at the time of surgical removal divided by the similarly normalized weight of the single remaining kidney at a specified period of time after removal. The normalized kidney weight is the weight of the kidney corrected for body weight using an empirically determined allometric scaling factor (i.e., an exponential factor which adjusts for the normal increase in kidney weight due to normal growth and development of the individual). Compensatory growth is the phenomenon in which the impaired function of one organ in a paired organ system or of part of an organ in a single organ system is followed by enlargement of the surviving organ or tissue so that functional capacity is maintained. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated measurement in which the difference in the volume of blood delivered to and/or exiting from the kidneys per unit time between two points in time or two conditions is divided by the weight (heaviness or degree to which a body is drawn toward the earth by gravity) of one or both kidneys, and presented as a ratio, fraction, quotient or percentage. The kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
ratio of change in renal blood flow rate to kidney weight
A measurement of the degree to which the blood vessels of the kidneys impede the flow of blood through them. Renal vascular resistance is calculated as the renal blood flow rate divided by the mean arterial pressure.
A measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
The difference in renal vascular resistance between two points in time or two conditions expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity. Renal vascular resistance is the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
absolute change in kidney vascular resistance
absolute change in renal vascular resistance
A calculated measurement of the slope, the ratio of vertical change to horizontal change, of the line of a graph designating the change in renal vascular resistance in response to a drug or other condition which causes constriction or reduction of the interior diameter of blood vessels. Renal vascular resistance is the degree to which the blood vessels of the kidneys impede the flow of blood through them. Blood vessels are the network of muscular tubes that carry blood throughout the body. Blood is the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. Kidney is the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
slope of constriction-induced renal vascular resistance curve
slope of contraction-induced kidney vascular resistance curve
slope of contraction-induced renal vascular resistance curve
The enumeration, i.e. measurement of the total number, of defects or lesions of the internal elastic lamina which are not hyperplastic or neoplastic in origin in a specified sample of artery. A lesion is a localized pathological change in structure of an organ or tissue due to injury or disease; especially one that is circumscribed and well defined. The internal elastic lamina (IEL) is a fenestrated (perforated) layer of elastic tissue, i.e., one having the property of returning to the original shape after being distorted, that is the outermost part of the intima (innermost layer) of an artery. The IEL is the elastic layer that is situated between the tunica intima (inner layers) and tunica media (middle layers) of artery walls. An artery is any one of the branching system of muscular, elastic blood vessels that carry blood away from the heart.
artery internal elastic lamina defect count
artery internal elastic lamina non-tumorous lesion count
The amount of plasma that perfuses the kidneys per unit time. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated measurement in which the effective renal plasma flow rate (eRPF) is divided by weight (i.e. the heaviness or the degree to which an object is drawn toward the earth by gravity) of both kidneys and presented as a ratio, fraction, quotient or percentage. The eRPF is the amount of plasma that perfuses the renal tubules per unit time, derived by measurement of the clearance rate of a non-metabolizable solute such as para-aminohippurate (PAH). Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
effective renal plasma flow rate to both kidney weight ratio
ratio of the effective renal plasma flow to the weight of both kidneys
A calculated measurement of the amount of plasma that perfuses the renal tubules per unit time, derived by measurement of the clearance rate of a non-metabolizable solute such as para-aminohippurate (PAH). The effective RPF is approximately 10% less than the actual RPF. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of plasma that perfuses the kidneys per unit time. Plasma is the fibrinogen-containing fluid portion of the blood in which the particulate components are suspended. The kidneys are the paired organs that function to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of only one of the kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the weight of both (the complete set of two) of the kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
A calculated measurement in which the weight after removal from the body but without desiccation of only the single right kidney is divided by the total weight of the body and presented as a ratio, fraction, quotient or percent, thus normalizing it to body weight and by extension to the size of the organism. The right kidney is the organ which lies on the right side of the body from the perspective of the subject.
individual right kidney wet weight to body weight ratio
right kidney wet weight to body weight ratio
A calculated measurement in which the weight after removal from the body but without desiccation of only the left kidney is divided by the total weight of the body and presented as a ratio, fraction, quotient or percent, thus normalizing it to body weight and, by extension, to the size of the organism. The left kidney is the organ which lies on the left side of the body from the perspective of the subject.
individual left kidney wet weight to body weight ratio
left kidney wet weight to body weight ratio
A calculated measurement in which the value for the volume of blood delivered to and/or exiting from the kidneys per unit time is divided by the weight (heaviness or degree to which an object is drawn toward the earth by gravity) of one or both kidneys, and presented as a ratio, fraction, quotient or percentage.
renal blood flow rate to kidney weight ratio
A calculated measurement in which difference in the mean arterial blood pressure between two or more dosages of a drug or chemical which reduces the interior diameter of blood vessels is divided by difference in the logarithm of the applied dosages and presented as a ratio, fraction, quotient or percentage. The value is calculated as the slope of the curve of the mean arterial blood pressure versus log of the vasoconstrictor dose [VC] graph, given by the equation (log[VC]2 - log[VC]1)/(MAP at [VC]2 - MAP at [VC]1). A logarithm is the power to which a base, such as 10, must be raised to produce a given number.
change in MAP to change in log[vasoconstrictor] ratio
change in mean arterial blood pressure to change in the logarithm of the vasoconstrictor dose ratio
Measurement of the length of a straight line passing through the center and connecting opposite points on the circumference of a circle delineating the outer limits of a glomerulosclerotic lesion.
kidney glomerulosclerotic lesion diameter
A calculated measurement in which the diameter of kidney glomerular injury is divided by the value of the mean arterial blood pressure and presented as a ratio, fraction, quotient or percentage, for example to give an index of kidney damage relative to the level of hypertension.
kidney glomerulosclerotic lesion diameter to mean arterial blood pressure ratio
Measurement of the physical form or structure of one or more blood vessels, the network of muscular tubes that carry blood through the body.
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of the aorta, the layered tissue which encloses and constitutes the structural component of the great artery arising from the left ventricle from which the systemic arterial system proceeds. A molecule is an aggregation of atoms, specifically a chemical combination of two or more atoms forming a specific chemical substance.
aortic wall molecular composition measurement
aorta wall molecular composition measurement
The amount of elastin in a specified sample of aorta wall tissue. Elastin is an elastic, fibrous mucoprotein, similar to collagen, and the major connective tissue protein of elastic fibers, such as those in arterial walls.
The amount of collagen in a specified sample of aorta wall tissue. Collagen refers to any of a family of extracellular, closely related proteins occurring as a major component of connective tissue, giving it strength and flexibility.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of the aorta.
calculated aortic wall molecular composition measurement
calculated aorta wall molecular composition measurement
A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of aorta wall is divided by the total weight after dessication of that sample of aorta wall, and the result presented as a ratio, fraction, quotient or percentage.
aortic wall elastin dry weight to total aortic wall dry weight ratio
aorta wall extracellular elastin dry weight to aorta wall dry weight ratio
A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of aorta wall is divided by the weight of extracellular collagen in that sample of aorta wall, and the result presented as a ratio, fraction, quotient or percentage.
aortic wall elastin dry weight to aortic wall collagen weight ratio
aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio
The total amount of protein extracted from within the cells of the aortic wall in a specified sample of aorta. Protein is any of a group of complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages.
aorta wall total intracellular protein level
The difference in mean arterial blood pressure between two points in time or two conditions expressed as a percentage (the proportion or rate per hundred parts).
percent change in mean arterial blood pressure
Average slope of the line defined by the change in heart rate (the number of contractions of the cardiac ventricles per unit of time) relative to the change in mean arterial blood pressure (the average force the blood exerts on an artery wall) over time and/or in response to a change in conditions.
change in heart rate to change in mean arterial blood pressure ratio
Maximum, largest or steepest slope of the line defined by the change in heart rate (the number of contractions of the cardiac ventricles per unit of time) relative to the change in mean arterial blood pressure (the average blood pressure within an artery over a specified period of time) over time and/or in response to a change in conditions.
maximum change in heart rate to change in mean arterial blood pressure ratio
The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of blood.
The amount of sterol, any of a group of steroids with a long (8 to 10 carbons) aliphatic side-chain at position 17 and at least one alcoholic group, in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of a specified tissue or set of tissues.
tissue molecular composition measurement
Determination of the number of mononuclear cells, i.e. leukocytes such as lymphocytes and monocytes with a single round or oval nucleus (including but not limited to such cells found in blood, lymph or spleen) found in a specified sample.
A calculated measurement in which .the number of kidney glomeruli displaying an abnormal (i.e., pathogenic) crescentic morphology is divided by the number of kidney glomeruli displaying normal morphology, and the result presented as a ratio, fraction, quotient or percentage.
kidney crescentic glomeruli count to kidney normal glomeruli count ratio
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of heart rate, the number of contractions of the cardiac ventricles per unit of time.
The difference between two points in time or two conditions in heart rate expressed as the ratio of the low frequency R-R interval component of the power spectrum analysis to the high frequency R-R interval component of the power spectrum analysis, expressed as the result of the subtraction in and of itself without comparison by ratio with another quantity.
absolute change in heart rate variability
absolute change in electrocardiographic low frequency R-R interval to high frequency R-R interval ratio
absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the tissue(s) of the heart left ventricle. A molecule is an aggregation of atoms, specifically a chemical combination of two or more atoms forming a specific chemical substance.
heart left ventricle molecular composition measurement
The amount in a specified sample of tissue from the heart left ventricle, of natriuretic peptide A (NPPA), a powerful vasodilator and peptide hormone secreted mainly by heart muscle cells and involved in control of extracellular fluid volume and electrolyte homeostasis.
heart left ventricle atrial natriuretic factor level
heart left ventricle natriuretic peptide A protein level
heart left ventricle natriuretic peptide A level
The amount of renin in a specified sample of kidney tissue. Renin, an aspartyl protease, catalyzes the cleavage of angiotensinogen to form angiotensin I, the first step in the activation pathway of angiotensinogen--a cascade that can result in aldosterone release,vasoconstriction, and increase in blood pressure.
Any quantification of the ability of a protein of the kidney to accomplish an effect, e.g. take part in a chemical reaction or carry out a specified molecular function.
Any quantification of the ability of a kidney enzyme, i.e. a protein located in the kidney that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions, to carry out its specified molecular function.
A calculated measurement in which the level of catalase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Catalase converts the reactive oxygen species hydrogen peroxide to water and oxygen.
kidney catalase activity to total protein level ratio
A calculated measurement in which the level of glucose-6-phosphate dehydrogenase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glucose-6-phosphate dehydrogenase catalizes the conversion of D-glucose 6-phosphate + NADP+ to 6-phospho-D-glucono-1,5-lactone + NADPH.
kidney G6PD activity to total protein level ratio
kidney glucose-6-phosphate dehydrogenase activity to total protein level ratio
A calculated measurement in which the level of glutathione reductase (GSR) enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. GSR reduces oxidized glutathione disulfide (GSSG) to the sulfhydryl form GSH.
kidney GSR activity to total protein level ratio
kidney glutathione reductase activity to total protein level ratio
A calculated measurement in which the level of glutathione peroxidase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glutathione peroxidases constitute a family of proteins that reduce lipid hydroperoxides to their corresponding alcohols and reduce free hydrogen peroxide to water.
kidney glutathione peroxidase activity to total protein level ratio
A calculated measurement in which the level of glutathione-S-transferase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Glutathione-S-transferase refers to any of a family of proteins with the ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification.
kidney glutathione-S-transferase activity to total protein level ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. superoxide dismutases constitute a family of proteins that convert naturally-occuring but harmful superoxide radicals to molecular oxygen and hydrogen peroxide.
kidney superoxide dismutase activity to total protein level ratio
A calculated measurement in which the level of paraoxonase 1 enzyme activity in a specified sample of kidney is divided by the weight of total protein in that sample. Paraoxonase 1 is an arylesterase that mainly hydrolyzes paroxon, an organophosphorus anticholinesterase compound, to produce p-nitrophenol.
kidney paraoxonase-1 activity to total protein level ratio
kidney paraoxonase1 activity to total protein level ratio
A calculated measurement in which the level of glutathione peroxidase enzyme activity in a specified sample of kidney is divided by the level of glutathione reductase enzyme activity in that same sample.
kidney glutathione peroxidase activity to glutathione reductase activity ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of catalase enzyme activity in that same sample.
kidney superoxide dismutase to catalase activity ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of glutathione peroxidase enzyme activity in that same sample.
kidney superoxide dismutase to glutathione peroxidase ratio
A calculated measurement in which the level of superoxide dismutase enzyme activity in a specified sample of kidney is divided by the level of paraoxonase 1 enzyme activity in that same sample.
kidney superoxide dismutase to paraoxonase-1 activity ratio
kidney superoxide dismutase to paraoxonase1 activity ratio
The amount of glutathione in a specified sample of kidney tissue. Glutathione (GSH/GSSG) is an antioxidant tripeptide with a gamma peptide linkage between the amine group of cysteine (which is attached by normal peptide linkage to a glycine) and the carboxyl group of the glutamate side-chain.
The amount of malondialdehyde in a specified sample of kidney tissue. Malondialdehyde is an organic compound with the formula CH2(CHO)2. It is a reactive species which occurs naturally, is generally found in the enol form (HOCH=CH-CHO), and is a marker for oxidative stress.
A calculated measurement in which the level of protein carbonyl (PCO) derivatives in a specified sample of kidney is divided by the total amount of protein in the sample. Protein carbonyl (PCO) derivatives are produced by the oxidation of amino acids and can be used as a marker of oxidative stress.
kidney protein carbonyl level to total protein level ratio
The amount of platinum, the chemical element with atomic number 78, in a specified sample of kidney tissue.
The amount of enzymatic activity of creatine kinase (CK) enzyme in a specified sample of serum. CK catalyses the reversible transfer of phosphate between ATP and various phosphogens such as creatine phosphate. Serum CK level is used as an enzymatic marker for myocardial infarction, rhabdomyolysis and acute renal failure.
serum creatine phosphokinase activity level
The amount of lipid peroxidation end products in a specified sample of kidney tissue. Lipid peroxidation is the oxidative degradation of lipids.
Measurement of the size of the three dimensional space occupied by a single kidney glomerulus.
Calculated measurement of a difference in the maximum arterial blood pressure, that is the pressure at the point of maximal contraction of the heart, between two points in time, one during the day and the other at night, expressed as a number (positive or negative), not as a ratio or percentage relative to another quantity.
absolute circadian change in systolic blood pressure
absolute diurnal change in systolic blood pressure
The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of blood. Cholesterol in the blood is generally associated with various lipoproteins.
The amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Cholesterol in the serum is associated with various lipoproteins.
A calculated measurement in which difference in the mean arterial blood pressure between two or more dosages of a drug or chemical which reduces or increases the interior diameter of blood vessels is divided by difference the applied dosages and presented as a ratio, fraction, quotient or percentage. The value is calculated as the slope of the curve of the mean arterial blood pressure versus the chemical dose graph.
beta coefficient of mean arterial blood pressure change
change in MAP to change in [vasoactive chemical] ratio
slope of the change in mean arterial blood pressure
change in mean arterial blood pressure to change in vasoactive chemical dose ratio
Ratio of the wall thickness (WT) of an artery to outer diameter (OD) of that artery at that location, usually expressed as a percentage, i.e. WT/OD x 100, but could also be expressed as a ratio, fraction or quotient. This measurement can be used to assess stenosis, a pathological narrowing of a blood vessel.
artery wall thickness as percentage of artery outer diameter
artery wall thickness as percentage of artery total diameter
artery wall thickness to artery total diameter ratio
Any value resulting from the quantification of a morphological or physiological parameter of leukocytes, largely colorless blood corpuscles capable of ameboid movement, whose chief function is to protect the body against microorganisms and other disease-causing entities.
A calculated measurement in which the number of white blood cells of one or more specific types in a specified sample of blood is divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
blood differential leukocyte count to total WBC count ratio
blood differential leukocyte count as percentage of total white blood cells
differential white blood cell percentage
blood differential leukocyte count to total leukocyte count ratio
Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of a morphological or physiological parameter of non-neoplastic lesions in the kidney.
calculated renal non-tumorous lesion measurement
calculated kidney non-tumorous lesion measurement
A calculated measurement in which the area occupied by renal protein casts is divided by the total, combined area of the outer stripe of the kidney outer medulla and the kidney cortex, and the result presented as a ratio, fraction, quotient or percentage. Renal protein casts are gelled proteins precipitated in the renal tubules and molded to the tubular lumen. The medulla outer stripe is the section of the renal medula adjacent to the renal cortex and contains portions of the nephron, including the straight proximal tubules, and portions of the loops of henle and outer medullary collecting ducts.
ratio of the area occupied by protein casts to the total area of the kidney outer medulla outer stripe and cortex
A calculated value in which the weight of the heart after removal from the body but without dessication is divided by the total weight of the body, and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight and, by extension, to the size of the organism.
heart wet weight as a percentage of body weight
A calculated measurement in which the difference between the contractile force of a blood vessel in response to a vasoconstrictor and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls.
vasoconstrictor-induced blood vessel contractile force expressed as percent of force at baseline
A calculated measurement in which the difference between the contractile force of a blood vessel in response to a specified dosage of phenylephrine and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. Phenylephrine is an adrenergic drug that is a powerful vasoconstrictor.
phenylephrine-induced blood vessel constriction expressed as percent of force at baseline
phenylephrine-induced blood vessel contractile force expressed as percent of force at baseline
A calculated measurement in which the difference between the contractile force of a blood vessel in response to a specified dosage of potassium chloride and the baseline contractile force exerted by that vessel in the absence of any external stimuli, is divided by the baseline contractile force measurement and the result expressed as a percentage. Potassium chloride is the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). It is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels.
KCl-induced blood vessel constriction expressed as percent of force at baseline
potassium chloride-induced blood vessel contractile force expressed as percent of force at baseline
Measurement of an organism's, organ's, tissue's or cell's capacity to respond, such as by a change in activity, state or condition, to potassium chloride, the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). Potassium chloride is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels.
potassium chloride response/sensitivity measurement
A calculated value for the concentration of potassium chloride (KCl) at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of KCl is halfway between the baseline value and the highest achievable value of such KCl-induced contractile energy. Potassium chloride is the salt of the potassium cation (K+) and the chlorine/chloride anion (Cl-). It is used as an eletroylyte replenisher and has mild vasoconstrictive properties when applied directly to blood vessels.
potassium chloride half maximal effective concentration (EC50)
KCl half maximal effective concentration (EC50)
concentration of potassium chloride at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of potassium chloride (KCl) at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of KCl is halfway between the baseline value and the highest achievable value of such KCl-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value.
potassium chloride Log half maximal effective concentration (Log EC50)
KCl Log half maximal effective concentration (Log EC50)
logarithm of the concentration of potassium chloride at which the force of blood vessel contraction is half the maximum value (Log EC50)
A calculated value for the concentration of a vasoconstrictor at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of the stimulus is halfway between the baseline value and the highest achievable value of such stimulus-induced contractile energy. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls.
vasoconstrictor half maximal effective concentration (EC50)
concentration of vasoconstrictor at which the force of blood vessel contraction is half the maximum value (EC50)
A calculated value for logarithm of the concentration of a vasoconstrictor at which the energy produced by the active reduction in the diameter of a blood vessel in response to the application of the stimulus is halfway between the baseline value and the highest achievable value of such stimulus-induced contractile energy. The logarithm of the concentration is the exponent indicating the power to which 10 must be raised to obtain that concentration value. A vasoconstrictor is any agent or condition that narrows blood vessels by constricting the smooth muscle in the vessel walls.
vasoconstrictor Log half maximal effective concentration (Log EC50)
logarithm of the concentration of vasoconstrictor at which the force of blood vessel contraction is half the maximum value (Log EC50)
The thickness or depth of the ventral/anterior wall of the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed. The ventral/anterior wall is the portion of the muscle enclosing the ventricle which is farthest from the spine and closest to the chest wall of the organism.
heart left ventricle end-diastolic ventral wall thickness
heart left ventricle end-diastolic anterior wall thickness
A calculated measurement in which the weight of the left ventricle of the heart is divided by its area at end-diastole, that is, when the heart muscle is maximally relaxed, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle weight to heart left ventricle end-diastolic area ratio
Any measurement of the movement of blood into, through or out of the heart.
Measurement of the speed at which blood flows into the ventricle during passive filling, that is, during the period when the blood flows from the atrium to the ventricle due to gravity rather than as a result of active contraction of the atrium.
An echocardiographic measurement of the amount of time between the maximum 'E point', that is, the maximum velocity of passive blood flow from the atrium to the ventricle, and the return to baseline at the end of early mitral flow.
Measurement of the decrease in transmitral blood flow velocity per unit time or the rate at which the velocity of passive blood flow from the atrium to the ventricle decreases over time as the ventricle fills and the atrium empties, calculated as the slope of transmitral velocity vs time.
Any measurement of the physical form or structure of a muscle fiber, any of the cells of skeletal or cardiac muscle tissue. Each cell is one fiber of the muscle.
Any measurementof the physical form or structure of a skeletal muscle fiber, a cylindrical multinucleate cell of skeletal muscle tissue containing contracting myofibrils and across which run transverse striations.
skeletal muscle fiber morphological measurement
The average number of capillaries associated with and/or surrounding an individual skeletal muscle fiber, a cylindrical multinucleate cell of skeletal muscle tissue containing contracting myofibrils and across which run transverse striations. Capillaries are the minute vessels connecting arterioles and venules, the walls of which act as a semipermeable membrane for interchange of various substances between the blood and tissue fluid.
number of capillaries per skeletal muscle cell
number of capillaries per skeletal muscle fiber
Any measurement, morphological or physiological of the minute vessels connecting arterioles and venules, the walls of which act as a semipermeable membrane for interchange of various substances between the blood and tissue fluid.
The length of time in the cardiac cycle between the end of left ventricular relaxation and the start of left ventricular filling. This represents the time in the cardiac cycle between closure of the aortic valve and opening of the mitral valve.
left ventricular isovolumetric relaxation time
The time interval from the completion of the mitral valve closure to the beginning of the aortic valve opening, that is, the period of contraction during which both the mitral and aortic valves are closed so that the volume of the ventricular space doesn't change.
left ventricular isovolumetric contraction time
The length of time in the cardiac cycle between the end of right ventricular relaxation and the start of right ventricular filling.
right ventricular isovolumetric relaxation time
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the length of time in the cardiac cycle between the end of left ventricular relaxation and the start of left ventricular filling.
calculated left ventricular isovolumetric relaxation time
A calculated measurement in which the value of the left ventricular isovolumetric relaxation time is corrected by the square root of the R-R interval [IVRT/(RR)1/2] on a simultaneously-recorded ECG.
heart rate-corrected left ventricular isovolumetric relaxation time
Measurement of the length of time between the closing of the mitral valve (the dual-flap valve in the heart that controls blood flow between the left atrium and the left ventricle) at the end of ventricular filling (that is, after atrial contraction) and its opening at the beginning of the next round of ventricular filling.
The time interval from the opening to the closing of the aortic valve (mechanical systole).
A calculated measurement comprised of the sum of left ventricular isovolumetric contraction time and isovolumetric relaxation time divided by the left ventricular ejection time.
Any measurement of the degree to which the presentation of any cardiovascular disease state, causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof.
cardiovascular disease severity measurement
Any measurement related to a deviation from or interruption of the normal structure or function of the cardiovascular system that is manifested by a characteristic set of symptoms and signs.
Any measurement of the degree to which the presentation of an arterial disease state, causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof. Arterial disease is a deviation from or interruption of the normal structure or function of one or more arteries, the vessels in which blood flows away from the heart carrying oxygenated blood, that is manifested by a characteristic set of symptoms and signs.
Measurement of the degree to which a tear or break in the continuity or configuration of the aorta (the great artery arising from the left ventricle and from which the systemic arterial system proceeds) causes pain or damage, or interferes with the normal functioning of an organism or of any part thereof.
The value or quantity determined by count of tears or breaks in the continuity or configuration of the fenestrated layer of elastic tissue that is the outermost part of the intima of an artery.
number of ruptures of internal elastic lamina in arteries
number of ruptures of internal elastic laminae in arteries
number of ruptures of arterial internal elastic lamina
The value or quantity determined by count of tears or breaks in the continuity or configuration of the internal elastic lamina (IEL) of the abdominal aorta and iliac arteries, that is, the distal segment of the descending aorta and the large arteries that originate from it.
number of RIEL in abdominal aorta and iliac arteries
number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries
The value or quantity determined by count of tears or breaks in the continuity or configuration of the internal elastic lamina (IEL) of the renal arteries, that is, the ateries which arise from the side of the abdominal aorta and which supply the kidneys with blood.
number of ruptures of the internal elastic lamina of the renal arteries
A measurement of the severity of tears or breaks in the arterial internal elastic lamina (IEL) which is derived from a combination of multiple measurements and/or objective or subjective severity scores according to a specified formula or set of criteria. The IEL is the fenestrated layer of elastic tissue that is the outermost part of the intima of an artery.
arterial internal elastic lamina rupture composite score
A calculated measurement in which the weight after dessication of the extracellular elastin in a specified sample of the wall of the aorta is divided by the length (that is, the distance between the two ends) of that segment, and the result presented as a ratio, fraction, quotient or percentage.
aorta wall extracellular elastin dry weight to aorta length ratio
A measurement of the existance and severity of a patent ductus arteriosus (PDA) when such a measurement is derived from a combination of multiple measurements and/or an objective or subjective ranking or rating system according to a specified formula or set of criteria. PDA is the abnormal persistence of an open lumen in the ductus arteriosus, between the aorta and the pulmonary artery, after birth.
Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins (complex high molecular weight organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur consisting of alpha-amino acids joined by peptide linkages) or peptides (low molecular weight compounds composed of at least two amino acids joined by peptide linkages) in a specified tissue or set of tissues.
tissue protein/peptide composition measurement
Any measurement involving the composition, that is, the absolute amount, relative amount or type of one or more proteins or peptides in a specified sample of tissue from the wall of the aorta.
aortic wall protein/peptide composition measurement
aorta wall protein/peptide composition measurement
A calculated parameter derived from a a sequence of blood pressure measurements taken sequentially and ordered in time. A parameter is a mathematical and statistical variable in a model system that partially or completely characterises the mathematical model.
blood pressure time series calculated parameter
A mathematical and statistical variable in a model system that partially or completely characterises the baroreceptor response in a blood pressure time series calculation. The baroreceptor response is the system whereby specific nerve terminals that stabilize moment to moment blood pressure variability in the carotid sinus and aortic arch sense deviations from the baseline pressure and initiate signals that dampens such deviations.
blood pressure time series baroreceptor response calculation parameter
The first order coefficient parameter derived from a blood pressure time series moving average (also known as a rolling average, running average, moving mean, or rolling mean) calculation.
blood pressure time series first order moving average coefficient
The fractal parameter derived from a blood pressure time series calculation based on a autoregressive fractionally integrated moving average time series model (ARFIMA, FARIMA, or fARIMA).
blood pressure time series fractal parameter
The experimental set point parameter of the blood pressure time series baroreceptor response calculation.
blood pressure time series experimental set point of the baroreceptor response
The average exponential scaling factor parameter of the blood pressure time series baroreceptor response calculation.
blood pressure time series average exponential scaling factor of the baroreceptor response
A parameter based on a blood pressure time series calculation using a first order mechanistic model.
blood pressure time series linear term first order parameter
A parameter based on a blood pressure time series calculation using a second order mechanistic model.
blood pressure time series linear term second order parameter
The thickness or depth (i.e. the measurement of the two-dimensional extent of the distance between the inner and outer surfaces) of the dorsal/posterior wall of the left ventricle of the heart at the end of diastole, that is, when the heart muscle is maximally relaxed. The dorsal wall is the portion of the muscle enclosing the ventricle which is closest to the spine and farthest from the chest wall of the organism.
end-diastolic heart left ventricle posterior wall thickness
heart left ventricle end-diastolic posterior wall thickness
A value resulting from the quantification of a morphological or physiological parameter of a blood-derived lipoprotein, any of a class of complex molecules found in blood that consist of a protein membrane surrounding a core of lipids.
Measurement of the amount of cholesterol, a eukaryotic sterol that in higher animals is the precursor of bile acids and steroid hormones and a key constituent of cell membranes, carried in lipoprotein molecules in a specified volume of blood. Lipoprotein particles are complex molecules that consist of a protein membrane surrounding a core of lipids.
The distance between the two ends, that is, of the extent of the longest dimension, of the aorta, the main trunk from which the arterial system proceeds.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the physical form or structure of the aorta, the main trunk from which the arterial system proceeds.
calculated aorta morphological measurement
A calculated measurement in which the weight of the aorta is divided by its length and the resulting quantity is divided by the total body weight of the organism.
aorta mass to aorta length to body mass ratio
aorta weight to aorta length to body weight ratio
A calculated measurement of the relative difference in pulse pressure between a treated state and a control state or between two points in time, expressed as a percentage.
Any quantification of the ability of a protein of the heart to accomplish an effect, e.g. take part in a chemical reaction or carry out a specified molecular function.
Any quantification of the ability of a heart enzyme, i.e. a protein located in the heart that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions, to carry out its specified molecular function.
Quantitation of the catalytic effect exerted by angiotensin I converting enzyme 2 (ACE2) in a specified sample of heart tissue. ACE2, an ACE homolog, is a zinc-dependent peptidase of the M2-metalloprotease family that is sensitive to chloride ion concentration, is a membrane-bound enzyme that acts as a monocarboxypeptidase, and is an essential regulator of heart function.
heart angiotensin II converting enzyme activity level
heart angiotensin I converting enzyme 2 activity level
Quantitation of the catalytic effect exerted by angiotensin I converting enzyme (ACE) in a specified sample of heart tissue. ACE is one of the enzymes of the renin-angiotensin system, and catalyzes the conversion of angiotensin I into a physiologically active vasoconstrictor peptide angiotensin II.
heart angiotensin I converting enzyme activity level
Quantitation of the catalytic effect exerted by angiotensin converting enzyme2 (ACE2) in a specified sample of kidney. ACE2, an ACE homolog, is a zinc-dependent peptidase of the M2-metalloprotease family that is sensitive to chloride ion concentration, and is a membrane-bound enzyme that acts as a monocarboxypeptidase and is an essential regulator of heart function.
kidney angiotensin II converting enzyme activity level
kidney angiotensin I converting enzyme 2 activity level
Quantitation of the catalytic effect exerted by angiotensin I converting enzyme (ACE) in a specified sample of kidney tissue. ACE is one of the enzymes of the renin-angiotensin system, and catalyzes the conversion of angiotensin I into a physiologically active vasoconstrictor peptide angiotensin II.
kidney angiotensin I converting enzyme activity level
Any measurement of the physical form or structure of a cardiac muscle fiber, a striated cardiac muscle cell (cardiomyocyte) that is responsible for heart contraction.
cardiac muscle cell morphological measurement
cardiac myocyte morphological measurement
heart muscle cell morphological measurement
cardiac muscle fiber morphological measurement
The length of a straight line passing through a cardiac muscle fiber, that is a cardiomyocyte, for instance through the center of its nucleus, and connecting opposite points on its periphery.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the amount of plasma that perfuses the kidneys per unit time per amount of body weight.
A calculated measurement in which glomerular filtration rate, an estimate of the volume of fluid filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time, is divided by the total weight of the body and the result is presented as a ratio, fraction, quotient or percentage.
glomerular filtration rate to body weight ratio
A calculated value in which the volume of glomeruli with lesions resulting from fibrosis, scarring or hyaline deposits is divided by the total volume of glomeruli in a specified sample of kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total volume of glomeruli.
kidney sclerotic glomerular volume to total kidney glomerular volume ratio
A calculated value in which the weight of the heart left ventricle is divided by the length of the tibia (the medial and larger of the two bones of the lower leg of bipeds or hindlimb of quadrupeds which articulates with the femur, fibula, and talus), and the result is presented as a ratio, fraction, quotient or percentage,thus normalizing it to the length of the leg and, by extension, to the size of the body.
heart left ventricle weight to tibia length ratio
Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the movement of blood into, through or out of the heart.
A calculated measurement in which the value of the E wave (that is, the velocity of the blood flow across the mitral valve during passive filling of the left ventricle in early diastole) is divided by the value of the A wave (that is, the velocity of the blood flow across the mitral valve during active filling of the left ventricle caused by atrial contraction in late diastole).
A calculated measurement in which the average width of the tunica media is divided by the inner diameter (that is, the diameter of the lumen) of the artery and the result is presented as a ratio, fraction, quotient or percentage.
artery tunica media width to artery inner diameter ratio
The thickness, width or depth of the septal wall of the heart ventricles (that is, the portion of the wall between the left and right ventricles that is shared between the two) at the end of diastole when the heart muscle is maximally relaxed.
heart intraventricular septum end-diastolic thickness
heart intraventricular end-diastolic wall thickness
The thickness, width or depth of the septal wall of the heart ventricles (that is, the portion of the wall between the left and right ventricles that is shared between the two) at the end of systole when the heart muscle is maximally contracted.
heart intraventricular septum end-systolic thickness
heart intraventricular end-systolic wall thickness
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour systolic blood pressure measurements.
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour diastolic blood pressure measurements.
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour mean arterial blood pressure measurements.
mean arterial blood pressure variability
A variability measurement in which the mean is calculated from the standard deviations or the standard deviation is calculated from the means of sequential one hour heart rate measurements.
A calculated value in which the number of glomeruli with microaneurysm (focal dilation of arteriocapillary junctions), is divided by the total number of glomeruli in the kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli.
ratio of number of glomeruli with microaneurysms to number of total glomeruli
A calculated value in which the area of glomeruli with activated mesangial cells (determined by the expression of α-smooth muscle actin), is divided by the total area of glomeruli counted in the kidney and presented as a ratio, fraction or quotient, thus normalizing it to the total number of glomeruli.
ratio of glomerular area occupied by activated mesangial cells to total glomerular area
Any measurement that has been normalized, adjusted or derived by a mathematical process or computation, of the glomeruli of one or both kidneys, the paired organ which functions to maintain proper water and electrolyte balance, regulate acid-base concentration, and filter the blood of metabolic wastes.
calculated kidney glomerulus morphological measurement
calculated kidney glomerulus measurement
Any measurement of the physical form or structure of one or more of the mesenteric arteries, which arise from the anterior surface of the abdominal aorta, just inferior to the origin of the celiac trunk, and supplies blood to the intestine from the lower part of the duodenum through two-thirds of the transverse colon, as well as the pancreas.
mesenteric artery morphological measurement
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the wall of one or more of the mesenteric arteries.
mesenteric artery molecular composition measurement
A measurement which has been normalized, adjusted or derived by a mathematical process or computation of the physical form or structure of any of the mesenteric arteries.
calculated mesenteric artery wall molecular composition measurement
calculated mesenteric artery molecular composition measurement
A calculated measurement in which mesenteric artery phosphorylated eNOS protein level is divided by aorta wall total eNOS protein level and presented as a ratio, fraction, quotient or percentage. Phosphorylation of eNOS is a mechanism that catylzes a structural change of the enzyme to an activated form.
mesenteric artery phosphylated eNOS protein level to total eNOS protein level ratio
mesenteric artery wall phosphylated eNOS level to total eNOS level ratio
mesenteric artery phosphylated eNOS level to total eNOS level ratio
A calculated measurement in which aorta wall phosphorylated eNOS protein level is divided by aorta wall total eNOS protein level and presented as a ratio, fraction, quotient or percentage. Phosphorylation of eNOS is a mechanism that catylzes a structural change of the enzyme to an activated form.
aorta wall phosphylated eNOS protein level to total eNOS protein level ratio
aorta wall phosphylated eNOS level to total eNOS level ratio
Monophasic action potentials (MAPs) are recorded using contact electrode catheters. The recordings provide local information about the actual cellular depolarization and repolarization process of myocardial tissue. They are different from body surface electrocardiographic (ECG) recordings or standard endocardial electrograms, which produce a summative or derivative view of the heart's electrical activity
Conduction velocity is calculated as the distance from pacing electrode to the monophasic action potential recording electrode across the epicardial surface, divided by the conduction time, the time from the pacing spike to monophasic action potential onset.
The E/E' is a ratio of peak velocity of early diastolic trans-mitral flow (E) to the peak velocity of early diastolic mitral annular motion (E')
E wave velocity to E' wave velocity ratio
Any quantitation of the molecules, atoms and/or ions which constitute the chemical make-up of the tissue(s) of the heart.
cardiac molecular composition measurement
Measurement of the amount of free fatty acids within the heart.
Measurement of the amount of triglycerides within the heart.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the end-systolic heart left ventricle posterior wall thickness.
calculated heart left ventricle end-systolic posterior wall thickness
A calculated measurement in which the heart left ventricle end-systolic posterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-systolic posterior wall index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart left ventricle end-systolic internal diameter.
calculated heart left ventricle end-systolic internal dimension
calculated heart left ventricle end-systolic internal diameter
A calculated measurement in which the heart left ventricle end-systolic internal diameter is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-systolic internal dimension index
heart left ventricle end-systolic internal diameter index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart ventricle end-systolic septal wall thickness.
calculated heart end-systolic intraventricular wall thickness
calculated heart ventricle end-systolic septal wall thickness
A calculated measurement in which the heart ventricle end-systolic septal wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart ventricle end-systolic septal wall index
Peak velocity of late atrial diastolic trans-mitral flow (A).
E' wave velocity is the peak velocity of early mitral annular diastolic motion.
A' wave velocity (A') is the peak velocity of late (atrial) diastolic mitral annular motion.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of cardiac output.
A calculated measurement in which the cardiac output is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of cardiac stroke volume.
A calculated measurement in which the cardiac stroke volume is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the left ventricular end-systolic blood pressure.
calculated left ventricular end-systolic blood pressure
Effective arterial elastance (Ea), defined as the ratio of left ventricular (LV) end-systolic pressure and stroke volume, lumps the steady and pulsatile components of the arterial load in a concise way.
Defined as the work performed by the left or right ventricle to eject the stroke volume into the aorta or pulmonary artery, respectively.
Defined as the work performed by the left ventricle to eject the stroke volume into the aorta.
Preload recruitable stroke work (PRSW) is determined by the linear regression of stroke work with the end-diastolic volume. The slope of the PRSW relationship is a highly linear index of myocardial contractility that is insensitive to preload and afterload.
preload recruitable left ventricle stroke work
A calculated measurement in which the maximum rate of positive change in left ventricular blood pressure is divided by the left ventricular end-diastolic volume, and the result presented as a ratio, fraction, quotient or percentage.
maximum rate of positive change in left ventricular blood pressure to left ventricular end-diastolic volume ratio
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the end-diastolic heart left ventricle posterior wall thickness.
calculated heart left ventricle end-diastolic posterior wall thickness
A calculated measurement in which the heart left ventricle end-diastolic posterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-diastolic posterior wall index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart left ventricle end-diastolic anterior wall thickness.
calculated heart left ventricle end-diastolic anterior wall thickness
A calculated measurement in which the heart left ventricle end-diastolic anterior wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricle end-diastolic anterior wall index
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the heart ventricle end-diastolic septal wall thickness.
calculated heart ventricle end-diastolic septal wall thickness
A calculated measurement in which the heart ventricle end-diastolic septal wall thickness is divided by the weight of the body, and the result presented as a ratio, fraction, quotient or percentage.
heart ventricle end-diastolic septal wall index
Renal medullary blood flow (MBF) is the volume of blood delivered to or exiting from the renal medulla per unit time.
Left ventricle end-diastolic elastance (Eed) is the estimate of the slope of the line Ped=Eed(Ved-V0), which is based on linear regression of points determined by iterative calculation of the LV end-diastolic pressurevolume relationship.
heart left ventricle end-diastolic elastance
Left ventricle end-systolic elastance (Ees) is the estimate of the slope of the line Pes=Ees(Ves-V0), which is based on linear regression of points determined by iterative calculation of the LV end-systolic pressurevolume relationship.
heart left ventricle end-systolic elastance
A measurement which has been normalized, adjusted or derived by a mathematical process or computation, of components of the periodic tightening and loosening of the muscles of a ventricle of the heart.
calculated ventricle contraction measurement
Left ventricle diastolic volume-axis intercept (V0) is determined by the line Ped=Eed(Ved-V0), which is based on linear regression of points determined by interative calculation of the LV end-diastolic pressurevolume relationship.
Heart left ventricle diastolic volume-axis intercept (V0)
Left ventricle systolic volume-axis intercept (V0) is determined by the line Pes=Ees(Ves-V0), which is based on linear regression of points determined by iterative calculation of the LV end-diastolic pressurevolume relationship.
Heart left ventricle systolic volume-axis intercept (V0)
A measurement of the volume of blood in ventricle immediately before a contraction which has been normalized or adjusted by a mathematical process or computation. .
A measurement of the volume of blood in a ventricle at the end of a contraction which has been normalized or adjusted by a mathematical process or computation.
The amount of adrenomedullin in a specified sample of kidney tissue.
The amount of adrenomedullin in a specified sample of medullary kidney tissue.
The amount of adrenomedullin in a specified sample of cortical kidney tissue.
Any measurement which has been normalized, adjusted or derived by a mathematical process or computation, of the volume of fluid filtered from the kidney glomerular capillaries into the Bowman's capsule per specified unit of time based on serum creatinine level, wieght and age of organism and other factors.
Any quantification of a morphological or physiological parameter of one or more nucleic acids in the heart. Nucleic acids are high-molecular-weight polymeric compounds composed of nucleotides, each consisting of a purine or pyrimidine base, a ribose or deoxyribose sugar, and a phosphate group, and are involved in the determination and transmission of genetic characteristics.
Any measurement of the absolute or relative amount(s) of one or more of the ribonucleic acids (RNAs) of which the heart is formed or composed.
heart ribonucleic acid composition measurement
heart insulin-like growth factor 1 mRNA level
Any measurement of the absolute or relative amount(s) of one or more of the ribonucleic acids (RNAs) of which the heart left ventricle is formed or composed.
heart left ventricle ribonucleic acid content
heart right ventricle insulin-like growth factor 1 mRNA level
The amount of ribonucleic acid (DNA), the molecule composed of the sugar ribose, phosphate groups and any combination of the bases adenine, guanine, cytosine, and/or uracil , extracted from or contained in the heart right ventricle, the lower chamber of the right side of the heart (from the perspective of the organism rather than the observer), which pumps venous blood through the pulmonary trunk and arteries to the capillaries of the lung.
heart right ventricle ribonucleic acid content
heart right ventricle molecular composition measurement
heart left ventricle insulin-like growth factor 1 mRNA level
heart insulin-like growth factor 1 receptor mRNA level
heart right ventricle insulin-like growth factor 1 receptor mRNA level
heart left ventricle insulin-like growth factor 1 receptor mRNA level
Filtration fraction is the ratio of the glomerular filtration rate (GFR) to the renal plasma flow (RPF). Filtration Fraction, FF = GFR/RPF. The filtration fraction, therefore, represents the proportion of the fluid reaching the kidneys which passes into the renal tubules.
glomerular filtration rate to kidney weight ratio
A calculated measurement to determine the volume of fluid filtered from the renal (kidney) glomerular capillaries of a single nephron into Bowman's capsule per unit time.
single nephron glomerular filtration rate
A calculated measurement to determine the ratio of the single nephron glomerular filtration rate (SNGFR) to the renal plasma flow (RPF). Single nephron filtration Fraction, SNFF = SNGFR/RPF. The single nephron filtration fraction, therefore, represents the proportion of the fluid reaching the kidneys which passes into the renal tubules from a single nephron.
calculated kidney morphological measurement
""A semiquantitative evaluation of the renal interstitium using a grading system with a score of 0 to 4+, which assesses the tubules and the interstitium for the presence of (1) tubular atrophy, (2) tubular dilatation, (3) interstitial inflammatory cell infiltrates, and (4) interstitial fibrosis. A score of 0 indicates no lesion (normal kidney), 1+ indicates a single, small focal lesion with very minimal tubular alterations and interstitial inflammatory cell infiltration, and 2+ to 4+ indicated increasing severity of tubular lesions, interstitial inflammatory cell infiltration, and/or fibrosis. A score of 4+ indicates involvement of approximately 50% or more of the renal parenchyma or interstitium." [PMID:PMID\:9369281]
A calculated value in which the weight of the left atrium, the upper chamber on the left side of the heart which empties into the lower left chamber, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight.
heart left atrium weight to body weight ratio
A measurement of the physical form or structure of the right atrium, the right upper chamber of the heart that receives blood from the vena cava and forces it into the right ventricle, which has been normalized, adjusted or derived by a mathematical process or computation.
calculated heart right atrium morphological measurement
A calculated value in which the weight of the right atrium, the upper chamber on the right side of the heart which empties into the lower right left chamber, is divided by the total weight of the body and the result presented as a ratio, fraction, quotient or percentage, thus normalizing it to body weight.
heart right atrium weight to body weight ratio
The weight of the septum of the heart, which is the portion of the heart left ventricle ventral/anterior wall and right ventricle dorsal/posterior wall which is shared between the ventricles, after removal from the body and separation from the rest of the heart.
The average number of podocytes in the kidney glomeruli.
number of podocytes per kidney glomerulus
A calculated measurement in which the average number of podocytes is divided by the average volume of kidney glomeruli.
number of podocytes to glomerular volume ratio
The average number of nucleated cells in the kidney glomeruli.
number of nucleated cells per kidney glomerulus
An injury score obtained by multiplying the degree of glomerular damage (0 to 4) with the percentage of the glomeruli with that type of injury (i.e., increase in mesangial matrix material or glomerulosclerosis).
Volume of blood plasma delivered to a single glomerulus per unit time
Force exerted on the luminal capillary wall from fluid flowing through the capillary.
Any measurement of one of the small blood vessels carrying blood between arteries and capillaries.
Resistance that must be overcome to push blood through arterioles to create flow.
Resistance to blood flow measured within the efferent arteriole proximal to a glomerular capillary network.
efferent glomerular arteriolar resistance
Resistance to blood flow measured within the afferent arteriole distal to a glomerular capillary network.
afferent glomerular arteriolar resistance
Total resistance to blood flow measured within the afferent arteriole proximal and distal to a glomerular capillary network (Rt = Ra + Re).
Rt; total glomerular arteriolar resistance
Measurement of the total amount of all proteins found in a specific volume of afferent arteriolar plasma.
afferent arteriolar plasma protein concentration
Measurement of the total amount of all proteins found in a specific volume of efferent arteriolar plasma.
efferent arteriolar plasma protein concentration
A form of osmotic pressure exerted by proteins, notably albumin, in the afferent arteriole's plasma that tends to pull water into the circulatory system. It is the opposing force to hydrostatic pressure. It has a major effect on the pressure across the glomerular filter.
A form of osmotic pressure exerted by proteins, notably albumin, in the efferent arteriole's plasma that tends to pull water into the circulatory system. It is the opposing force to hydrostatic pressure. It has a major effect on the pressure across the glomerular filter
A measure of a membrane's permeability to water; specifically, the volume of fluid filtered in unit time through a unit area of membrane per unit pressure difference, and it is defined as the glomerular filtration rate (GFR) for both kidneys per millimeter of mercury (mmHg) of filtration pressure.
glomerular capillary ultrafiltration coefficient
A calculated measurement in which the area occupied by renal cysts is divided by the total the kidney, and the result presented as a ratio, fraction, quotient or percentage.
ratio of the area occupied by cysts to the total area of the kidney
Force exerted on the luminal surface of the proximal tubule from fluid flowing through the tubule.
mean proximal tubular hydraulic pressure
Force exerted on the luminal vessel wall from fluid flowing through the efferent arteriole.
efferent glomerular arteriolar hydraulic pressure
The difference between the force exerted on the luminal glomerular capillary wall and the force exerted on the luminal proximal tubular membrane (Pgc - Pt = delta P).
glomerular transcapillary hydraulic pressure gradient
calculated left ventricular end-diastolic blood pressure measurement
A calculated measurement in which the pressure in the heart left ventricle at the end of diastole, the period when the heart is in a state of relaxation and expansion and the ventricles fill with blood, divided by the diameter across the left ventricle of the heart at the end of diastole and the result presented as a ratio, fraction, quotient or percentage.
heart left ventricular end-diastolic blood pressure to heart left ventricular end-diastolic diameter ratio
Rate-pressure product is defined as the product of the heart rate (the number of contractions of the cardiac ventricles per unit of time) and mean arterial blood pressure (the average force the blood exerts on an artery wall).
A calculated measurement of the average width of the tunica media (the middle coat of the arterial wall) divided by the artery total diameter (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall).
artery tunica media to artery total diameter ratio
A calculated measurement of the average width of the artery lumen (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the inner surface of the blood vessel wall) divided by the artery total diameter (measured as the length of a line which crosses a transverse view of an artery, passing through its center and ending on either side at the outer surface of the blood vessel wall).
artery lumen to artery total diameter ratio
the role of a material entity to prevent, diagnose, treat, or study disease and/or its effects
clinical drug role
a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
William Hogan
drug product
active ingredient role
a role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism
William R. Hogan
active ingredient
role of a scattered molecular aggregate
a role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes
role of scattered molecular aggregate
administration of a drug product to an organism
a treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism
drug administration
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
A political association with effective dominion over a geographic area.
Place or area with clustered or scattered buildings and a permanent human population.
A feature that has been constructed by deliberate human effort.
"constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
A permanent walled and roofed construction.
A geographical region whose affairs and population are administered by an authority.
An environmental feature that is, or can be, contained and is predominantly composed of one or a few types of stuff.
An object which is large enough to be visible to humans, but small enough that humans can handle the object (i.e. transport it, examine it, etc) in its entirety with little to no technological assistance.
This is a legacy class from ENVO's early versions. It will be depopulated and filled in by inference using a PATO quality. Not to be confused with "mesoscopic" as defined in physics, which deals with objects typically between 10e-6 and 10-8 meters in diameter.
physical object of mesoscopic geological size
A material entity which determines an environmental system.
A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products.
anthropogenic abiotic mesoscopic feature
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
A system which has the disposition to environ one or more material entities.
In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
A building part is a construction which is part of a building.
Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat.
Outer space is a hard vacuum containing a low density of particles, predominantly a plasma of hydrogen and helium as well as electromagnetic radiation, magnetic fields, neutrinos, dust and cosmic rays that exists between celestial bodies.
outer space
A settlement with a high density of buildings and inhabitants.
See also: http://www.ecotope.org/anthromes/v1/guide/urban/12_dense_settlements/default.aspx
The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request.
dense settlement
A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning.
See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work.
human dwelling
A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement.
This class may be split. "urban village" doesn't sit well and prevents relations to village biomes.
village
An object which is naturally occuring, bound together by gravitational or electromagnetic forces, and surrounded by space.
Astronomical bodies are usually cohesive, thus the use of the term 'object' sensu BFO 'object'.
astronomical body
An object which is composed of one or more gravitationally bound structures that are associated with a position in space.
If there is only one astronomical body involved, this class is equivalent to ENVO:01000799. This may be problematic with reasoning, but it seems to be true to the rather fuzzy definitions found thus far.
astronomical object
A material part of an astronomical body.
astronomical body part
A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
A process during which a natural environmental system is altered by human action.
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
A part of an astronomical body which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology and which are within the gravitational sphere of influence of that body.
An environmental system which includes, as parts, all the entities which have been constructed or manufactured by humans or their technology within the gravitational sphere of influence of an astronomical body.
technosphere
A planned process during which raw or recycled materials are transformed into products for use or sale using labour and machines, tools, chemical and biological processing, or formulation.
The term may refer to a range of human activity, from handicraft to high tech, but is most commonly applied to industrial production, in which raw materials are transformed into finished goods on a large scale.
manufacturing process
An process during which natural or manufactured materials and products are processed and arranged by humans or their technology into structures.
The nature of "structures" must be further specified.
construction process
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
A quality which inheres in a astronomical body or astronomical body part by virtue of the variation in its material composition, participation in geological processes, and the variation in is land- and hydroforms.
Materials which are usually assessed when appraising geodiversity include minerals, rocks, sediments, fossils, soils and water. Landforms factored into geodiversity metrics typically include folds, faults, and other expressions of morphology or relations between units of earth material. Natural processes that are included in measures of geodiversity are those which either maintain or change materials or geoforms, including tectonics, sediment transport, and pedogenesis. Geodiversity does not usually factor in anthropogenic entities.
geodiversity
A process during which an ecosystem, its parts, or the processes it participates in are modified by human intervention to accomplish an objective.
Umweltmaßnahme
active ecosystem management process
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
A planned process during which humans access and obtain resources, benefits, or services from a natural or anthropised ecosystem.
planned environmental usage process
A planned environmental usage process during which an environment supports the settlement and dwelling of a community of humans.
This class does not include environments which are primarily used for commerce or industry.
usage of an environment for residential activity
A building which is primarily used for the long-term habitation of humans.
domestic building
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process during which humans apply technology to alter the magnitude, duration, rate, or impact of an environmental process.
Relabel the obo foundry unique label to be generic process
anthropogenic modulatory intervention process
An environmental process which is driven by the action of humans.
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
Experimental class for structural purposes not recommended for annotation.
material transport process
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean.
Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding.
Any abnormality of the cardiovascular system.
Abnormality of the cardiovascular system
Elevated body temperature due to failed thermoregulation.
A condition in which the stomach contents leak backwards from the stomach into the esophagus through the lower esophageal sphincter.
A lack or loss of appetite for food (as a medical condition).
An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles.
Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.
An atrial arrhythmia characterized by disorganized atrial activity without discrete P waves on the surface EKG, but instead by an undulating baseline or more sharply circumscribed atrial deflections of varying amplitude an frequency ranging from 350 to 600 per minute.
Stridor is a high pitched sound resulting from turbulent air flow in the upper airway.
An abnormal accumulation of fluid beneath the skin of the legs.
An abnormality of the gastrointestinal tract.
Abnormality of the gastrointestinal tract
Abnormal functionality of the cardiovascular system.
Abnormality of cardiovascular system physiology
An infection of the upper or lower respiratory tract.
Edema (swelling) of the bulbar conjunctiva.
A functional anomaly of the nervous system.
Abnormality of nervous system physiology
Abnormal structure of the gastrointestinal tract.
Morphological abnormality of the gastrointestinal tract
Abnormal functionality of the gastrointestinal tract.
Functional abnormality of the gastrointestinal tract
A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.
Abnormality of the digestive system
A functional anomaly of the digestive system.
Abnormality of digestive system physiology
A high-pitched whistling sound associated with labored breathing.
An anomalous (adventitious) sound produced by the breathing process.
Abnormal breath sounds characterized by discontinuous clicking or rattling.
Abnormal breath sounds characterized by low-pitched, snoring or rattle-like sounds.
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Melanie Courtot
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
Answers the question, why did you do this experiment?
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
datum label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
Person: Alan Ruttenberg
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
a numeral that denotes an integer
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
directive information entity
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
density plot
Density plot of SSC-H and FSC-H.
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photograph
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
a textual entity intended to identify a particular publication
document title
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
table
| T F --+----- T | T F F | F F
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
hypothesis textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses an assertion that is intended to be tested.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
Person:Chris Stoeckart
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
A planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
line chart
WEB: http://en.wikipedia.org/wiki/Line_chart
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
Person:Bjoern Peters
Person:Melanie Courtot
assigning a centrally registered identifier
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
Entries in a Column of which the header is "Pubmed ID"
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
CRID
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
author information textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
PERSON: Bill Baumgartner
case report textual entity
Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that needs to be perceived.
A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.
social act
the claim of a piece of land, the obligation to pay rent to the owner of a rental property
Socio-legal generically dependent continuants are generically dependent continuants that come into existence through declarations and are concretized as roles. They differ from information content entities in that they are not about something, but exist as quasi-abstract social entities. Socio-legal generically dependent continuants are not concretized as qualities inhering in independent continuants, but only as realizable entities borne by an organism or an aggregate of organisms.
socio-legal generically dependent continuant
my consenting verbally to buy a used TV set for $ 500, Jane Doe's signing of the divorce papers, John Robie's taking of Mrs. Steven's jewels
A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or revokes a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
Mathias Brochhausen
declaration
A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
document act input document
a judge's role of signing a court order, a hospital committee's to sanction conformance to a specific guideline for hospital employees.
A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
declaration performer role
A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.
The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. For instance, whereas the NCIt definition restricted informed consent forms to clinical trials, the present definition does not.
Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte
informed consent document
NCIt C16468
See curator note for 'incomplete informed consent form'.
informed consent form
A social act that is a part of an informed consent process and has output of a signed informed consent form. The signing process leads to a legal obligation.
Alla Karnovsky, Frank Manion, Yongqun He, Jihad Obeid, Chris Stoeckert, and Mathias Brochhausen
This class is under group discussion as of 03/26/2019.
Signing here does not mean that we have to sign with a pen. It may happen in terms of signing a piece of a paper or an electronic form.
signing an informed consent form
A document act input document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and whose purpose is to assist in obtaining consent.
J. Neil Otte
Note: instances of 'incomplete informed consent form' include both blank informed consent forms that are waiting to be used in a process of informed consent, as well as those that have been left blank by a patient, whether on purpose or in error. Those that have been left blank on purpose have been used in a process of informed consent, where the patient must have reached a decision.
incomplete informed consent form
A document act input document that has, as part, an incomplete informed consent form, along with some additional parts, such as a signature, stamp, or initials, which serve as a record to an act of consent that had the incomplete informed consent form as a specified input.
complete informed consent form indicating consent
An information content entity that is a handwritten depiction of a name.
Jonathan Vajda, Cooper Stansbury, J. Neil Otte.
signature
Sudden and sustained deterioration of the kidney function characterized by decreased glomerular filtration rate, increased serum creatinine or oliguria.
Progressive kidney disorder caused by vascular damage to the glomerular capillaries, in patients with diabetes mellitus. It is usually manifested with nephritic syndrome and glomerulosclerosis.
Impairment of the renal function secondary to chronic kidney damage persisting for three or more months.
A misfolded protein that has the ability to transmit its misfolded shape onto normal variants of the same protein.
Homo sapiens
An individual's total number of brothers and sisters.
The age of the subject at the time of the vaccination.
A group of people characterized by the practice of a common religion.
A member of the Jewish faith whose ancestors lived in North Africa, the Middle East, Portugal or Spain.
Individuals who do not necessarily identify with any particular race or others who do not wish to self select into a racial category(ies).
The age at which permanent cessation of menses occurs.
The age at which permanent cessation of menses occurred. (NCI)
A person having origins in the original peoples of Asia, but not China, India, Korea, the Philippine Islands or Vietnam.
A person having origins in the original peoples of the Pacific Islands, but not Guam, Hawaii, the Mariana Islands or Samoa.
A person of Mexican or Mexican American culture or origin, regardless of race.
A person of Cuban culture or origin, regardless of race.
A person of Spanish culture or origin, but not Cuban, Mexican, Puerto Rican, South or Central American, regardless of race.
The time elapsed between the day of conception and the day of delivery.
Chronological age reduced by the number of weeks born before 40 weeks of gestation; most appropriately used to describe children up to 3 years of age who were born preterm.
Best estimate of the first day of last menstrual period to birth plus time elapsed from day of birth.
A person's optimum weight as calculated by a standard methodology.
The money received by retired workers who have paid in to the Social Security system during their working years.
A fixed sum paid regularly to a person by their former employer.
The pressure within the left ventricle following the completion of diastolic filling, just prior to systole.
The pressure within the left ventricle of the heart at the end of the period when the chambers of the heart refill with blood and just before the contraction begins.
The pressure in the left ventricle at any point prior to the ejection of its contents into the aorta (systole).
The pressure within the left ventricle of the heart during the contraction of the left ventricle of the heart.
An approximate calculation of the gestational age of the fetus.
The number of education years that a subject has competed.
The number of years of education that a person has completed.
The age at which the first episode occurred.
The age at which the first hospitalization event occurred.
The age at which the first treatment event occurred.
The age at which the first treatment for the condition occurred.
The maternal body weight adjusted for the weight of the gravid uterus. This is derived by subtracting the gravid uterus weight from the total maternal body weight.
Gravid Uterus Adjusted Maternal Body Weight
An estimate or direct measurement of the heaviness of a fetus.
A measurement of the average weight of all live fetuses.
A measurement of the average weight of all live female fetuses.
A measurement of the average weight of all live male fetuses.
A measurement of the total weight of all live fetuses.
The age at which a minor assumes legal control over their person, actions, and decisions.
Denotes a person whose ancestry is in any of the countries of the central part of the African continent: Burundi, the Central African Republic, Chad, the Democratic Republic of the Congo, and Rwanda.
Denotes a person whose ancestry is in any of the countries of the northern part of the African continent: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia, and Western Sahara.
Denotes a person whose ancestry is in the country of South Africa.
Denotes a person whose ancestry is in any of the countries of the Americas or the Caribbean where Spanish or Portuguese is spoken.
Denotes a person whose ancestry is in any of the countries of South America.
Denotes a person whose ancestry is in any of the Asian countries south of China, east of India, west of New Guinea and north of Australia.
Denotes a person whose ancestry is in any of the Asian countries between the Caspian Sea in the west, China in the east, Afghanistan in the south, and Russia in the north.
Denotes a person whose ancestry is in the country or continent of Australia.
Denotes a person whose ancestry is in the country of New Zealand.
Denotes a person whose ancestry is in the country of Iceland.
Denotes a person whose ancestry is in the countries of Scandinavia: Denmark, Norway and Sweden. Finland and Iceland are generally included as part of the Scandinavian region.
A collection of ethnic geographical categories including African American, North American, Latin American, Caribbean, and South American.
A collection of ethnic geographical categories including Australian and New Zealander.
A collection of ethnic geographical categories including Middle Eastern and Hispanic.
Denotes a person of African ancestral origins whose family settled in America.
A person having origins in the original peoples of sub-Saharan Africa and the United States.
A person having origins in the original peoples of sub-Saharan Africa or the Caribbean.
Denotes a person of African ancestral origins whose family settled in Central America.
A person having origins in the original peoples of sub-Saharan Africa and Central America.
Denotes a person of African ancestral origins whose family settled in South America.
A person having origins in the original peoples of sub-Saharan Africa and South America.
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa and Central America.
A person having origins in the original peoples of Europe, the Middle East, or North Africa, and Central America.
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa and South America.
A person having origins in the original peoples of Europe, the Middle East, or North Africa, and South America.
The maximum pressure exerted into the systemic arterial circulation during the contraction of the right ventricle of the heart.
Blood pressure within the left atrium. It is commonly measured indirectly by a pulmonary capillary wedge pressure.
The estimated arithmetic average of atrial pressure.
An approximate determination of the weight of a body.
An approximate determination of the weight of the subject.
The result of a body mass index measurement.
Indicates a body mass index measurement less than 19.
Indicates a body mass index measurement greater than or equal to 19 but below 21.
Indicates a body mass index measurement greater than or equal to 21 but below 23.
Indicates a body mass index measurement greater than or equal to 23.
Body Mass Index Greater Than or Equal to 23
An indication that an individual's age is or was greater than 85 years.
An indication that an individual's age is or was between 80 and 85 years.
An indication that an individual's age is or less than 80 years.
A quantitative estimate of the pressure in a given cardiovascular structure during ventricular systole.
The age at which the full-time use of an entity occurred.
The age at which the full-time use of a pre-specified object first occurred.
Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, and who was either born in the United States or who was naturalized as a citizen of the United States.
A person having origins in the original peoples of Asia and the United States.
A person having origins in any of the Black racial groups of Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American". (OMB)
A person having origins in any of the black racial groups of Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American." (FDA)
A general indicator of the body fat an individual is carrying based upon the ratio of weight to height.
A general indicator of the body fat an individual is carrying based upon the ratio of weight to height. (NCI)
A measure that relates body weight to height. BMI is sometimes used to measure total body fat and whether a person is a healthy weight. Excess body fat is linked to an increased risk of some diseases including heart disease and some cancers.
A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease.
Denotes social groups with a shared history, sense of identity, geography, and cultural roots.
A group of individuals united by a common factor (e.g., geographic location, ethnicity, disease, age, gender)
Any finite or infinite collection of subjects from which a sample is drawn for a study to obtain estimates for values that would be obtained if the entire population were sampled. [AMA style Manual]
A subjective and comparative term describing a lack of sufficient wealth (usually understood as capital, money, material goods, or resources especially natural resources) to live what is understood in a society as a "normal" life: for instance, to be capable of raising a healthy family, and especially educating children and participating in society. A person living in this condition of poverty is said to be poor. The meaning of "sufficient" varies widely across the different political and economic areas of the world.
An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.
A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. The term, "Spanish origin," can be used in addition to "Hispanic or Latino." (OMB)
A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. (NCI)
Characteristics of a person such as education and occupation, used to describe the person's position in stratification systems, access to services, etc.
Ashkenazi Jews, also called Ashkenazim, are Jews who are descendants of Jews from Germany, Poland, Austria and Eastern Europe.
One of two major ancestral groups of Jewish individuals, comprised of those whose ancestors lived in Eastern Europe (Germany, Poland, Russia). The other group is designated Sephardic Jews and includes those whose ancestors lived in North Africa, the Middle East, and Spain. Most Jews living in the United States are Ashkenazi Jews.
Denotes a person having origins in any indigenous people of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment. The concept refers to population subgroups such as Eskimos, Aleuts, Inupiat, Yupik, Alutiiq, Egegik,and Pribilovian, Alaskan Athabascan, Tlingit, and Haida. The concept refers also to individuals who classify themselves as such.
A demographic parameter indicating the average amount of earnings made by a family in a particular population or/and during a particular period of time.
a demographics parameter useful for identifying socio-economic groups.
The distinguishing qualities or prominent aspects of an individual person.
Age of first menstruation. A risk factor for breast cancer
The age at which the first menstruation event occurred. (NCI)
The age at which a woman gave birth to her first live child.
An indication of a person's current tobacco and nicotine consumption as well as some indication of smoking history.
Current Tobacco and Nicotine Consumption Status
How long something has existed; elapsed time since birth.
How long something has existed; elapsed time since birth. (NCI)
The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart.
The maximum blood pressure in the systemic arterial circulation during the cardiac cycle.
The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling.
The minimum blood pressure in the systemic arterial circulation during the cardiac cycle.
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. (NCI)
A system, commonly called the INR, established by the World Health Organization (WHO) and the International Committee on Thrombosis and Hemostasis for reporting the results of blood coagulation (clotting) tests. All results are standardized using the international sensitivity index (ISI) for the particular thromboplastin reagent and instrument combination utilized to perform the test; the ratio of a patient's clotting time to the lab's mean reference value is normalized against the ISI. (from medterms.com and medicine.ucsf.edu)
A birth weight that is less than 2500 grams.
The length of a person's life, stated in months since birth.
The length of a person's life, stated in years since birth.
A gain or recurrent benefit during a period of time, usually measured in money that derives from capital or labor.
Income is one of the major demographic parameters used in population-based biomedical research.
A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. (OMB)
Native Hawaiian or Other Pacific Islander
Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuu. (FDA)
A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race.
A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification. (NCI)
Denotes a person of African ancestral origins whose family settled in the Caribbean region.
A person having origins in the original peoples of sub-Saharan Africa and the Caribbean.
A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB)
A person having origins in any of the original peoples of North and South America (including Central America), and who maintains tribal affiliation or community attachment. (FDA)
A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB)
A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent including, for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (FDA)
A person having origins in any of the original peoples of Europe, the Middle East, or North Africa. (OMB)
Denotes a person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. (FDA)
A person having origins in the original peoples of the Indian sub-continent.
A person having origins in any of the original peoples of the Indian subcontinent.
The concept is close to the term South Asian but several major South Asian populations such as Pakistani and Bangladeshi may not identify with it.
Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka.
Denotes a person with African ancestral origins who self identifies, or is identified, as African. The concept does not refer to those of other ancestry, for example, European and South Asian. In practice, the term mainly refers to people originated from forty-eight sub-Saharan Africa nations; and excludes individuals from North Africa countries, e.g. such as Algeria, Morocco, Egypt, Tunisia with Arab and Berber ethnicity.
A person having origins in any of the original peoples of sub-Saharan Africa.
Aleutian - a person having origins from the Aleut indigenous group of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment.
The native people inhabiting the Arctic of northern Canada, Greenland, Alaska, or eastern Siberia. The two main groups referred to as Eskimo are the Yupik and Inuit. A third group, the Aleut, is related. In Canada and Greenland, the term Eskimo has fallen out of favor, as it is considered pejorative by the natives and has been replaced by the term Inuit.
A person having origins in any of the original peoples of China.
A person having origins in any of the original peoples of Japan..
A person having origins in any of the original peoples of the Philippine Islands.
A person having origins in any of the original peoples of the Philippines.
A person having origins in any of the original peoples of Hawaii.
A person having origins in any of the original peoples of Korea.
A person having origins in any of the original peoples of North and South Korea.
A person having origins in any of the original peoples of Viet Nam.
Denotes the inhabitants of Laos, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Laos.
Denotes a person having origins in any of the original Hmong people originating in China around the Yellow River or Hoang Ho.
The native people originating in China around the Yellow River or Hoang Ho.
Early in the 19th century, the Hmong migrated to French Indochina, which comprised Vietnam, Cambodia and Laos. In 1947, Hmong officially became citizens of Loas. Later a number of Hmong emigrated to Thailand and the United States.
Denotes the inhabitants of Cambodia (formerly Kampuchea), a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Cambodia (formerly Kampuchea).
Denotes the inhabitants of Thailand, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Thailand.
Denotes a person from any of the islands in the western pacific encompassing the area from the Philippines in the west, Indonesia to the south west, Papua New Guinea and Melanesia to the south, and Polynesia to the south-east and east.
A person having origins in any of the original peoples of Micronesia.
Denotes any of the indigenous Chamorro people of Guam and the Mariana Islands or persons of that ancestry.
Denotes the inhabitants of Guam, a person from there, or their descendants elsewhere.
Denotes a person from any of the over 1,000 islands in the central and southern Pacific Ocean bounded by a triangle with its three corners at Hawaii, New Zealand, and Easter Island or a person of that ancestry.
A person having origins in any of the original peoples of Polynesia.
Denotes the inhabitants of Tahiti, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Samoa.
Denotes the inhabitants of Tonga, a person from there, or their descendants elsewhere.
Denotes a person from any of the islands in the region extending from the west Pacific to the Arafura Sea, north and north-east of Australia. or of that ancestry.
A person having origins in any of the original peoples of Melanesia.
Denotes the inhabitants of Fiji, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Papua New Guinea, a person from there, or their descendants elsewhere.
Primarily refers to a person having origins in the original peoples of the Indian sub-continent, a subset of which formed Pakistan. The term also refers to a person from Pakistan, whether or not ancestors were from India.
A person having origins in any of the original peoples of Pakistan.
Denotes the inhabitants of Bangladesh, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Bangladesh.
Denotes the inhabitants of Sri Lanka, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Sri Lanka.
Denotes the inhabitants of Bhutan, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Bhutan.
Denotes the inhabitants of Myanmar (formerly Burma), a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Myanmar (formerly Burma).
Denotes the inhabitants of Taiwan, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Taiwan.
Denotes the inhabitants of Indonesia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Indonesia.
Denotes the inhabitants of Malaysia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Malaysia.
Denotes the inhabitants of the japanese island of Okinawa, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Okinawa.
Denotes the inhabitants of Iwo Jima, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Iwo Jima.
Denotes the inhabitants of the Maldives, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the Maldives.
Denotes the inhabitants of Nepal, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Nepal.
Denotes the inhabitants of Singapore, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Singapore.
Denotes the inhabitants of Madagascar, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Madagascar.
Denotes the inhabitants of Barbados, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Barbados.
Denotes the inhabitants of Dominica, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Dominica.
Denotes the inhabitants of Haiti, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Haiti.
Denotes the inhabitants of Jamaica, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Jamaica.
Denotes the inhabitants of Tobago, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Tobago.
Denotes the inhabitants of Trinidad, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Trinidad.
Denotes the inhabitants of the West Indies, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the West Indies.
Denotes the inhabitants of Botswana, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Botswana.
Denotes the inhabitants of Ethiopia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Ethiopia.
Denotes the inhabitants of Liberia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Liberia.
Denotes the inhabitants of Namibia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Namibia.
Denotes the inhabitants of Nigeria, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Nigeria.
Denotes the inhabitants of the Democratic Republic of the Congo (formerly Zaire), a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Zaire.
Denotes the inhabitants of Tokelau, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Guam or the Mariana Islands.
Denotes the inhabitants of the Northern Mariana Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Marshall Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Palau, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Caroline Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Kosrae, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Pohnpei, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Saipan Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Kiribati, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Chuuk, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the island of Yap, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the Solomon Islands, a person from there, or their descendants elsewhere.
Denotes the inhabitants of the islands of Vanuatu, a person from there, or their descendants elsewhere.
Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Europe.
Denotes the inhabitants of Armenia, a person from there, or their descendants elsewhere.
Denotes the inhabitants of England, a person from there, or their descendants elsewhere.
Denotes the inhabitants of France, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Germany, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Ireland, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Italy, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Poland, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Scotland, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Russia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Russia.
Denotes the inhabitants of Sweden, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Norway, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Ukraine, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Mongolia, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of Mongolia.
Denotes the inhabitants of Finland, a person from there, or their descendants elsewhere.
Denotes a person from any of the countries of southwest Asia and northeastern Africa; this region includes those countries east of Egypt and south of Turkey and extending to Iran in the east.
A collective term used to identify indigenous peoples of northern Iraq and neighboring areas of Syria and Turkey, who also identify themselves as Aramaeans and Chaldeans. They are the survivors of the formerly extensive Aramaic- or Syriac- speaking Christian community of northern Iraq, southeastern Turkey, and northwestern Iran.
Denotes the inhabitants of Egypt, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Iran, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Iraq, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Lebanon, a person from there, or their descendants elsewhere.
Denotes those persons of mainly Arabic speakers who regard themselves as a distinct branch of the Arabic-speaking peoples, with family origin in Palestine being the defining characteristic.
Denotes the inhabitants of Syria, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Afghanistan, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Israel, a person from there, or their descendants elsewhere.
Denotes a person with ethnic origins in the Semitic people originally from the Arabian peninsula and surrounding territories in the Middle East and northern Africa.
A person having origins in any of the original peoples of the Arabian peninsula and surrounding territories in the Middle East and northern Africa.
Denotes a person having origins in one of the indigenous peoples of North America, who lived on the continent prior to the European colonization. The term includes individuals belonging to a large number of tribes, states, and ethnic groups, many of them still enduring as communities.
The native people inhabiting the territory spanning the Norton Sound on the Bering Sea to the Canadian border.
The native Yupik people inhabiting the coast of the Chukchi Peninsula in the far northeast of the Russian Federation and on St. Lawrence Island in Alaska.
The native people inhabiting western, southwestern, and southcentral Alaska and the Russian Far East.
Central Council of Tlingit and Haida Tribes
The mean pressure of the blood within the arterial circulation. The arterial pressure may be directly measured by insertion of an intra-arterial catheter connected to a transducer. The mean arterial pressure (MAP) can be calculated by subsequent analysis of the waveform. MAP can be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure.
The mean pressure of the blood within the arterial circulation. The arterial pressure may be directly measured by insertion of an intra-arterial catheter connected to a transducer. The mean arterial pressure (MAP) can be calculated by subsequent analysis of the waveform. MAP can be approximated without an invasive procedure using the following formula: diastolic pressure plus 1/3 of the pulse pressure, where pulse pressure is systolic pressure - diastolic pressure. (NCI)
The pressure of the circulating blood against the walls of the blood vessels.
The force of circulating blood on the walls of the arteries. Blood pressure is taken using two measurements: systolic (measured when the heart beats, when blood pressure is at its highest) and diastolic (measured between heart beats, when blood pressure is at its lowest). Blood pressure is written with the systolic blood pressure first, followed by the diastolic blood pressure (for example 120/80).
A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life.
Having ancestors of several or various races.
A person living in the United States of Mexican, Puerto Rican, Cuban, Central or South American, or other Spanish culture or origin. The concept does not include Brazilian Americans or Portuguese Americans.
A person of Puerto Rican culture or origin, regardless of race.
Denotes an american citizen of Mexican descent.
A person of Mexican and American descent.
Denotes a person from or of Cuba or an American citizen of Cuban descent.
Denotes the inhabitants of the Dominican Republic, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the Dominican Republic.
Denotes a person from the area between north and south America including persons from Belize, Costa Rica, El Salvador, Guatemala, Honduras, Nicaragua, Panama, and the Panama Canal zone.
Denotes a person from Spain or of Spanish descent.
A person from Spain or of Spanish descent.
Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day.
Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day.
An adult who has smoked 100 cigarettes in his or her lifetime and who currently smokes cigarettes. Includes daily smokers and non-daily smokers (also known as occasional smokers).
A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life.
Indicates a person who is known to have smoked but whose current smoking status is unknown.
Indicates that a person's smoking status is unknown.
Denotes the inhabitants of the Bahamas, a person from there, or their descendants elsewhere.
A person having origins in any of the original peoples of the Bahamas.
A person who inhales or has inhaled combustible products of organic material during their lifetime.
The age of a person at the start of a specific event.
The age of a patient on the first occurrence of an event, such as the first use of a medication.
The age of a person who is the subject in a study.
Age of patient who is the subject of observations.
A demographic parameter indicating the amount of earnings made by a family.
The first weight of a newborn obtained after birth.
A measured weight of a newborn obtained immediately or shortly after birth.
Denotes a person having origins in one of the indigenous people of South or Central America such as Mayans or Incas.
Denotes a person having origins in one of the indigenous people of the Caribbean.
Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe.
A person having origins in any of the original peoples of the countries surrounding the Mediterranean sea.
Denotes a person of European, Middle Eastern, or North African ancestral origins whose family settled in a North American country such as the United States of America or Canada.
Denotes a person having origins in a northern country of Africa such as Egypt, Sudan, Libya, Algeria, Morocco, or Tunisia.
A person having origins in any of the original peoples of North Africa.
Denotes a person having origins in any of the countries of northern Europe such as Belgium, Denmark, Austria, Switzerland, Norway, Sweden, or Great Britain.
A person having origins in any of the original peoples of Northern Europe.
Denotes a person having origins in any of the black racial groups of Africa whose family settled in a South or Central American country such as Argentina, Brazil, or Mexico.
Denotes a person with European, Middle Eastern, or North African ancestral origin whose family settled in the Caribbean region.
A person having origins in the original peoples of Europe, the Middle East, or North Africa, and the Caribbean.
Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France.
A person having origins in any of the original peoples of Western Europe.
Denotes a person of European ancestral origins whose family settled in a South or Central American country such as Argentina, Brazil, or Mexico.
Denotes a person having origins in any of the countries of Eastern Europe such as Czechoslovakia, Poland, Croatia, Hungary, Slovenia, Former Soviet Union, or Finland. It also includes persons who call themselves Gypsies from this region.
A person having origins in any of the original peoples of Eastern Europe.
Denotes a person having origins in the region of southwest Asia, between the India subcontinent and Europe, including Kuwait, Turkey, Lebanon, Israel, Iraq, Iran, Jordan, Saudi Arabia, lands east of Pakistan or the other countries of the Arabian Peninsula. Also includes people of Jewish ethnicity including Sephardic and Ashkenazic.
A person having origins in any of the original peoples of the Middle East.
A person's total income before taxes, exclusions, and deductions.
A general term for a group of culturally similar indigenous peoples inhabiting the Arctic regions of Canada, Greenland, Russia and the United States. In Alaska, the term Eskimo is commonly used, because it includes both Yupik and Inupiat, while Inuit is not accepted as a collective term. In Canada and Greenland, the term Eskimo has fallen out of favor, as it is considered pejorative by the natives and has been replaced by the term Inuit.
The systolic and diastolic blood pressure of the newborn upon examination; the normal range of the systolic blood pressure is 60 - 90, while the normal range of the diastolic blood pressure is 20-60.
The weight of a subject at a specified end point.
The weight of a subject at a specified end point. (NCI)
a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
WEB: http://en.wikipedia.org/wiki/Adverse_event
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
WEB: http://wiki.answers.com/Q/What_is_medical_intervention
a medical intervention where a patient is administered with a drug
an adverse event that has an outcome of abnormal sign in a musculoskeletal or connective tissue.
musculoskeletal and connective tissue disorder AE
WEB: http://www.cdc.gov/niosh/programs/msd/
A musculoskeletal disorder is an injury or disorder of the muscles, nerves, tendons, joints, cartilage, or supporting structures of the upper or lower limbs, neck, or lower back that are caused, precipitated, or exacerbated by sudden exertion or prolonged exposure to physical factors such as repetition, force, vibration, or awkward posture
an adverse event that shows a complication that occurs after a medical procedure and is directly related to the precedure itself.
a procedure complication AE that occurs after a surgery.
The key difference between a surgery and a procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. Technically speaking, a surgery is a specific type of procedure. A procedure is a broad general term that refers to any series of pre-defined steps that should be followed to achieve a desired result. Therefore, a “surgical procedure” is synonymous with a “surgery.” See more: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm.
Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery.
WEB: http://en.wikipedia.org/wiki/Surgery
WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
a musculoskeletal and connective tissue AE that displays an outcome of fistula, a permanent abnormal passageway between two organs in the body or between an organ and the exterior of the body.
WEB: http://medical-dictionary.thefreedictionary.com/fistula
a serious AE that is due to an allergic brochospasm, which causes a serious problem with breathing and requires treatment in an emergency room.
URL: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
URL: https://en.wikipedia.org/wiki/Bronchospasm
allergic brochospasm AE that requires treatment in emergency
a sensory capability AE that has an outcome of pain in a patient
a sudden death AE that occurs to an infant.
According to the Vaccine Adverse Event Reporting System (VAERS), 'sudden infant death' is an adverse event that was mentioned in 808 VAERS reports (0.6%) during1991-2001 (Reference: PMID: 12825543).
an AE that occurs in cardiovascular system.
an adverse event that has an outcome of an abnormal behavior and neurological phenotype.
WEB: http://www.psychguides.com/guides/behavioral-disorder-symptoms-causes-and-effects/
any anomaly in the actions, reactions, or performance of an organism in response to external or internal stimuli compared to controls
a behavior and neurological AE that has an outcome of inability or altered ability to respond to a sensory stimulus
a urinary system AE that results in the presence of blood in the urine
UMLS CUI: C0018965 (hematuria AND haematuria); UMLS CUI: C0947999 (blood urine presence)
WEB: http://kidney.niddk.nih.gov/kudiseases/pubs/hematuria/
Hematuria AE can be caused by menstruation, vigorous exercise, sexual activity, viral illness, trauma, or infection, such as a urinary tract infection (UTI), along with more serious disorders such as cancer, disease, and clotting.
an adverse event that has an outcome of urinary system AE is a functional anomaly of any of the organs involved in the production or excretion of urine
serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death.
WEB: http://en.wikipedia.org/wiki/Serious_adverse_event
WEB: http://www.google.ca/url?sa=t&source=web&ct=res&cd=1&ved=0CA4QFjAA&url=http%3A%2F%2Fwww.irrd.ca%2Fethics%2Fimages%2FAdverse-event-definition.doc&ei=eqFMS-yFNZSoswOt6siKAQ&usg=AFQjCNGnQcwI8OXH7dqxwo4RgZEEn8X6lg&sig2=UNngkCdO5ZTFvbIB1pKuaA
a serious adverse event that has an outcome of death.
a serious AE that is suspected to put the patient at substantial risk of dying at the time of the adverse event, or that the use or continued use of the device or other medical product might have resulted in the death of the patient.
a serious adverse event that leads to hospitalization. Such an adverse event resulted in an admission to the hospital or prolongation of hospitalization.
adverse event leading to hospitalization
a serious adverse event that leads to disability or permanent damage. Such an adverse event results in a substantial disruption of a person's ability to conduct normal life functions, i.e., the adverse event resulted in a significant, persistent or permanent change, impairment, damage or disruption in the patient's body function/structure, physical activities and/or quality of life.
a serious adverse event that resulted in congenital anomaly and bith defect, leading to suspicions that an exposure to a medical product prior to conception or during pregnancy resulted in an adverse outcome in the child.
adverse event leading to congenital anomaly
WEB: http://www.thefreedictionary.com/birth+defect
a serious adverse event which is an adverse event that requires intervention to prevent permanent impairment or damage leads to suspicions that the use of a medical product may result in a condition which requires a medical or surgical intervention to preclude permanent impairment or damage to a patient.
adverse event that requires intervention to prevent permanent impairment or damage
an cardiovascular adverse event that is a collection of blood outside the blood vessels, generally the result of hemorrhage, or more specifically, internal bleeding. It is commonly called a bruise.
YH: MedDRA ID: 10018852 is for "haematoma"; MedDRA ID: 10019428 is for "hematoma".
WEB: http://en.wikipedia.org/wiki/Hematoma
CTCAE: E13775 (hematoma); CTCAE: E11666 (brruising)
NCIt: C37921 (Bruising); NCIt: C50579 (Hematoma)
an adverse event that has an outcome of disease in the biological tissue that supports, binds together and protects organs
WEB: http://medical-dictionary.thefreedictionary.com/connective+tissue+disease
a connective tissue disorder AE that occurs in the non-skeletal tissue, usually subcutaneous and muscle tissue
WEB: http://www.reference.md/files/D018/mD018461.html
a death AE that has an outcome of unexpected death, 1 to 24 hours after the onset of symptoms
WEB: http://medical-dictionary.thefreedictionary.com/sudden+death
a process quality that represents the level of severity of an adverse event.
severity of adverse event
a severity of AE that shows sign and symptom within normal limits.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_0_Adverse_Event
Note the AE severity Grade 0 equals to CTCAE G0 AE severity.
AE severity G0
a severity of AE that shows asymptomatic, or involves mild or minor symptoms, or is of marginal clinical relevance, or consists of clinical or diagnostic observations alone, or where intervention is not indicated, or where only non-prescription intervention is indicated.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_1_Adverse_Event
Note the AE severity Grade 1 equals to CTCAE G1 AE severity.
AE severity G1
a severity of AE for which only minimal, local, or noninvasive intervention (e.g. packing, cautery) is indicated, or that limits instrumental activities of daily living (ADLs, e.g., shopping, laundry, transportation, or ability to conduct finances).
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_2_Adverse_Event
Note the AE severity Grade 2 equals to CTCAE G2 AE severity.
AE severity G2
a severity of AE that shows an outcome which is medically significant but not life-threatening; or for which inpatient care or prolongation of hospitalization are indicated; or that is an important medical event that does not result in hospitalization, but may jeopardize the patient or may require intervention either to prevent hospitalization, to prevent the AE from becoming life-threatening or causing death; or that is disabling; or that results in persistent or significant disability, incapacity, or limitation of self care activities of daily living (ADLs, getting in and out of bed, dressing, eating, getting around inside, bathing, or using the toilet).
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_3_Adverse_Event
Note the AE severity Grade 3 equals to CTCAE G3 AE severity.
AE severity G3
a severity of AE that has life-threatening consequences, for which urgent intervention is indicated, that puts the patient is at risk of death at the time of the event if immediate intervention is not undertaken, or that causes blindness or deafness (need to decide if unilateral or bilateral).
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_4_Adverse_Event
Note the AE severity Grade 4 equals to CTCAE G4 AE severity.
AE severity G4
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_5_Adverse_Event
Note the AE severity Grade 5 equals to CTCAE G5 AE severity.
AE severity G5
a hospitalization AE that leads to an intial hospitalization.
initial hospitalization AE
a hospitalization AE that leads to a prolonged hospitalization.
prolonged hospitalization AE
an adverse event that shows a result of injury or procedural complication.
injury or procedural complication AE
a pain AE that has marked discomfort sensation on the lateral side of the body in the region below the ribs and above the hip.
a death AE that has death in utero; failure of the product of conception to show evidence of respiration, heartbeat, or definite movement of a voluntary muscle after expulsion from the uterus, without possibility of resuscitation.
a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
medical procedure
a behavioral quality where the behavior in an organism is abnormal.
WEB: https://en.wikipedia.org/wiki/Abnormality_(behavior)
behavior abnormal quality
a death AE that has cessation of life occurring during the first 28 days of life.
An adverse event of hematoma in the subcapsular space of the kidney. This event occurs after a medical intervention, and may be caused by a tumor, trauma, vasculitis, renal infarction, or other disease process.
subcapsular hematoma AE
An adverse event of hematoma occurring around the kidney.
perinephric hematoma AE
arteriovenous fistula AE
An adverse event of surgery that leads to the puncturing of an adjacent organ. For example, a needle to the kidney may puncture the adjacent organs.
puncturing of adjacent organ AE
A date of specimen collection for the first collection of blood from a donor.
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
A date of specimen collection for the first collection of a tissue from a donor.
A date of specimen collection on which the surgery was performed during which the specimen was collected.
A data item that indicates the time when the collection of a specimen occurred.
Alice Nzinga
date of specimen preparation
It is denoted by Date in ISO-standard (8601) time format.
date of specimen collection
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
a worker role comprised of handling the administrative duties of a trial or study.
Person:Jennifer Fostel
clinical research coordinator role
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
OBI branch derived
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
evaluant role
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
PlanAndPlannedProcess Branch
measuring
scientific observation
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
Jennifer Fostel
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
Buffer, dye, a catalyst, a solvating agent.
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
PERSON:Matthew Brush
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation role
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Person: Jennifer Fostel
responsible party role
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
specimen role
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker role
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
sponsor role
a responsible party role involved with any of the following activities: initiating, managing and funding a study
CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Glucose in blood (measured in an assay to determine the concentration of glucose).
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
analyte role
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
hypothesis driven investigation
is an investigation with the goal to test one or more hypothesis
hypothesis generating investigation
is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
transfer function
A transfer function is a function to displace a material from one location to another.
extract
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
artifact creation objective
material transformation objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters.
An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism.
the sodium and chloride ions in a glass of salt water
A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
scattered molecular aggregate
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
A planned process with the objective of collecting a specimen.
Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
a material obtained from an organism in order to be a representative of the whole
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
A material entity that has the material sample role
An objective specification maintains some or all of the qualities of a material over time.
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
A measurement datum that is reported on a categorical scale
A biologist who uses a sequencing services fulfills the role of a service consumer
a role which inheres in a person who uses a service
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
A specimen that has been intentionally physically modified.
A tissue sample that has been sliced and stained for a histology study.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
An organism has been injected 1ml of vaccine
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An device that is used to determine the order of amino acids in protein sequences.
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
specimen from organism
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
tissue specimen
A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material.
Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process.
A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization
A service which has a material entity as specified input and/or specified output.
Services performing DNA sequencing or Cell Analysis
A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer.
A service that offers liquid nitrogen stroage.
A storage service in which a service consumer provides some material as input which a service provider stores and returns as output.
specimen identifier
A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
Person: Chris Stoeckert, Jie Zheng
specimen ID
NIAID GSCID-BRC metadata working group
selection criterion
rats should be aged between 6 and 8 weeks and weight between 180-250grams
A directive information entity which defines and states a principle of standard by which selection process may take place.
Person: Philippe Rocca-Serra
selection rule
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
specimen repository organization
An organization that provides a service to store and distribute specimens
sequencing facility organization
An organization that provides sequence determination service
comment on investigation
A textual entity that is about any of the aspects of an investigation worth noting
specimen identifier assigned by specimen repository
A specimen identifier which is assigned by a specimen repository
specimen identifier assigned by sequencing facility
A specimen identifier which is assigned by a sequencing facility
sequencing service
A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized.
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
selection
PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
selection process
A value specification that is specifies one category out of a fixed number of nominal categories
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
molecular analysis facility organization
An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs.
An organization that provides molecular analysis service.
An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
chemotherapy treatment exclusion criterion
An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
chemotherapy treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years.
An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
radiation treatment within the recent past exclusion criterion
An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years.
An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death.
An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process.
history of metastatic cancer exclusion criterion
An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
intravenous drug use exclusion criterion
Donor eligibility based on history of intravenous drug abuse in the last 5 years.
An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of blood borne infection exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
history of sex with someone with a history of intravenous drugs exclusion criterion
Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years.
An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process.
exposure to blood borne infectious disease exclusion criterion
Donor eligibility based on whether the donor has been exposed to HIV/AIDS.
An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process.
measurand role
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
health status inclusion criterion
‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
MIABIS2.0
clinically relevant lifestyle inclusion criterion
'smoking behavior’
An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process.
clinically relevant exposure inclusion criterion
'exposure to cigarette smoke’, ‘exposure to lead through drinking water'
An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process.
gravidity inclusion criterion
'pregnant’, ‘not pregnant'
An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process.
inclusion based on age, sex, and living region (rural area or specified city).
An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
defined population inclusion criterion
age group inclusion criterion
"18-33 years old"
An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
minimum age value specification
A value specifcation that specifies the youngest age when specifying an age range.
maximum age value specification
A value specifcation that specifies the oldest age when specifying an age range.
use of medication inclusion criterion
"received at least 2 days of vancomycin"
An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
hospital patient inclusion criterion
"included hospital patients"
An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
family status inclusion criterion
"included married and unmarried patients", "included divorced individuals"
An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
sex inclusion criterion
"included males and females", "included male patients"
An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
country of residence inclusion criteria
"include US residents"
An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
ethnicity inclusion criterion
"include only Hispanic individuals"
An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
WEB: http://en.wikipedia.org/wiki/Organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
extraction
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
inclusion condition
inclusion rule
exclusion rule
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
human subject enrollment
enlisting familiy members of HIV patients into a study
A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
As with group assignment, should the specified output here be an organism which bears a role
IEDB
criteria come from plan / clinical trial branch
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
maintaining cell culture
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
requested by Helen Parkinson for MO. Could be defined class
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
A specimen that is derived from some bodily fluid
Christian Stoeckert ORCID:0000-0002-5714-991X
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A representation of an image that supports an inference to an assertion about some quality of a patient.
A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A bodily process that is clinically abnormal.
The representation of a conclusion of a diagnostic process.
TODO: Define.
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure.
At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.
A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes.
social security number
A social role inhering in a human being.
human social role
party to a legal entity
party to a legal proceeding
party to a legal agreement
party to a marriage contract
party to a power of attorney
A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
male gender
male gender role
A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
female gender
female gender role
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
health care role
human health care role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
Amanda Hicks
patient
CAFE domain expert working group.
In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
patient role
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
physician
physician role
A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
nurse
based on: http://en.wikipedia.org/wiki/Nursing
nurse role
Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division).
health care provider organization role
person health care provider role
A health care provider organization role that inheres in an organization consisting of two or more physicians.
physician practice
A health care provider organization role that inheres in an organization that is comprised of other organizations.
integrated delivery network
An object aggregate of organisms.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
collection of organisms
An object aggregate all of whose components are human beings.
collection of humans
A role inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A role in human social processes that inheres in an organization.
Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
organization social role
A role in human social processes that inheres in an organism.
William R. Hogan Mathias Brochhausen
Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
Previous definition: A role in human social processes played by an organism.
organism social role
An organization social role that is realized by a health care process.
Previous definition: An organization social role played by an organization in health care processes.
organization health care role
A patient role that inheres in a human being.
human patient role
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
A role that inheres in an organism and is realized by habitually smoking tobacco products.
smoker role
material entity role
A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
hospital role
An organization social role that inheres in an organization and is realized by providing formal education to students.
school role
An organization that is the bearer of a school role.
school organization
A human social role that is realized by the process of formal education that the bearer undergoes.
student role
nursery school role
primary school role
secondary school role
A trauma patient role that inheres in a homo sapiens who is under the age of 15 years.
pediatric trauma patient
The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years."
pediatric trauma patient role
A patient role that inheres an organism suffering one or more injuries.
injured patient
The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries.
injured patient role
A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn.
The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn.
burn patient
burn patient role
A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient.
physiatrist
The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine.
Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine.
physiatrist role
A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury.
trauma patient
The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury.
trauma patient role
A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity.
residence function
A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function.
household
employee role
A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person.
http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015
US Census reference person role
A role that concretizes a socio-lega generically dependent continuant
socio-legal human social role
A socio-legal human social role that concretizes a socio-legally generically dependent continuat that was created by a declaration performed by an organization.
human role within an organization
employer role
payer role
party to an insurance policy
A US Census unemployed role is a human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff.
US Census unemployed role
A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon.
US physician assistant role
A physician role that inheres a human being and, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or by making decisions independently of a supervising physician regarding the adminstration of such medication.
anesthesiologist role
surgeon role
A surgeon role realized by its bearer using performing neurosurgery.
neurosurgereon role
A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products.
heavy smoker role
A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products.
light smoker role
employment data
income data
government assistance health care plan data
health care plan data
government assistance income data
WIC data
socio-economic data
A planned process that achieves the planned objective of precision medicine objective. Specifically, it is a medical process that includes the customization of healthcare, with medical decisions, treatments, practices, or products being tailored to the individual patient.
precision medicine process
An investigation that is targeted for precision medicine
precision medicine investigation
the number of people living together supported jointly by an household income
We may use IRS's definition: https://www.healthcare.gov/income-and-household-information/household-size/
household size
more than 5.5 pounds (2500 grams) birth weight
less than 5.5 pounds (2500 grams) birth weight
unknown birth weight
birth weight declined to answer
individual plan insurance (paid by the member)
group plan insurance through employee union
USA government health plan insurance
no insurance status
body temperature measured orally
body temprature by ear (tempanic, aural)
body temprature by forhead
arterial line body temperature
body temprature by other measurement
An education level that indicates a grade of higher than 7th but lower than 12 as the highest level of educational achievement.
higher than 7th but less than 12th Grade education level
direct serum bilirubin level
precision medicine objective
An education level that indicates the 7th grade complete or less as the highest level of educational achievement.
less than 8th Grade education level
An education level that indicates that the highest level of education achievement for a person is a high school completion, GED, or equivalent
high school completion, GED or equivalent
An information content entity that is the answer to a specific question
answer to question
An answer to question where the answer is Yes.
yes answer to question
An answer to question where the answer is No.
no answer to question
An answer to question that indicates the response to the specified question is unknown.
unknown answer to question
A do not know answer to question that is answered due to data unavailable
do not know due to data unavailable answer to question
An answer to question where one declines to answer the specified question.
declined to answer to question
An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box
other answer to question
An answer to question that is not listed in the whole list of response options
none answer to question
A textual entity that is a question presented in text
textual question
medical history form
A form with questions that is used to assess a person's eligibility to participate in a specific study (e.g., kidney precision medicine project).
eligibility assessment form
A form with questions that includes statistical data related to particular groups within a population where a person belongs to
demographic information form
physical measurement form
A textual question that includes a list of enumerated answers
question with enumerated responses
A question that has two primary and definitive answers: Yes and No, and there may be other given options like Don't know or Decline to answer.
question with yes and no responses
A question with enumerated responses where one can only choose one answer.
question with enumerated responses where only one answer chosen
A question with enumerated responses where one can choose multiple answers.
question with enumerated responses where multiple answers may be chosen
A case report form (or CRF) is a paper or electronic questionnaire specifically used in clinical trial research
Oliver He, Edison Ong, Fred Dowd, Hong Yu
case report form
laboratory result form
new patient form
biopsy procedure form
kidney biopsy procedure form
consent form
paper form
Medical records release form is usually required to be a paper form that should be signed by the patient who agrees to have his/her medical records released.
paper form with signature required
A public health process that involves clean drinking water and adequate treatment and disposal of human and animal excreta and sewage.
sanitation
A form that includes the information of contact for a person
contact information form
biosample collection form
clinic reception form
medications form
participant study status form
hospitalization form
personal history form
AKI hospitalization form
CKD hospitalization form
participant reported outcome measures form
health literacy questionnaire form
biopsy safety checklist form
post biopsy form
A clinical report form that covers the information about the tracking of biopsied tissue
tissue tracking form
pathology images upload form
diagnostic core .jpg images QC form
diagnostic core - disease categories form
central path quality metrics assessment Dx core form
central path quality metrics assessment interrogation core form
post-biopsy patient experience survey form
adverse event entry form
month of year
The first month of the year in the Gregorian calendar
January
The second month of the year in the Gregorian calendar.
February
The third month of the year in the Gregorian calendar.
March
The4th month of the year in the Gregorian calendar
April
The 5th month of the year in the Gregorian calendar
May
The 6th month of the year in the Gregorian calendar
June
The 7th month of the year in the Gregorian calendar
July
The 8th month of the year in the Gregorian calendar
August
The 9th month of the year in the Gregorian calendar
September
The 10th month of the year in the Gregorian calendar
October
The 11th month of the year in the Gregorian calendar
November
The 12th month of the year in the Gregorian calendar
December
A day of a calendar week that includes covers 24 hours each day.
day of week
Monday
Tuesday
Wednesday
Thursday
Friday
Saturday
Sunday
A day when an organism (e.g., a human) is born.
day of birth
the anniversary of the birth of a person
There is a difference between birthday and birthdate: The former, such as February 29, occurs each year, while the latter is the exact date a person was born (e.g., January 15, 2001).
birthday
information associated with an individual
personal information
A name of a person, which can have different types
person name
person first name
person last name
person middle name
患者本人在公安户籍管理部门正式登记注册的姓氏和名称
Suyuan Peng, Hong Yu, Yongqun He
《电子病历基本数据集 第10部分：住院病案首页》WS 445.10-2014
person full name
A person name that identifies a person for legal, administrative and other official purposes
person legal name
birth name
A person name that is used for a person to access a computer system.
person login username
maiden name
A person name that is fictitious and generated for a person to perform a particular social role.
pseudonym
Personal information that indicates a person's status in marriage
marital status
married marital status
single marrital status
divorced marrital status
A marital status that indicates no marriage status due to the death of his/her spouse and no remarriage.
widowed marrital status
legally separated marital status
not married marital status
An education level that indicates that the highest level of education achievement for a person.
education level
A telephone number is a sequence of digits assigned to a fixed-line telephone subscriber station connected to a telephone line or to a wireless electronic telephony device, such as a radio telephone or a mobile telephone, or to other devices for data transmission via the public switched telephone network (PSTN) or other public and private networks.
telephone number
A telephone number used for a phone at home
home telephone number
A telephone number used for a phone at work
work telephone number
A telephone number that is used in a cellular device
cell phone number
The status of actively looking for employment, but not being currently employed.
unemployment status
home postal address
work postal address
A series of letters or digits or both, sometimes including spaces or punctuation, included in a postal address for the purpose of sorting mail.
postal code
A ZIP Code is a postal code used by the United States Postal Service (USPS). The term ZIP is an acronym for Zone Improvement Plan.
ZIP code
The personal information that indicates an individual's or his/her family's economic and social position in relation to others, based on income, education, and occupation.
socioeconomic status
An socioeconomic status that indicates the status of being employed in an occupation to perform an activity or service for wage or salary. It is the status of a worker in a company or institute on the basis of the contract of work or duration of work done.
employment status
A state of employment in which a person works for a minimum number of hours defined as full-time by their employer.
full time employment status
a status of employment that carries fewer hours per week than a full-time job.
part time employment status
an employment status where the work is arranged and paid on a hourly basis.
hourly employment status
The state of working for oneself rather than an employer.
self-employment status
An employment situation where the working arrangement is limited to a certain period of time based on the needs of the employing organization.
temporary employment status
An education level that indicates that the highest level of education achievement for a person is a Master's degree.
Master's degree education level
An education level that indicates that the highest level of education achievement for a person is an academic Doctorate degree
academic Doctorate degree education level
An education level that indicates that a person does not have formal school education.
no formal school education level
An education level that indicates that the highest level of education achievement for a person is a high school completion.
high school education level
An education level that indicates that the highest level of education achievement for a person is a Bachelor's degree
Bachelor's degree education level
An education level that indicates that a person has obtained a degree allowing them to practice a profession, such as law, medicine, music, or ministry.
professional doctorate degree education level
M.D. completion education level
Pharmacy complete education level
An education level that indicates that the highest level of education achievement for a person is kindergarten completion.
kindergarten completion education level
An education level that indicates that the highest level of education achievement for a person is preschool.
preschool completion education level
An education level that indicates that the highest level of education achievement for a person is the pass of a General Education Development (GED) tests. The GED tests are a group of four subject tests which, when passed, provide certification that the test taker has United States or Canadian high school-level academic skills.
GED education level
An education level that indicates that the highest level of education achievement for a person is the 1st Grade elementary school completion.
1st Grade education level
An education level that indicates that the highest level of education achievement for a person is the second Grade elementary school completion.
2nd Grade education level
An education level that indicates that the highest level of education achievement for a person is the third Grade elementary school completion.
3rd Grade education level
An education level that indicates that the highest level of education achievement for a person is the 4th Grade elementary school completion.
4th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 5th Grade elementary school completion.
5th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 6th Grade elementary school completion.
6th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 7th Grade elementary school completion.
7th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 8th Grade elementary school completion.
8th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 9th Grade elementary school completion.
9th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 10th Grade elementary school completion.
10th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 11th Grade elementary school completion.
11th Grade education level
An education level that indicates that the highest level of education achievement for a person is the 12th Grade elementary school completion.
12th Grade education level
An education level that indicates that the highest level of education achievement for a person is a degree from a 2 year college program.
associate academic degree education level
An education level that indicates that the highest level of education achievement for a person is a degree from an occupational, technical, or vocational program
vocational program completion education level
The code in the specific coding system for the payment method of the expenses incurred in a single hospitalization of the patient
患者单次住院诊疗所发生费用的支付方式的特定编码体系中的代码
医疗付费方式
health insurance plan
A joint federal and state program that helps with medical costs for some people with limited income and resources.
Medicaid
Medicare is a national health insurance program in the United States, begun in 1966 under the Social Security Administration and now administered by the Centers for Medicare and Medicaid Services (CMS).
Medicare
private health insurance plan
worker compensation insurance plan
body weight
A body weight that is obtained immediately after birth
birth weight
emergency contact phone number
care provider
primary care provider
a centrally registered identifier symobol that refers to a specific study
centrally registered study identifier symbol
secondary care provider
tertiary care provider
An email address that is used secondary after the de fault first email address.
2nd email address
age question
A textual question that asks whether a person's age is less than 18 years old
Whether age less than 18 years old
An eligibility assessment form that is designed and used by the Kidney Precision Medicine Project (KPMP; http://kpmp.org) organization.
KPMP eligibility assessment form
BMI question
Whether BMI greater than 40 kg per m2
BMI greater than 40 kg per m2
question about blood transfusion
Whether unwilling to receive blood transfusion
pregnancy question
A pregnancy question that asks whether a person is pregnant at the moment of being questioned
Whether pregnant
transplant question
A transplant question that asks whether a person has received some transplant (includes solid transplant and bone marrow). Example transplants are kidney transplant and heart transplant.
Whether transplant recipient
A transplant question that asks whether a person has received a kidney transplant.
Whether kidney transplant recipient
KPMP clinical report form
A biopsy procedure form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP biopsy procedure form
A biosample collection form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP biosample collection form
An adverse event entry form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP adverse event entry form
A biopsy safety checklist form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP biopsy safety checklist form
A clinic reception form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP clinic reception form
A contact information form that is designed and used by the Kidney Precision Medicine Project (KPMP) organization.
KPMP contact information form
KPMP demographic information form
KPMP health literacy questionnaire form
A textual question that is about eligibility of a person to participate in a project.
eligibility question
KPMP AKI hospitalization form
KPMP CKD hospitalization form
KPMP laboratory result form
KPMP medical history form
This form is the end of a successful screening process
KPMP consent form
KPMP medications form
KPMP new patient form
KPMP participant reported outcome measures form
KPMP participant study status form
KPMP pathology images upload form
KPMP patient experience survey form
KPMP personal history form
KPMP physical measurement form
KPMP post biopsy form
KPMP tissue tracking form
KPMP Dx core - .jpg images QC form
KPMP Dx core - disease categories form
KPMP central path quality metrics assessment Dx core form
KPMP central path quality metrics assessment interrogation core form
The last four digits of a social security number, which is often asked in a survey form.
last four digits of social security number
A question in a survey form may ask whether a provided email address belongs to self
The self is an individual person as the object of his or her own reflective consciousness.
self
email question
An email question that asks the exact email address
What email address
An email question that asks whether the email address provided belongs to the person being surveyed.
Whether self owns email address
Who owns email address
A textual question that asks the birthday of the person being surveyed
What is your birthday
The textual name of the contact person or organization
contact name
The textual name of the contact person or organization that will be contacted during emergency
emergency contact name
Who owns the 2nd email address
Who owns the 3rd email address
physician information
physician specialty information
Health care or healthcare is the maintenance or improvement of health via the prevention, diagnosis, and treatment of disease, illness, injury, and other physical and mental impairments in human beings.
health care
A health care rendered for the benefit of a patient.
patient care
Primary care refers to the work of health professionals who act as a first point of consultation for all patients within the health care system
primary care
Secondary care includes acute care: necessary treatment for a short period of time for a brief but serious illness, injury, or other health condition. This care is often found in a hospital emergency department. Secondary care also includes skilled attendance during childbirth, intensive care, and medical imaging services.
secondary care
Tertiary care is specialized consultative health care, usually for inpatients and on referral from a primary or secondary health professional, in a facility that has personnel and facilities for advanced medical investigation and treatment, such as a tertiary referral hospital.
tertiary care
The term quaternary care is sometimes used as an extension of tertiary care in reference to advanced levels of medicine which are highly specialized and not widely accessed.
quaternary care
A patient care that is provided in hospital.
It is sometimes the synonym of secondary care. However, many secondary care providers, such as psychiatrists, clinical psychologists, occupational therapists, most dental specialties or physiotherapists do not necessarily work in hospitals. Some primary care services are delivered within hospitals. Depending on the organization and policies of the national health system, patients may be required to see a primary care provider for a referral before they can access secondary care.
hospital care
nephrology care
endocrinology care
physician question
What physician's specialty
hospital question
what name of hospital
address question
What street name
What city
What state
What Zip code
What street number and name
What apartment
What country
Do you have physician who provides your usual medical care?
Whether have physician for usual medical care
nephrology care provider
patient condition question
Whether diabetic kidney disease (DKD)
Whether hypertensive CKD (H-CKD)
Whether diabetic nephropathy resisters percutaneous biopsy
Whether AKI percutaneous biopsy
Whether AKI open biopsy
Whether biopsy
CRF filled up by patient
What postal code
CRF filled up by research coordinator
CRF filled up by biopsy operator
biopsy-related CRF
post biopsy hospitlization form
A clinical report form that is related to the processing and analysis of tissue of diseased patient.
pathology CRF
screening and patient tracking CRF
enrollment CRF
A eligibility question that asks whether a patient is eligible to consent to participate in a project.
Whether patient eligible to consent
HIPAA release
Whether patient signed HIPPA release form
When HIPAA release form signed
Whether scanned HIPAA release form uploaded
A chronic kidney disease that is accompanied with elevated blood pressure or hypertension
Oliver note: This term is not shown in MONDO or DOID. May request an addition.
hypertensive chronic kidney disease
a process that obtains a tissue from a living body in order to discover the presence, cause, or extent of a disease, or perform further biomeidcal investigation
biopsy
A systematized collection of patient and population electronically-stored health information in a digital format
NCIT definition: A digital version of a patient's medical history. [def-source: NCI]
electronic health record
A biopsy that takes a small piece of tissue out of a living body through the skin, using only a tiny incision
percutaneous biopsy
AKi percutaneous biopsy
A biopsy process in which a surgical incision (cut) is made through the skin to expose and remove tissues
open biopsy
AKI open biopsy
diabetic nephropathy resisters percutaneous biopsy
The state of being free from illness or injury
health status
The medical state or condition of a patient
medical condition
Whether diseased
Whether kidney diseased
the date or time on which a visit occurs
visit temporal region
a machine-readable centrally registered identifier that is represented in a visual format on a surface
barcode
a barcode that represents a specific specimen
specimen barcode
A planned process that tracks the tissue specimen including tissue vial number, storage location, time of vial arrival to storage, storage temperature, etc.
tissue tracking
A centrally registered identifier that is assigned for a specific clinical trial registered in the ClinicalTrials.gov. The format for the ClinicalTrials.gov registry number is “NCT” followed by an 8-digit number, e.g.: NCT00000419.
Qingliang Leon Li, Asiyah Yu Lin, Oliver He
USA National Clinical Trial identifier
A textual entity that is the title of a clinical trial
title of clinical trial
A title of clinical trial that is recorded as official
official title of clinical trial
A title of clinical trial that is meant for lay people understanding
lay title of clinical trial
A person who performs an investigation task and takes the role of an investigator role.
investigator
An investigator who is involved in a clinical trial and is responsible for ensuring that an investigation is conducted according to the signed investigator statement, the investigational plan, and applicable regulations; for protecting the rights, safety, and welfare of subjects under the investigator's care; and for the control of drugs under investigation.
clinical investigator
study start date
The (estimated) date on which the clinical study is open for recruitment of participants, or the actual date on which the first participant is enrolled.
clinical trial start date
study completion date
The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated.
clinical trial study completion date
The date that the final participant was examined or received an intervention for the purposes of final collection of data for the primary outcome, whether the clinical study concluded according to the pre-specified protocol or was terminated. In the case of clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all of the primary outcomes.
clinical trial primary completion date
The main objective of the intervention(s) being evaluated by the clinical trial.
clinical trial primary purpose specification
date of registration
A primary outcome measure used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment.
primary health outcome measurement datum
The current stage of a clinical study and whether it is or will be open for enrollment
recruitment status
A case report form that is presented in an electronic format
electronic case report form
A human being who is a candidate to participant in a clinical study
clinical study participant candidate
answering textual question
today's date
CRF filled up by participant candidate
pregnancy test positive
hemoglobin test finding
In KPMP, the hemoglobin < 9 g/dl is considered as hemoblobin test positive.
hemoglobin test positive with result < 9 g/dl
a date when a test is performed at the first time
date of first test
date of test
a date when a test is performed at the second time
date of second test
A person name that includes both the first and last name
person first and last name
sign date
status
study status
patient status
a selection criterion (rule) which defines and states the exclusion condition for an entity to be considered as suitable for a given task or participation in a process.
exclusion criterion - obsolete
An exclusion criterion that relates to the process of bleeding
bleeding exclusion criteria
A case report form of PROMIS: Patient-Reported Outcomes Measurement Information System. PROMIS is a set of person-centered measures that evaluates and monitors physical, mental, and social health in adults and children. It can be used with the general population and with individuals living with chronic conditions.
PROMIS form
kit identifier
A centrally registered identifier that is for a kit used in biopsy
biopsy kit identifier
A PROMIS form that is designed and used by the KPMP project (http://kpmp.org).
KPMP PROMIS form
biopsy pass
needle biopsy
A textual question about health condition
health status question
A health status question that asks about the condition of a person's heath, which can be a selection from different options such as Excellent, Very good, Good, Fair, or Poor.
what health status
excellent health status
very good health status
good health status
fair health status
poor health status
quality of life
excellent quality of life
very good quality of life
good quality of life
fair quality of life
poor quality of life
consent status
A consent status that indicates a participant unwilling to receive a procedure of blood transfusion
unwilling to receive a blood transfusion
A consent status that indicates a participate willing to receive a procedure of blood transfusion
willing to receive a blood transfusion
year
A textual quesition thta is about medical history of a person
medical history question
What birth weight
Japan clinical trial identifier
A Japan clinical trial identifier provided by the University Hospital Medical Information Network Center (UMIN-CTR)
UMIN-CTR clinical trial identifier
JAPIC clinical trial identifier
JMACCT clinical trial identifier
European clinical trial registry identifier
A clinical trial that covers both Phase 1 and 2
Phase I/II clinical trial
combinational intervention
The quality of a clinical trial that studies a drug or biological product. The phase is based on the study's objective, the number of participants, and other characteristics. According to USA FDA, there are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4.
clinical trial phase
A clinical trial phase that represents the first-in-man trial, which tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects.
clinical trial phase 1
A clinical trial phase that is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI]
clinical trial phase 2
A clinical trial phase that is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI]
clinical trial phase 3
A clinical trial phase that is designed for a randomized, controlled trial to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed. [def-source: NCI]
clinical trial phase 4
A clinical trial phase that is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI]
clinical trial phase 0
A clinical trial that covers both Phase 2 and 3
Phase II/III clinical trial
radiation
genetic intervention
A medical intervention that involves a behavioral process to control, prevent, or treat a behavior problem.
behavioral intervention
study accession identifier
title of study
A livinging individual who is or becomes a participant in research, either as a recipient of a test article or as a control. A subject may be either a healthy human or a patient. Based on the NIH definition, a living individual about whom an investigator (whether professional or student) conducting the following research: (1) Obtains information or biospecimens through intervention or interaction with the individual, and uses, studies, or analyzes the information or biospecimens; or (2) Obtains, uses, studies, analyzes, or generates identifiable private information or identifiable biospecimens.
human subject
In clinicaltrials.gov, contact information character limits: First Name: 62 characters Last Name: 62 characters Degree: 30 characters Phone: 30 characters Phone Ext: 14 characters Email: 254 characters Citation: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials
A person who serves as a contact role and has disclosed specified information to be reached. Usually the contact information, such as email and phone number, is provided.,
Leon, Asiyah, Oliver: Since each contact needs to provide some contact information, we may need to define the contact information.
contact person
A contact person for each facility participating in a study.
facility contact
biosample identifier
GSM identiifier
ImmPort biosample identifier
Person to contact if Facility Contact is not available (that is, a second contact person).
facility contact backup
contact of scientific queries
An investigation agent role that is taken by a human individual
investigator role
a role taken by a person who serves as a contact for some process.
contact person role
Topical ocular hypotensive eye drops
contact for public queries
A person who is responsible for the overall scientific leadership of the protocol, including study principal investigator
overall study official
A person to whom questions concerning enrollment at any location of the study can be addressed.
central contact person of study
A person to contact if Central Contact is not available.
central contact backup of study
information content entity about a contact person
contact person information
A sponsor role taken by an individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. The Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder.
primary sponsor role
A sponsor role taken by an additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship.
A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. by WHO (https://www.who.int/ictrp/network/trds/en/)
In clinicaltrials.gov, the secondary sponsor role can be taken by a project collaborator (Reference: https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf). However, a secondary sponsor may serve as a collaborator role, but a collaborator may not serve as a secondary sponsor role.
secondary sponsor role
An investigator role taken by an individual who is designated as responsible party by the sponsor
principal investigator role
An investigator role taken by an individual who both initiates and conducts the study
sponsor investigator role
An investigation agent role taken by an agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them.
A secondary sponsor may serve as a collaborator role. However, a collaborator may not serve as a secondary sponsor role.
investigation collaborator role
a selection criterion (rule) which defines and states the inclusion condition for an entity to be considered as suitable for a given task or participation in a process.
Oliver He, Edison Ong, Leon Li, Asiyah Lin
inclusion criterion - obsolete
A centrally registered unique identifier assigned by the primary registry to a study including a clinical trial.
primary registry identifier
An individual, organization, group or other legal entity that involves with any of the following activities: initiating, managing and funding a study
sponsor
investigation agent
The individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. In clinical trial, the Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder.
primary sponsor
An additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship.
A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. Reference: https://www.who.int/ictrp/network/trds/en/
secondary sponsor
A centrally registered unique identifier besides the primary registry identifier allocated by the Primary Registry, if any.
secondary registry identifier
An agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them.
collaborator
An investigator who is designated as responsible party by the sponsor
principal investigator
sponsor investigator
A role taken by a string (which may have mixed integer and text) that serves as a unique record.
identifier role
obsolete class
An identifier role that inheres in a unique record which provides an identifier secondary to the primary registry identifier.
secondary registry identifier role
An identifier role that is assigned by a primary registry and provides a unique record.
primary registry identifier role
a human who is a recipient of a health care service performed by healthcare professionals.
A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research.
human subject study
A collection of humans who share a defining characteristic, typically those who are collectively experiencing a common event (e.g., a clincal trial study) in a selected period.
human cohort
A material entity that is composed of organic structure and is capable of self-replication (with or without host support). Various types of self-replicating organic structures can be found at: https://en.wikipedia.org/wiki/Template:Self-replicating_organic_structures.
A self-replicating organic structure that is composed of one cell or multiple cells and embodies the properties of life.
cellular self-replicating organic structure
cellular organism
A self-replicating organic structure that does not have the unit of cell but it may use the cells to replicate.
non-cellular self-replicating organic structure
non-organism self-replicating organic structure
acellular self-replicating organic structure
An non-organism infectious agent that is composed solely of a short strand of circular, single-stranded RNA and has no protein coating.
viroid
A process of a dynamic system that produces an identiical or similar copy of itself.
self-replication
organic chemical entity
A measurement datum that is about the age of human subject
human subject age data
For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, a child is defined as an individual under the age of 18 years.
child age data of human subject (by NIH)
The regular aged adult group is defined here as an individual over 18 years of age.
adult age data of human subject
For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, an older adult is defined as an individual 65 years of age or older.
older adult data of human subject (by NIH)
The representation of a positive conclusion of a diagnostic process, which indicates that the patient is diagnozed as positive for a hypothetic disease.
positive diagnosis
The representation of a negative conclusion of a diagnostic process, which indicates that the patient is diagnozed as negative for a hypothetic disease.
negative diagnosis
The representation of a presumptive positive conclusion of a diagnostic process, which indicates that the patient is diagnozed as presumptive positive for a hypothetic disease.
presumptive positive diagnosis
A human subject classified as adult, which is defined by NIH as an individual under the age of 18 years. For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, a child is defined as an individual under the age of 18 years.
child human subject
A human subject classified as adult, which is defined by NIH as an individual 65 years of age or older. For the purposes of the NIH Policy and Guidelines on the Inclusion of Individuals Across the Lifespan as Participants in Research Involving Human Subjects, an older adult is defined as an individual 65 years of age or older.
older adult human subject
A human subject classified as adult, which is defined by NIH as an individual over 18 years of age.
adult human subject
Yingtong Liu, Anthony Huffman, Oliver He
biomarker role
immune signature role
cytokine signature role
inflammatory cytokine signature role
A material entity that has a measurable quality or process profile(s), which can be used as an indicator of an underlying biological state or identity.
The NIH Biomarkers and Surrogate Endpoint Working Group defined a biomarker as “A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention” (https://pubmed.ncbi.nlm.nih.gov/11240971/). However, the definition of 'characteriistc' is unclear, so we do not use the exact definintion in the ontology.
biomarker
A biomarker that is indicative of an immune response
immune biomarker
cytokine biomarker
inflammatory cytokine biomarker
disease biomarker role
A biomarker that is indicative of a disease
disease biomarker
A biomarker that is an indicator of a cell lineage or cell type
cell lineage biomarker
molecular biomarker
Cellular biomarkers are marked cells that can be isolated, sorted, quantified and characterized by their morphology and physiology, and used in both clinical and laboratory settings for different biomarker applications. An example of a cellular biomarker sorting technique is Fluorescent-activated cell sorting.
cellular biomarker
imaging biomarker
A biomarker that can predict clincal outcome.
predictive biomarker
A biomarker that provides information about the patient's overall outcome, regardless of therapy.
prognostic biomarker
A biomarker that can serve a role in narrowing down diagnosis, which can lead to diagnosis that is significantly more specific to individual patients.
diagnostic biomarker
A molecular biomarker at the DNA gene level
DNA biomarker
RNA biomarker
A molecular biomarker at the protein level
protein biomarker
A biomarker that is indicative of a disease and achieved through imaging.
imaging disease biomarker
A disposition that a material entity (e.g., gene or protein) is susceptible to be up or down-regulated in an organism or virus.
susceptibility to biological regulation
imaging disease biomarkers by magnetic resonance imaging
imaging disease biomarkers by MRI
A biomarker that is indicative of the presence of cancer in the body
cancer marker
A disposition that a material entity (e.g., gene or protein) is susceptible to be up-regulated in an organism or virus.
susceptibility to biological up-regulation
A disposition that a material entity (e.g., gene or protein) is susceptible to be down-regulated in an organism or virus.
susceptibility to biological down-regulation
A Unified Social Credit Identifier is issued to registered companies and other types of organization by the Chinese government.
Unified Social Credit Identifier
healthcare organization
A centrality registered identifier for a medical record.
medical record number
A centrally registered identifier that is uniquely assigned to a person.
person ID
指患者在本医疗机构住院诊治的次数
Suyuan Peng, Hong Yu, Oliver He
《卫生部关于修订住院病案首页的通知》卫医政发〔2011〕84号
住院次数
number of hospital admissions
A time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's admission to a hospital
指患者实际入病房的接诊时间
《住院病案首页数据填写质量规范（暂行）》国卫办医发〔2016〕24号
入院时间
date of hospital admission
A year when an organism (e.g., a human) is born.
year of birth
A month when an organism (e.g., a human) is born.
month of birth
This term is generated to be equivalent to the "birth_datetime" in OMOP. Also note: in OMOP v6.0, DATETIME fields were made mandatory and date fields were made optional. Reference: https://ohdsi.github.io/CommonDataModel/cdm60.html#PERSON
birth datetime
A time measurement datum that is about a human being who bears a patient role and specifies the date of the patient's discharge from a hospital
出院时间是指患者治疗结束或终止治疗离开病房的时间，其中死亡患者是指其死亡时间；记录时间应当精确到分钟
The number of health card for residents of the People's Republic of China
在已统一发放“中华人民共和国居民健康卡”的地区填写健康卡号码，尚未发放“健康卡”的地区填写“-”
健康卡号
residents health card number
birth-related time
A care site is a uniquely identified institutional (physical or organizational) unit where healthcare delivery is practiced, for example, office, ward, hospital, clinic, etc.
According to OMOP, care site does not consider the provider (human) information such a specialty. Instead, care site is considered at the institutional level.
care site
A centrally registered identifier that refers to where the care provider typically provides the primary care.
care site identifier
A medical occurrence where a person engages with the healthcare system for a duration of time.
medical visit
A centrally registered identifier that refers to a specific visit occurrence. This identifier identifies a unique interaction between a person and the health care system.
visit occurrence identifier
A vist ocurrence in which the patient's condition requires admission to a hospital.
inpatient visit
A vist ocurrence in which a patient attends an outpatient clinic with no plan to stay beyond the duration of the visit.
outpatient visit
emergency room visit
The date on which a visit starts. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction.
visit start date
The date on which a visit ends. For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.
visit end date
A temporal region that covers the time period from the visit start time to the visit end time.
visit duration
The date and time on which a visit starts. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction.
visit start datetime
The date and time on which a visit ends. For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.
visit end datetime
A visit occurrence that occurs for the person prior to the given visit. There could be a few days or a few years in between.
preceding medical visit
A vist ocurrence that includes a visit to the emergency room followed by a subsequent inpatient visit.
emergency room and inpatient visit
A visit to a dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock
non-hospital institution visit
A visit where a provider visits a person, without a care site, within one day, delivering service
home medical visit
A visit in which a patient engages with a Provider through communication media. A patient can use digital information and communication technologies, such as computers and mobile devices, to access health care services remotely and manage their health care.
telehealth visit
A visit to the pharmacy for dispensing of drug, at a care site, within one day
pharmacy visit
A visit to a dedicated institution, at a care site, within one day, for the purpose of a measurement. The visit is carried out in a medical laboratory or clinical laboratory where tests are carried out on clinical specimens to obtain information about the health of a patient to aid in diagnosis, treatment, and prevention of disease
laboratory medical visit
A medical visit occurrence that involves an interaction with the healthcare system, without a care site, within a day, with no providers involved, for the administrative purpose of patient case management.
case management visit
A site that is used as a permanent or semi-permanent residence for one or many humans.
home
A centrally registered identifier that refers to the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS). NPI is assigned for use in all administrative and financial transactions specified by HIPAA.
National Provider Identifier
A centrally registered identifier that is issued by the Drug Enforcement Administration (DEA), a US federal agency, that allows a provider to write prescriptions for controlled substances.
DEA identifier
A medicl occurrence that is ordered by, or carried out by, a healthcare provider on a patient with a diagnostic or therapeutic purpose.
medical procedure occurrence
A centrally registered identifier that refers to a procedure occurrence, which is an activity or process that is ordered by, or carried out by, a healthcare provider on a patient with a diagnostic or therapeutic purpose.
procedure occurrence identifier
A temporal region that is associated with a procedure
procedure temporal region
procedure start date
The date and time when a procedure starts
procedure start datetime
procedure end date
procedure end datetime
The information content entity that represents the origin of record such as the clinical form as the origin record of death.
provenance of record
As part of the OMOP CDM, PROCEDURE TYPE CONCEPT best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’.
A provenance of record that determines the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
provenance of procedure record
death diagnosis status
A provenance of record that designates the source (provenance) of the cost data.
provenance of cost record
As part of the OMOP CDM, use the type concept that be reflects the source of the death record. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.
A provenance of record that determines the provenance of the death record, i.e., where it came from.
provenance of death record
A provenance of record that determines the provenance of the record, as in whether the record is from administrative claims or EHR.
provenance of device record
As part of the OMOP CDM, choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug.
A provenance of record that determines the provenance of a drug prescription, which delineates prescriptions written, prescriptions dispensed, medication history, patient-reported exposure, etc.
provenance of drug record
A provenance of record that determines the provenance of the Episode record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
provenance of episode record
A provenance of record that determines the provenance of the Measurement record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.
provenance of measurement record
As part of the OMOP CDM, the provenance of the notes most likely will be EHR.
A provenance of record that determines the provenance of the note.
provenance of note record
A provenance of record that determines the provenance of the Observation record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.
provenance of observation record
A provenance of record that determines the source of the specimen record, as in an EHR system.
provenance of specimen record
As part of the OMOP CDM, populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim.
A provenance of record that determines the provenance of the visit record, or where the record comes from.
provenance of visit record
A provenance of record that determines the provenance of the Condition record, as in whether the condition was from an EHR system, insurance claim, registry, or other sources.
provenance of condition occurrence record
The primary diagnosis refers to the patient condition that demands the most provider resources during the patient’s stay.
There is often confusion surrounding primary and principal diagnoses and, consequently, the terms are commonly used interchangeably. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis
primary diagnosis status
A medicl occurrence where a person presents a disease or medical condition stated as a diagnosis, a sign, or a symptom, which is either observed by a Provider or reported by the patient.
medical condition occurrence
the date or time on which a condition occurs
condition temporal region
condition end date
The date and time on which a clinical condition ends.
condition end datetime
condition start date
The date and time on which a condition starts.
In OMOP CDM, most often data sources do not have the idea of a start date for a condition. Rather, if a source only has one date associated with a condition record it is acceptable to use that date for both the CONDITION_START_DATE and the CONDITION_END_DATE. Reference: https://ohdsi.github.io/CommonDataModel/cdm54.html#CONDITION_OCCURRENCE
condition start datetime
The state or status at the point during the visit the diagnosis was given (admitting diagnosis, final diagnosis), whether the diagnosis was determined due to laboratory findings, if the diagnosis was exclusionary, or if it was a preliminary diagnosis, among others.
In OPMI, we treated medical condition status as a status, which is a realizable entitry. One major section of the branch is various diagnosis condition status. There are basically two types of diagnosis: one type diagnosis is treated as a condition status, the other is diagnosis (OGMS_0000073) as a type of clinical data item. One good example to illustrate the difference is the difference between primary and principal diagnoses. While these can be (and frequently are) the same diagnosis in practice, their definitions are distinct. While a principal diagnosis is the underlying cause of patient symptoms, the primary diagnosis is used for healthcare billing purposes and is a type of medical condition status. Reference: https://www.definitivehc.com/resources/glossary/primary-diagnosis
medical condition status
An action specification that indicates why a Condition is no longer valid with respect to the purpose specified within the source data.
In OMOP CDM, a Stop Reason does not necessarily imply that the condition is no longer occurring.
medical condition stop reason specification
The status of have the primary admission diagnosis
primary admission diagnosis status
confirmed diagnosis status
Principal diagnosis describes the underlying cause behind a patient’s initial hospital admission and is assigned only after a physician has completed necessary tests and examinations.
principal diagnosis
A discharge diagnosis is a final diagnosis given a patient before release from the hospital after all testing, surgery, and workup are complete.
discharge diagnosis status
A postoperative diagnosis is a diagnosis or diagnoses discovered or confirmed during the surgery. Often it is the same as the preoperative diagnosis.
postoperative diagnosis status
preliminary diagnosis status
A preoperative diagnosis is a surgical diagnosis or diagnoses that are assigned to the patient before the surgical procedure, and is the reason for the surgery. A preoperative diagnosis is, in the opinion of the surgeon, the diagnosis that will be confirmed during surgery.
preoperative diagnosis status
An admitting diagnosis is defined as the initial working diagnosis documented by the patient's admitting or attending physician who determined that inpatient care was necessary.
admission diagnosis status
A cause of death is an official determination of conditions resulting in a human's death, which may be recorded on a death certificate. A cause of death is determined by a medical examiner.
cause of death status
primary referral diagnosis status
A referral is a written request from one health professional to another health professional or health service, asking them to diagnose or treat you for a particular condition.
referral diagnosis status
A secondary diagnosis is a condition that coexists at the time of admission, that develops subsequently, or that affects the treatment received and/or length of stay.
secondary diagnosis status
secondary discharge diagnosis status
secondary referral diagnosis status
preliminary admission diagnosis status
preliminary discharge diagnosis status
condition to be diagnosed by procedure status
A contributory cause of death is a significant condition that unfavourably influences the course of the morbid process and thus contributes to the fatal outcome, but which is not related to the disease or condition directly causing death.
contributory cause of death status
An immediate cause of death is a final disease, injury, or complication directly causing the death
immediate cause of death status
A process of a person’s exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes through a mechanism beyond chemical action. Devices include implantable objects (e.g. pacemakers, stents, artificial joints), medical equipment and supplies (e.g. bandages, crutches, syringes), other instruments used in medical procedures (e.g. sutures, defibrillators) and material used in clinical care (e.g. adhesives, body material, dental material, surgical material).
medical device exposure
primary discharge diagnosis status
the date or time on which a device exposure occurs
device exposure temporal region
The date on which a device exposure ends.
"Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure end date
The date and time on which a device exposure ends.
"If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure end datetime
secondary admission diagnosis status
A medical condition status in which the subject is not presently experiencing the condition or situation and there is a negligible perceived risk of the condition or situation returning.
resolved condition status
The underlying cause of death refers to the disease or injury that initiated the train of morbid events leading directly to death or the circumstances of the accident or violence that produced the injury.
underlying cause of death status
The date on which a device exposure starts.
"Valid entries include a start date of a procedure to implant a device, the date of a prescription for a device, or the date of device administration." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure start date
The date and time on which a device exposure starts.
"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DEVICE_EXPOSURE
device exposure start datetime
the date or time on which a drug exposure occurs in a patient
drug exposure temporal region
The date on which a drug exposure starts.
"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE." http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure start date
The date and time on which a drug exposure starts.
"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)." http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure start datetime
The date on which a drug exposure ends for a patient.
drug exposure end date
The date and time on which a drug exposure ends for a patient.
"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)". http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure end datetime
The reason a person stopped a medication as it is represented in the source. Reasons include regimen completed, changed, removed, etc.
This information is often not populated in source data and it is a valid etl choice to leave it blank if the information does not exist. This field will be retired in v6.0 of the OMOP CDM, . http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug exposure stop reason specification
An action specification that represents the intended refills at time of the prescription.
drug refills specification from prescription
This is only filled in when the record is coming from a prescription. http://ohdsi.github.io/CommonDataModel/cdm54.html#DRUG_EXPOSURE
drug refills specification
The end date of a drug exposure as it appears in the source data
drug exposure verbatim end date
An exposure or contact of a person to a drug. The drug exposure includes drug dispensing or administration for a person.
This term is used in OMOP CDM. This term appears similar to 'drug administration'. However, drug exposure also covers involuntary, but drug administration usually means voluntary. More discussion is needed.
drug exposure
In drug exposure, the quantity refers to number of pieces, e.g. tablets. In the example: 20 Ingredient dose= quantity x amount_value [amount_unit_concept_id] Acetaminophen dose = 20 x 500mg = 10,000mg Daily dose = Acetaminophen dose/drug duration
The quantity of drug exposure refers to the number of drug pieces, e.g. tablets, that are exposed to a person.
quantity of drug exposure
This days of the supply of a drug that is given on the prescription.
days of drug supply
A period time when an observation is conducted.
In OMOP, the observation table contains records that defines spans of time during which two conditions are expected to hold: (i) Clinical Events that happened to the Person are recorded in the Event tables, and (ii) absense of records indicate such Events did not occur during this span of time.
observation period
A temporal region that is associated with an observation
observation temporal region
observation period start date
observation period end date
measurement time
measurement date
A datetime when a measurement is conducted.
measurement datetime
A unique key given to a Measurement record for a Person. Such record can be used in the ETL for how duplicate Measurements during the same Visit were handled.
clnical measurement identifier
Payer plan is a plan specification that captures the details of the period of time that a person is continuously enrolled under a specific health Plan benefit structure from a given payer. Each person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies.
payer plan
A temporal region that is associated with the payment process defined in a payer plan
payer plan temporal region
A period time of the payment that is covered by a payer plan for a person.
payer plan period
payer plan period start date
payer plan period end date
A process that a patient experiences over a period of time.
medical occurrence
An electronic health record that records the information of medical condition.
condition occurrence record
An electronic health record that records the information of medical cost.
electronic health cost record
An electronic health record that records the information of the death record of a person.
electronic death record
An electronic health record that records the information of medical device usage.
electronic device record
An electronic health record that records the information of drug usage including drug prescriptions written, prescriptions dispensed, medication history, patient-reported exposure, etc.
electronic drug record
A data item that captures clinical facts about a patient obtained in the context of examination, questioning or a procedure.
This term is dervied from OMOP:Observation term. Observations differ from Measurements in that they do not require a standardized test or some other activity to generate clinical fact. Typical observations are medical history, family history, the stated need for certain treatment, social circumstances, lifestyle choices, healthcare utilization patterns, etc.
medical observation data
An electronic health record that records the information of medical Episode record.
electronic episode record
An electronic health record that records the information of medical measurement record.
electronic measurement record
An electronic health record that records the information of medical notes.
electronic health note record
An electronic health record that records the information of medical observational record.
electronic health observation record
An electronic health record that records the information of Procedure record.
electronic health procedure record
An electronic health record that records the information of the specimen record.
electronic specimen record
An electronic health record that records the information of medical visit.
electronic medical visit record
preliminary diagnosis
preliminary admission diagnosis
preliminary discharge diagnosis
The primary diagnosis is a diagnosis of the patient condition that demands the most provider resources during the patient’s stay.
primary diagnosis
primary admission diagnosis
primary discharge diagnosis
primary referral diagnosis
A secondary diagnosis is a diagnosis made at the time of admission, that develops subsequently, or that affects the treatment received and/or length of stay.
secondary diagnosis
secondary admission diagnosis
secondary discharge diagnosis
secondary referral diagnosis
admission diagnosis
confirmed diagnosis
death diagnosis
discharge diagnosis
postoperative diagnosis
A medical occurrence in which a patience is exposed to a medical related material entity such as drug or medical device. Medical exposure refers primarily to exposure incurred by patients for the purpose of medical diagnosis or treatment.
medical exposure
preoperative diagnosis
referral diagnosis
An acellular self-replicating organic structure that is composed of nucleic acid
self-replicating nucleic acid
A self-replicating nucleic acid that can move around within a genome, or that can be transferred from one species or replicon to another.
mobile genetic element
A mobile genetic element that is composed of a generally circular extrachromosomal DNA molecule and is able to replicate and be transmitted independent of chromosomal DNA.
plasmid
A mobile genetic element that is composed of a DNA sequence and can move and replicate in different parts of a cell's genome.
transposon
A age quality that is measured by the value of less than 18 years old
age less than 18 years
GFR 30-59 mL/min/1.73m2
eGFR >=60 mL/min/1.73m2 with urine albumin excretion >= 30 mg/g creatinine
eGFR >= 60 mL/min/1.73m2 with urine protein excretion >= 150 mg/g creatinine
A role of a person (e.g., a study participant, participant's family member, or participant's physician) who provides the medical history information.
medical history information provider role
A role of a person who is a family member of a participant in an investigation study.
study participant's family member role
a role of a physician who takes care of a study participant
study participant's physician role
An age when a disease is first diagnosed
age at diagnosis of disease
age at diagnosis of kidney disease
Whether chronic kidney disease
Whether acute kidney injury
time of biopsy
year of kidney biopsy
time of kidney biopsy
month of kidney biopsy
age at the start of kidney stone
An age when a disease started in a patient
age at the start of disease
Whether diabetes
age at diagosis of diabetes
What disease
What type of diabetes
treatment question
medicatoin treatment question
surgical treatment question
Whether taking medication for diabetes
age at the start of medication
age at the start of taking medication for diabetes
What medication
What medication taken for diabetes
Whether insulin taken for diabetes
Whether diabetes during pregnancy
a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc.
clinical trial
A clinical trial that is at Early Phase 1 or Phase 0
A clinical trial that is at an Early Phase i or Phase 0, which is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI]
Early Phase 1 clinical trial
A clinical trial that is at Phase 1, which is often the first-in-man trial, and it tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects.
Phase 1 clinical trial
A clinical trial that is at Phase 2, which is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI]
Phase 2 clinical trial
A clinical trial that is at Phase 3, which is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI]
Phase 3 clinical trial
Phase 4 clinical trial
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A time quality inhering in a bearer by virtue of how long the bearer has existed.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
患者生理性别在特定编码体系中的代码
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
A physical quality inhering in a bearer that has mass near a gravitational body.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
See comments of relational quality of a physical entity.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A quality that inheres in an entire organism or part of an organism.
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
A material entity that consists of two or more organisms, viruses, or viroids.
A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.
ecological community
A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other.
community
A collection of organisms that consists of two or more organisms from at least two species.
multi-species collection of organisms
A material entity that is one or more organisms, viruses or viroids.
organismal entity
An anatomical entity that is or was part of a plant.
entidad anat&#243mica vegetal (Spanish, exact)
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A stage that is part of the embryo stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
The liquid component of blood, in which erythrocytes are suspended.
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
The post-cranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
an organ that functions as a secretory or excretory organ
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
A vascular network consisting of blood vessels.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
We explicitly merge the NCITA terms here
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Anatomical system that consists of all the joints of the body.
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A part of a wall of an organ that forms a layer.
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
An epithelial sheet bent on a linear axis.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
Mesenchyme that is part of a developing trunk.
A portion of tissue that is part of an embryo.
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
A delimited region of dense mesenchyme within looser mesenchyme.
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
Of or pertaining to the period of time immediately following birth, or to the newborn.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
A presumptive structure that has the potential to develop into a paraxial mesoderm.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO]
connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
An epithelial tube open at both ends that allows fluid flow.
Mesenchyme with little extracellular matrix.
this class will be an important part of the NC reorganization
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
the FMA def is Transudate contained in a serous sac
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
An anatomical structure that has more than one cell as a part.
Mesenchyme that has the potential to develop into a dermis.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints.
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A cardiovascular system that is part of a conceptus.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
Epithelium that derives from the mesoderm. [Automatically generated definition].
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
A organ component layer that is part of a integumental system.
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
A portion of tissue that will develop into vasculature.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
A mammalian developmental stage that covers the period from birth until weaning.
Nursing stage that follows the neonate stage in mammals and ends at weaning.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
organ region with floating fiat boundary
The primordial mouth region of the developing head.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
A unit which is a standard measure of the dimension in which events occur in sequence.
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
a medical intervention that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intent to invoke an adaptive immune response.
Part of the landmass of Eurasia, with the western portion of the latter occupied by Europe, lying east of the Suez Canal, east of the Ural Mountains, and south of the Caucasus Mountains and the Caspian and Black Seas. It is bounded on the east by the Pacific Ocean, on the south by the Indian Ocean, and on the north by the Arctic Ocean.
A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.
United Kingdom of Great Britain and Northern Ireland
An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.
A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.
A group of islands off the northwest coast of continental Europe that include the islands of Great Britain and Ireland, and over six thousand smaller islands. There are two sovereign states located on the islands: the United Kingdom and the Republic of Ireland. The British Isles also include two dependencies of the United Kingdom: the Isle of Man and, by tradition, the Channel Islands, although the latter are not physically a part of the island group.
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
KPMP organization
participant candidate 1
participant candidate 2
participant candidate 3
filled CRF by candidate 1
filled CRF by candidate 2
filled CRF by candidate 3
European Union Drug Regulating Authorities Clinical Trials
EudraCT
ClinicalTrials.gov is a resource provided by the U.S. National Library of Medicine.
Clinicaltrials.gov
SDY269 study
SDY269
human subject SUB112829
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
Adam Goldstein
Albert Goldfain
Barry Smith
Carlo Torniai
Chris Stoeckert
Christian A. Boelling
Darren Natale
David Osumi-Sutherland
Gwen Frishkoff
Holger Stenzhorn
James A. Overton
James Malone
Jonathan Rees
Larisa Soldatova
Lawrence Hunter
Matt Brush
Melanie Courtot
Michel Dumontier
Paolo Ciccarese
Pat Hayes
Philippe Rocca-Serra
Randy Dipert
Ron Rudnicki
Satya Sahoo
Sivaram Arabandi
Werner Ceusters
William Duncan
Yongqun (Oliver) He
An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO
IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html
This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
Bill Bug
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Jay Greenbaum
Jeffrey Grethe
Jessica Turner
Joe White
John Westbrook
Kevin Clancy
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Phillip Lord
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
An ontology for the annotation of biomedical and functional genomics experiments.
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
One of the large, unbroken masses of land into which the Earth's surface is divided.
A reference to a place on the Earth, by its name or by its geographical location.
The convention used in gaz.obo is that the Europe-Asia boundary follows the watershed of the Ural Mountains from near Kara, Russia on the Kara Sea to the source of the Ural River, then follows that river to the Caspian Sea. The border then follows the watershed of the Caucasus Mountains from the Caspian Sea to the Black Sea.
A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.
DrOn contains content developed by the National Library of Medicine in RxNorm. In creating DrOn, we have used RxNorm content only with SAB = RXNORM.
When citing DrOn, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/dron.owl. When referencing a specific component of the DrOn, such as a class, object property, annotation property, or individual, use the Uniform Resource Identifier (URI) of that component.
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 186 Logical Axioms: 30]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 132 Logical Axioms: 23]
ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ Please see www.environmentontology.org for more information and citations.
Desikan Jagannathan
An ontology for the annotation of the adverse event domain.
Vision Release; 1.2.19
Product version
Shelley Zhang
Meiu Wong
The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
OAE: Ontology of Adverse Events
Bingjian Yang
MIABIS_v2_accepted and UPenn Biobank ontology
The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.
development version
Ontology for BIoBanking (OBIB)
The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl The OGMS developer site is https://github.com/OGMS/ogms If you are interested in participating in the development of OGMS, please send email to baeverma
This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
Swetha Garimalla
The Ontology of Medically Related Social Entities
Shariq Tariq