The TURBO application ontology
type: Ontology
version IRI: turbo merged.owl
editor note: Converting UO terms from classes to individuals (offline, in a triplestore): (Most recently did mmHg with Ontofox, then converted in text editor... may not survive next merge.) PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX : <http://purl.obolibrary.org/obo/uo.owl#> insert { graph :individualized { ?s a ?super } } where { values ?super { <http://purl.obolibrary.org/obo/UO_0000001> <http://purl.obolibrary.org/obo/UO_0000002> } ?s rdfs:subClassOf ?super ; rdfs:label ?sublab . ?super rdfs:label ?superlab . } --- PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX : <http://purl.obolibrary.org/obo/uo.owl#> insert { graph :individualized { ?s a <http://purl.obolibrary.org/obo/UO_0000051> } } where { values ?super { <http://purl.obolibrary.org/obo/UO_0000052> } ?s rdfs:subClassOf ?super ; rdfs:label ?sublab . ?super rdfs:label ?superlab . } --- PREFIX : <http://purl.obolibrary.org/obo/uo.owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> construct { ?s ?p ?o . ?s a owl:NamedIndividual . } where { graph :individualized { ?s a ?t } ?s ?p ?o . filter(?o != owl:Class) filter(?p != rdfs:subClassOf) } --- save results of construct statement to uo_individualized.ttl and import into TURBO Used a similar strategy for Gleason terms from NCIT: asserted (though inserts into a new named graph) that the subclasses of http://purl.obolibrary.org/obo/NCIT_C28107 and http://purl.obolibrary.org/obo/NCIT_C28084 are instances of NCIT_C28107 and NCIT_C28084. Then constructed those assertions, along with all annotations on the terms except for subClassOf, into a turtle file. Other NCIT terms were imported earlier on just by cutting and pasting between RDF files. That's the case for any term that isn't native to TURBO or didn't come from OntoFox or OntoDog (including parent terms imported to satisfy MIREOT)
Contributor: Chris Stoeckert
Contributor: Mark A. Miller
Source: OBO foundry ontologies, especially the ontology for biobanking, OBIB.
comment: Basic approach: used ontodog to extract a base ontology view from OBIB Then used ontofox to get additional classes and properties from other OBO foundry ontologies After merging and tidying up, save as turbo_merged.owl (AND turbo_merged.rdf or turbo_merged.ttl for TopBraid Composer) ---- some manual tidying that might be required: Make [molecular entity](http://purl.obolibrary.org/obo/CHEBI_23367) a direct subclass of [material entity](http://purl.obolibrary.org/obo/BFO_0000040) and remove [chemical entity](http://purl.obolibrary.org/obo/CHEBI_24431) from [material entity](http://purl.obolibrary.org/obo/BFO_0000040). [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) isn't a direct sbclasses of [entity](http://purl.obolibrary.org/obo/BFO_0000001), only [continuant](http://purl.obolibrary.org/obo/BFO_0000002) Haven't been using [Anatomical location](http://purl.obolibrary.org/obo/FMA_50707) ... hasn't appeared at all in recent ontoanimal exports GO cellular_component appearing as direct subclass of Thing... dragged into material entity a la OBI ... hasn't appeared at all in recent ontoanimal exports ---- April 2019 manual changes (attributed to OntoFox extract, possibly from hypertension related terms?) - BFO_0000051 was erroneously labeled "part of" in addition to the correct label "has part" - [sign](http://purl.obolibrary.org/obo/OGMS_0000024) was moved out of [quality](http://purl.obolibrary.org/obo/BFO_0000019) and into [entity](http://purl.obolibrary.org/obo/BFO_0000001) ---- removed [physical object quality](http://purl.obolibrary.org/obo/PATO_0001241) from [Phenotypic abnormality](http://purl.obolibrary.org/obo/HP_0000118) removed [blood pressure](http://purl.obolibrary.org/obo/VSO_0000004) from [vital sign](http://purl.obolibrary.org/obo/OGMS_0000029)
comment: This ontology is intended to support a semantic linked data reimplementation of biobanking and related data, typically originating in a relational format. The first implementation will be at the Penn Medicine Biobank.
comment: todo: make a better log of terms pasted into turbo.owl with text editor or merged through any route other than ontodog or ontofox. may include BMI, DOB, mmHg, systolic blood pressure measurement datum. ICD-9 and ICD-10 as individuals. ---- https://github.com/PennTURBO/Turbo-Ontology/issues/2 Foreign terms that have asserted super-classes in turbo.owl proper, as opposed to an import file: - **Present in OBI** - Note two different styles for NCIT terms - Note inconsistency re UO terms as instances vs classes ---- - http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C49474 - http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C53489 - http://purl.obolibrary.org/obo/CL_0001061 - http://purl.obolibrary.org/obo/HTN_00000000 - http://purl.obolibrary.org/obo/HTN_00000001 - http://purl.obolibrary.org/obo/MONDO_0004992 - http://purl.obolibrary.org/obo/MONDO_0045024 - http://purl.obolibrary.org/obo/NCIT_C28084 - http://purl.obolibrary.org/obo/NCIT_C28107 - http://purl.obolibrary.org/obo/OGMS_0000031 - http://purl.obolibrary.org/obo/OGMS_0000078 - http://purl.obolibrary.org/obo/OGMS_0000096 - http://purl.obolibrary.org/obo/UO_0000009 - http://purl.obolibrary.org/obo/UO_0000015 - http://purl.obolibrary.org/obo/VSO_0000005 - http://purl.obolibrary.org/obo/VSO_0000006 - http://www.ebi.ac.uk/efo/EFO_0004340 ---- Moved to ontofox import: - **http://purl.obolibrary.org/obo/GO_0005575** - **http://purl.obolibrary.org/obo/IAO_0000010** - **http://purl.obolibrary.org/obo/IAO_0000594** - **http://purl.obolibrary.org/obo/UBERON_0001013**

BFO OWL specification label
type: AnnotationProperty
editor preferred label: BFO OWL specification label
definition: 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.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
editor preferred label: BFO CLIF specification label
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example
editor preferred label: example of usage
has curation status: ready for release
definition: 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
definition: 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred label: has curation status
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
definition source: OBI_0000281

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
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.
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
definition editor: PERSON:Daniel Schober
alternative term: DEFINITION
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative_term: DEFINITION
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
definition: 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: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
has db xref: IAO:0000116
has OBO namespace: uberon
id: editor_note
is metadata tag: true
shorthand: editor_note
is metadata tag: 1

definition editor
type: AnnotationProperty
editor preferred label: definition editor
editor preferred label: term editor
has curation status: ready for release
definition: 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
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred label: alternative term
has curation status: pending final vetting
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: ready for release
definition: 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
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
definition: 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.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
database_cross_reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: 1
shorthand: curator_notes
label: curator notes

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

ontology term requester
type: AnnotationProperty
has curation status: pending final vetting
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty
editor preferred label: expand expression to
example of usage: ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
definition editor: Chris Mungall

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: 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 .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

elucidation
type: AnnotationProperty
editor preferred label: elucidation
definition editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: 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)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

is allocated id range
type: AnnotationProperty
editor preferred label: is allocated id range
definition: Add as annotation triples in the granting ontology
definition: Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
definition editor: PERSON:Alan Ruttenberg

term replaced by
type: AnnotationProperty
editor preferred label: term replaced by
has curation status: pending final vetting
definition: Add as annotation triples in the granting ontology
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: ready for release
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
definition editor: Person: Alejandra Gonzalez-Beltran
definition editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative term

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: ready for release
definition: An alternative term used by the IEDB.
definition editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative term

symbol from nomenclature authority
type: AnnotationProperty
definition: the symbol assigned by the nomenclature authority
definition editor: Oliver He, Yue Liu

full name from nomenclature authority
type: AnnotationProperty
definition: the full name assigned by the nomenclature authority
definition editor: Oliver He, Yue Liu

NCBI GeneID
type: AnnotationProperty
definition: A GeneID in the NCBI Gene database
definition editor: Oliver He, Yue Liu

NCBI LocusTag
type: AnnotationProperty
definition: the NCBI LocusTag name of a gene
definition editor: Oliver He, Yue Liu

gene map location
type: AnnotationProperty
definition: the map location of a gene
definition editor: Oliver He, Yue Liu

modification date
type: AnnotationProperty
definition: a date of content modification
definition editor: Oliver He, Yue Liu

organism NCBITaxon ID
type: AnnotationProperty
definition: The NCBITaxon ontology ID of an organism.
definition editor: Oliver He, Yue Liu

chromosome ID of gene
type: AnnotationProperty
definition: A chromosome ID where a gene is located.
definition editor: Oliver He

type of gene
type: AnnotationProperty
definition: an annotation property that specifies the type of a gene
definition editor: Oliver He

nomenclature status
type: AnnotationProperty
definition: an annotation property that specifies a nomenclature status
definition editor: Oliver He

has GO association
type: AnnotationProperty
definition: an annotation property that shows the GO information associated with a specific gene.
definition editor: Yongqun He
comment: YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association.
domain: gene

has PubMed association
type: AnnotationProperty
definition: An annotation property that represents a gene's association with PubMed publication(s).
definition editor: Yongqun He
comment: YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).

temporal interpretation
type: AnnotationProperty
editor preferred label: temporal interpretation
definition: 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.
sub property of: logical macro assertion on an object property

logical macro assertion
type: AnnotationProperty
definition: 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 on a property
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

is homeomorphic for
type: AnnotationProperty
example of usage: part-of is homeomorphic for independent continuants.
definition: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
created by: cjm
creation date: 2018-10-21T19:46:34Z
comment: R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
sub property of: logical macro assertion on an object property

taxon_notes
type: AnnotationProperty
definition: Notes on the how instances of this class vary across species.
database_cross_reference: UBPROP:0000008
has_obo_namespace: uberon
id: taxon_notes
is metadata tag: true
shorthand: taxon_notes

external_ontology_notes
type: AnnotationProperty
definition: Notes on how similar or equivalent classes are represented in other ontologies.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000012
has_obo_namespace: uberon
id: external_ontology_notes
is metadata tag: true
shorthand: external_ontology_notes

has_rank
type: AnnotationProperty
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy

translated by
type: AnnotationProperty
definition: A person how is responsible for translating the entity annotations from English to another language.
definition editor: PERSON:Fernanda Farinelli
range: Name

translated to Portuguese by
type: AnnotationProperty
definition: A person how is responsible for translating the entity annotations from English to Portuguese.
definition editor: PERSON:Fernanda Farinelli
sub property of: translated by
range: Name

Contributor
type: AnnotationProperty
description: 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.
comment: An entity responsible for making contributions to the content of the resource.

Creator
type: AnnotationProperty
description: 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.
has_obo_namespace: uberon
id: dc-creator
is metadata tag: true
shorthand: dc-creator
comment: An entity primarily responsible for making the content of the resource.
label: creator

Date
type: AnnotationProperty
description: 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.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: 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.
comment: An account of the content of the resource.

Format
type: AnnotationProperty
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).
comment: The physical or digital manifestation of the resource.

Resource Identifier
type: AnnotationProperty
description: Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
comment: An unambiguous reference to the resource within a given context.

Source
type: AnnotationProperty
description: 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.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: 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.
comment: The topic of the content of the resource.

license
type: AnnotationProperty
definition editor: Mark Miller
date: 2018-05-11T13:47:29Z

interdependent with shortcut
type: AnnotationProperty
editor preferred label: interdependent with shortcut
example of usage: For example, both a 'shortcut health care encounter to diagnosis code symbol' and a 'shortcut health care encounter to diagnosis code registry URI string'might be required to create a fully-formed CRID for a diagnosis code
definition: X 'interdependent with shortcut' Y means it would not make sense, or might not even be possible, to expand shortcut X in the absence of shortcut Y.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-09-05T17:02:53Z
comment: In general, if a shortcut triple appears in the absence of its interdependencies, the turbo expansion method should throw an exception. how to assert that both the domain and range are <http://transformunify.org/ontologies/TURBO_0000670> instantiation hybrid shortcut?

retires
type: AnnotationProperty
editor preferred label: retires
definition: Links a 'retired placeholder' to to the corresponding class that is subject to 'referent tracking' X retires Y means that an instance of class Y will appear as an instance of class X after 'referent tracking'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-31T13:29:27Z
range: Thing
domain: retired placeholder

replaced with IUI
type: AnnotationProperty
editor preferred label: replaced with IUI
definition: the subject of this property has been demoted in the course of referent tracking, and the corresponding entity in reality is now better known by the following IUI:
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2017-04-12T14:00:00-05:00
sub property of: term replaced by

referent tracked?
type: AnnotationProperty
editor preferred label: referent tracked?
definition: A boolean property that is asserted true for individuals that have been referent tracked.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-04-12T14:00:00-05:00
comment: this property should only be true for individuals whose URI (in RDF/OWL perspective) is a IUI, containing a UUID (according to TURBO rules)
range: boolean
domain: entity

conclusionated?
type: AnnotationProperty
editor preferred label: conclusionated?
definition: this data item is the output of a turbo conclusionation process
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-10-05T18:34:04Z
range: boolean
domain: entity

previous URI text
type: AnnotationProperty
editor preferred label: previous URI text
example of usage: :Consenter1 and :ConsenterID1 were instantiated (by Karma?) because there was a column with the semantic type 'biobank consenter symbol', with a value of '1' on some row. (Assuming other interdependent shortcut requirements are met.) If :Consenter1 and :ConsenterID1 end up in a triplestore containing other biobank consenters with 'biobank consenter symbol' values of '1' ( :Consenter2 and :ConsenterID2) and referent trcking is performed, it may be concluded that :Consenter1 and :Consenter2 are the same individual in reality. I that case, :Consenter1 and :Consenter2 would be replaced with two 'retired placeholder for biobank consenter's and one new IUI/UUID-identified referent tracked 'biobank consenter'. To document these results of referent tracking, triples would be inserted saying :ConsenterRT 'previous URI text' "Consenter1" . :ConsenterRT 'previous URI text' "Consenter2" .
definition: 'previous URI text' has subproperties that are applicable to the URIs that are inputs into and outputs from shortcut expansion and referent tracking. The shortcut expansion case follows a similar pattern to the referent tracking case. X 'previous URI text' Y means that X is some referent tracked individual, and that before referent tracking was performed, there was an individual identified by a URI with string value Y that is now identified singularly and uniquely by X. One X can have anywhere from one to an infinite number of Y X 'previous URI text's
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
range: string
domain: entity

pre-expansion URI text
type: AnnotationProperty
editor preferred label: pre-expansion URI text
definition: A ‘previous URI text’ property asserted as a result of shortcut expansion
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-09-27T17:38:47Z
sub property of: previous URI text
range: string
domain: entity

pre-reftracking URI text
type: AnnotationProperty
editor preferred label: pre-reftracking URI text
definition: A ‘previous URI text’ property asserted as a result of referent tracking
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-09-27T17:39:47Z
sub property of: previous URI text
range: string
domain: entity

expands to
type: AnnotationProperty
definition editor: Mark A. Miller
date: 2019-03-02T22:25:42Z

has OMOP concept ID
type: AnnotationProperty
range: integer
domain: entity

maps to
type: AnnotationProperty
definition: A maps to B means that URI-identified class A has some relationship between URI-identified class B, outside of rdfs:subClassOf or owl:equivalentClass. Classes A and B will generally be defined and or asserted in different upstream ontologies (or other RDF artifacts) Similar in some ways to 'relatedMatch' from https://en.wikipedia.org/wiki/Simple_Knowledge_Organization_System, although SKOS defines that term an an object property.
range: Thing

evidence code for disease
type: AnnotationProperty
definition: A 'maps to' relationship in whose subject is a code (from a system like ICD or SNOMED) and the object is a disease (preferable form MonDO) This property does not imply any certainty or causality, only that some path can be drawn from the code to the disease. This path justifying each 'evidence code for disease' should be exposed in an RDF graph, possibly by grouping all assertions from one path into the same named graph, which would be annotated with a definition etc. If you have a need to find people in an EHR who 'have' a disease, looking for the mapped code is a reasonable but noisy start.
sub property of: maps to

PDS R_MEDICATION suggests drug term
type: AnnotationProperty
definition: A 'maps to' relationship in which the subject is an RDF model of a R_MEDICATION row from the 'master data management' schema in the Penn Data Store relational database used by the University of Pennsylvania Healthcare System. The object would be the term for a drug (ingredient, generic product or branded product) from RxNorm, DrOn, ChEBI, etc.
comment: This term might not ever be used per se. Rather, relationships are more likely to be drawn between an R_MEDICATION, some search results, and the predicted drug term. 19 August 2019: repo XXX has a <http://example.com/resource/rxnav_mapping> named graph containing the results of submitting PDS R_MEDICATION FULL_NAMEs to RxNav's approximateTerm API. +---------------------+----------------------------------------------------+ | predicate | object | +---------------------+----------------------------------------------------+ | mydata:R_MEDICATION | mydata:802ab5cc-bd6b-11e9-910d-713b0667bca7 | +---------------------+----------------------------------------------------+ | mydata:rank | 1 | +---------------------+----------------------------------------------------+ | mydata:rxcui | http://purl.bioontology.org/ontology/RXNORM/307719 | +---------------------+----------------------------------------------------+ | mydata:score | 100 | +---------------------+----------------------------------------------------+ | rdf:type | mydata:rxnav_mapping | +---------------------+----------------------------------------------------+ This says that PDS R_MEDCIATION mydata:802ab5cc-bd6b-11e9-910d-713b0667bca7 +-------------------------+----------------------------------------------------+ | predicate | object | +-------------------------+----------------------------------------------------+ | mydata:FULL_NAME | .Acetylcysteine Inhalation Solution 20%. | +-------------------------+----------------------------------------------------+ | mydata:ORDERCOUNT | 324 | +-------------------------+----------------------------------------------------+ | mydata:PK_MEDICATION_ID | 50665 | +-------------------------+----------------------------------------------------+ | mydata:RXNORM | http://purl.bioontology.org/ontology/RXNORM/307719 | +-------------------------+----------------------------------------------------+ has a high quality match against RxNorm term 307719 (Acetylcysteine 200 MG/ML Inhalat…
sub property of: maps to

data retained between expansion steps
type: AnnotationProperty
comment: these properties can be used to temporarily link data values to a non-data-model class. they can be used for retaining data from a "data model with shortcut properties" when the expansion needs to be processed in two or more steps, due to a limitation of federated SAPRQL queries in some triple stores: it's hard to build a link between two service blocks with a data literal appearing in both blocks.

previous visit id from omop visit
type: AnnotationProperty
sub property of: data retained between expansion steps
range: integer
domain: health care encounter

patient id from omop visit
type: AnnotationProperty
sub property of: data retained between expansion steps
range: integer
domain: health care encounter

visit id from omop visit
type: AnnotationProperty
comment: this could be different from the symbol part of the denoter. in the case of instantiating data in from an OMOP schema, the symbol might come from the source identifier and this annotation might come from the OMOP primary key
sub property of: data retained between expansion steps
range: integer
domain: health care encounter

visit concept from omop visit
type: AnnotationProperty
comment: this could be used to determine a more specific type (inpatient, outpatient, ER) for a healthcare encounter instance
sub property of: data retained between expansion steps
range: integer
domain: health care encounter

commented SPARQL query for expansion
type: AnnotationProperty

race concept from omop person
type: AnnotationProperty
sub property of: data retained between expansion steps
range: integer
domain: Homo sapiens

ethnicity concept from omop person
type: AnnotationProperty
sub property of: data retained between expansion steps
range: integer
domain: Homo sapiens

gender concept from omop person
type: AnnotationProperty
sub property of: data retained between expansion steps
range: integer
domain: Homo sapiens

person id from omop person
type: AnnotationProperty
sub property of: data retained between expansion steps
range: integer
domain: Homo sapiens

definition_citation
type: AnnotationProperty
definition: A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty
database_cross_reference: oboFormat:xref
  type: database_cross_reference
  has_URI: http://purl.org/oboInOwl/owl/oboInOwlFormat#oboInOwlFormat_xref
database_cross_reference: oboFormat:xref
  type: database_cross_reference
  has_URI: http://purl.org/oboInOwl/owl/oboInOwlFormat#oboInOwlFormat_xref
label: has_dbxref

alternative_term
type: AnnotationProperty
definition: An alternative label for a given entity such as a commonly used abbreviation or synonym.
definition: 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.
alternative_term: FULL_SYN
alternative_term: Synonym with Source Data
label: has exact synonym
label: has_exact_synonym

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_URI
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty
comment: The TURBO ontology is moving away from human-readable URIs towards the OBO Foundry practice of NAMESPACE_XXXXXXX identifiers, where the X's are numerical digits. Our software developers would like to continue using mnemonics to refer to ontology terms. Presumably this will be implemented with sameAs or equivalentClass/equivalentProperty relationships. This has_mnemonic datatype property has been created to facilitate and maintain these relationships, most likely with some SPARQL construct statements.

label
type: AnnotationProperty
editor preferred label: label

see also
type: AnnotationProperty
has_obo_namespace: uberon
id: seeAlso
is metadata tag: true
shorthand: seeAlso

is part of
type: ObjectProperty
equivalent property:
  inverse of: has part
sub property of: overlaps
sub property of: topObjectProperty
inverse of: has part
type: TransitiveProperty
domain: entity
domain: Thing
range: entity
range: Thing
editor preferred label: is part of
editor preferred label: part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: part of
alternative term: part_of
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
temporal interpretation: axiom holds for all times
is homeomorphic for: continuant
is homeomorphic for: occurrent
is homeomorphic for: independent continuant
is homeomorphic for: realizable entity
is homeomorphic for: quality
is homeomorphic for: specifically dependent continuant
is homeomorphic for: generically dependent continuant
label: part of

has part
type: ObjectProperty
equivalent property:
  inverse of: is part of
sub property of: overlaps
sub property of: topObjectProperty
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: has_part
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: pr.owl
imported from: ro.owl
temporal interpretation: axiom holds for all times
database_cross_reference: BFO:0000051
has_obo_namespace: protein
id: has_part
shorthand: has_part
label: has_part

inheres in at all times
type: ObjectProperty
sub property of: specifically depends on at all times
domain: specifically dependent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
BFO OWL specification label: inheres-in_at
BFO CLIF specification label: inheresInAt
definition: b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
editor note: BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
editor note: BFO2 Reference: independent continuant that is not a spatial region
editor note: BFO2 Reference: specifically dependent continuant
imported from: ogg.owl
has associated axiom(fol): (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
sub property of: topObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/ro.owl
elucidation: [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])
comment: 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
type: ObjectProperty
equivalent property:
  inverse of: realized in
sub property of: topObjectProperty
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/ro.owl
elucidation: 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])
comment: 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

concretized by at some time
type: ObjectProperty
inverse of: concretizes at some time
domain: generically dependent continuant
range: specifically dependent continuant
BFO OWL specification label: concretized-by_st
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
example of usage: [copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
editor note: [copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
imported from: ogg.owl
elucidation: [copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])

concretizes at some time
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
BFO OWL specification label: concretizes_st
BFO CLIF specification label: concretizesAt
example of usage: You may concretize a piece of software by installing it in your computer
example of usage: You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
example of usage: you may concretize a poem as a pattern of memory traces in your head
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
imported from: ogg.owl
elucidation: b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
has associated axiom(nl): if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
has associated axiom(fol): (forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
has associated axiom(fol): (forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]

preceded by
type: ObjectProperty
sub property of: temporal relation
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: preceded by
definition: 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.
editor note: 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.
alternative term: is preceded by
alternative term: preceded_by
imported from: obi.owl
imported from: ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: precedes
definition: 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.
imported from: obi.owl
imported from: ro.owl

specifically depends on at all times
type: ObjectProperty
sub property of: specifically depends on at some time
BFO OWL specification label: s-depends-on_at
BFO CLIF specification label: specificallyDependsOn
example of usage: A pain s-depends_on the organism that is experiencing the pain
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
example of usage: a shape s-depends_on the shaped object
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
editor note: BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
imported from: ogg.owl
elucidation: To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has associated axiom(nl): If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
has associated axiom(nl): If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
has associated axiom(nl): If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
has associated axiom(nl): an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
has associated axiom(nl): if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
has associated axiom(fol): (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]

occupies spatial region at some time
type: ObjectProperty
inverse of: has spatial occupant at some time
domain: independent continuant
range: spatial region
BFO OWL specification label: located-at-r_st
BFO CLIF specification label: occupiesSpatialRegionAt
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: BFO2 Reference: independent continuant
editor note: BFO2 Reference: spatial region
imported from: ogg.owl
elucidation: b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has associated axiom(nl): every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
has associated axiom(nl): if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
has associated axiom(fol): (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
has associated axiom(fol): (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
has associated axiom(fol): (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]

exists at
type: ObjectProperty
inverse of: during which exists
domain: entity
range: temporal region
BFO OWL specification label: exists-at
BFO CLIF specification label: existsAt
editor note: BFO2 Reference: entity
editor note: BFO2 Reference: temporal region
imported from: ogg.owl
elucidation: b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])

has occurrent part
type: ObjectProperty
inverse of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
example of usage: [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
imported from: ogg.owl
elucidation: [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]

has proper occurrent part
type: ObjectProperty
sub property of: has occurrent part
inverse of: proper part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-has-ppart
BFO CLIF specification label: hasProperOccurrentPart
definition: [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
definition: b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
imported from: ogg.owl

has spatial occupant at some time
type: ObjectProperty
domain: spatial region
range: independent continuant
BFO OWL specification label: r-location-of_st
editor note: [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
imported from: ogg.owl
elucidation: [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])

has specific dependent at some time
type: ObjectProperty
inverse of: specifically depends on at some time
domain: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
range: Class
  union of: process
  union of: specifically dependent continuant
BFO OWL specification label: has-s-dep_st
example of usage: [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
example of usage: [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
example of usage: [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
editor note: [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
editor note: [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
imported from: ogg.owl
elucidation: [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64

has spatiotemporal occupant
type: ObjectProperty
inverse of: occupies spatiotemporal region
domain: spatiotemporal region
range: occurrent
BFO OWL specification label: occupied-by
editor note: [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
imported from: ogg.owl
elucidation: [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])

occupies spatiotemporal region
type: ObjectProperty
domain: occurrent
range: spatiotemporal region
BFO OWL specification label: occupies
BFO CLIF specification label: occupiesSpatiotemporalRegion
editor note: BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
imported from: ogg.owl
elucidation: p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])

part of occurrent
type: ObjectProperty
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-part-of
BFO CLIF specification label: occurrentPartOf
example of usage: Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: the first set of the tennis match occurrent_part_of the tennis match.
definition: [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: BFO2 Reference: occurrent
imported from: ogg.owl
elucidation: b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(nl): occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
has associated axiom(nl): occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
has associated axiom(nl): occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
has associated axiom(nl): occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
has associated axiom(nl): occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
has associated axiom(fol): (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
has associated axiom(fol): (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]

proper part of occurrent
type: ObjectProperty
sub property of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: o-ppart-of
BFO CLIF specification label: properOccurrentPartOf
definition: [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
definition: b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
imported from: ogg.owl
has associated axiom(fol): (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]

temporal part of
type: ObjectProperty
sub property of: part of occurrent
type: TransitiveProperty
domain: occurrent
range: occurrent
BFO OWL specification label: t-part-of
BFO CLIF specification label: temporalPartOf
example of usage: the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: the process boundary which separates the 3rd and 4th years of your life.
example of usage: your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
definition: b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
alternative term: TPO
imported from: ogg.owl
has associated axiom(nl): if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
has associated axiom(fol): (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
has associated axiom(fol): (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
has associated axiom(fol): (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]

projects onto spatial region at some time
type: ObjectProperty
inverse of: spatial projection of spatiotemporal at some time
domain: spatiotemporal region
range: spatial region
BFO OWL specification label: st-projects-onto-s_st
imported from: ogg.owl

spatial projection of spatiotemporal at some time
type: ObjectProperty
domain: spatial region
range: spatiotemporal region
BFO OWL specification label: s-projection-of-st_st
imported from: ogg.owl

projects onto temporal region
type: ObjectProperty
sub property of: exists at
inverse of: temporal projection of spatiotemporal
domain: spatiotemporal region
range: temporal region
BFO OWL specification label: st-projects-onto-t
imported from: ogg.owl

temporal projection of spatiotemporal
type: ObjectProperty
sub property of: during which exists
domain: temporal region
range: spatiotemporal region
BFO OWL specification label: t-projection-of-st
imported from: ogg.owl

occupies temporal region
type: ObjectProperty
sub property of: exists at
inverse of: has temporal occupant
domain: occurrent
range: temporal region
BFO OWL specification label: spans
BFO CLIF specification label: occupiesTemporalRegion
alternative term: OTR
imported from: ogg.owl
elucidation: 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
type: ObjectProperty
sub property of: during which exists
domain: temporal region
range: occurrent
BFO OWL specification label: span-of
BFO CLIF specification label: spanOf
imported from: ogg.owl
imported from: bfo.owl
elucidation: [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])

during which exists
type: ObjectProperty
domain: temporal region
range: entity
BFO OWL specification label: during-which-exists
editor note: [copied from inverse property 'exists at'] BFO2 Reference: entity
editor note: [copied from inverse property 'exists at'] BFO2 Reference: temporal region
imported from: ogg.owl
elucidation: [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])

bearer of at all times
type: ObjectProperty
sub property of: has specific dependent at all times
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: specifically dependent continuant
BFO OWL specification label: bearer-of_at
BFO CLIF specification label: bearerOfAt
definition: b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
editor note: BFO2 Reference: independent continuant that is not a spatial region
editor note: BFO2 Reference: specifically dependent continuant
imported from: ogg.owl
has associated axiom(fol): (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]

has disposition at all times
type: ObjectProperty
sub property of: bearer of at all times
range: disposition
BFO OWL specification label: has-d_at
BFO CLIF specification label: hasDispositionAt
definition: a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.
imported from: ogg.owl
has associated axiom(fol): (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]

has specific dependent at all times
type: ObjectProperty
sub property of: has specific dependent at some time
BFO OWL specification label: has-s-dep_at
imported from: ogg.owl

specifically depends on at some time
type: ObjectProperty
domain: Class
  union of: process
  union of: specifically dependent continuant
range: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
BFO OWL specification label: s-depends-on_st
BFO CLIF specification label: specificallyDependsOn
example of usage: A pain s-depends_on the organism that is experiencing the pain
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
example of usage: a shape s-depends_on the shaped object
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
editor note: BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
editor note: BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
editor note: BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
imported from: ogg.owl
elucidation: To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has associated axiom(nl): If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
has associated axiom(nl): If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
has associated axiom(nl): If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
has associated axiom(nl): an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
has associated axiom(nl): if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
has associated axiom(fol): (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]

part of continuant at some time
type: ObjectProperty
inverse of: has continuant part at some time
domain: continuant
range: continuant
BFO OWL specification label: c-part-of_st
BFO CLIF specification label: continuantPartOfAt
example of usage: Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
example of usage: the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
editor note: BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: BFO2 Reference: continuant
editor note: BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
editor note: [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
imported from: ogg.owl
elucidation: b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has associated axiom(nl): continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
has associated axiom(nl): continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
has associated axiom(nl): continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
has associated axiom(nl): continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
has associated axiom(nl): continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
has associated axiom(nl): if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
has associated axiom(fol): (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
has associated axiom(fol): (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
has associated axiom(fol): (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]

has continuant part at some time
type: ObjectProperty
domain: continuant
range: continuant
BFO OWL specification label: c-has-part_st
BFO CLIF specification label: hasContinuantPartAt
example of usage: [copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
example of usage: [copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
editor note: [copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
editor note: [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
imported from: ogg.owl
elucidation: [copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has associated axiom(fol): (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]

part of continuant at all times that whole exists
type: ObjectProperty
sub property of: part of continuant at some time
type: TransitiveProperty
domain: continuant
range: continuant
BFO OWL specification label: c-part-of-object_at
definition: [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
editor note: This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
editor note: [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
imported from: ogg.owl

has continuant part at all times that part exists
type: ObjectProperty
sub property of: has continuant part at some time
type: TransitiveProperty
domain: continuant
range: continuant
BFO OWL specification label: c-has-part-object_at
example of usage: [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
example of usage: [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
editor note: This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
editor note: [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
editor note: [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
imported from: ogg.owl
elucidation: [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])

has_sequence
type: ObjectProperty
inverse of: is_sequence_of
range: biological sequence
definition: A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.
alternative term: has_sequence_component
alternative term: has_state
imported from: geno.owl
database_cross_reference: VMC:state
comment: 'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.

is_sequence_of
type: ObjectProperty
domain: biological sequence
imported from: geno.owl

varies_with
type: ObjectProperty
type: SymmetricProperty
definition: A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part).
imported from: geno.owl
comment: This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)

has_location
type: ObjectProperty
domain: sequence_feature
range: sequence feature location
definition: A relation linking a sequence feature to the location it occupies on some reference sequence.
alternative term: occupies
imported from: geno.owl

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label
imported from: obi.owl

is about
type: ObjectProperty
domain: information content entity
editor preferred label: is about
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 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.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: ico.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

mentions
type: ObjectProperty
sub property of: is about
has curation status: pending final vetting
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition editor: PERSON: Jonathan Rees
definition editor: Person: Alan Ruttenberg
imported from: pdro.owl

denotes
type: ObjectProperty
sub property of: is about
domain: information content entity
range: Thing
example of usage: 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.
definition: 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
editor note: 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
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
imported from: pdro.owl

is quality measurement of
type: ObjectProperty
equivalent property:
  inverse of: is quality measured as
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: quality
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
definition editor: Alan Ruttenberg
imported from: obi.owl
imported from: ontoneo.owl

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
has curation status: metadata complete
definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg

is quality measured as
type: ObjectProperty
equivalent property:
  inverse of: is quality measurement of
has curation status: metadata complete
definition: inverse of the relation of is quality measurement of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
imported from: obi.owl
imported from: ontoneo.owl

has time stamp
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: information content entity
range: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
definition editor: Alan Ruttenberg
comment: IAO domain: [time stamped measurement datum](http://purl.obolibrary.org/obo/IAO_0000582) I would also like to use this with data items like prescriptions and diagnoses

has measurement datum
type: ObjectProperty
sub property of: has part
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the measurement datum that was measured
definition editor: Alan Ruttenberg

designates
type: ObjectProperty
inverse of: is designated by
type: AsymmetricProperty
type: IrreflexiveProperty
domain: information content entity
range: entity
definition: x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
definition editor: Mathias Brochhausen
imported from: pdro.owl
creator: Mathias Brochhausen

is designated by
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
definition editor: Mathias Brochhausen
imported from: pdro.owl

has material basis in
type: ObjectProperty
imported from: doid.owl

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
editor preferred label: is_supported_by_data
example of usage: 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.
has curation status: ready for release
definition: 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
definition editor: OBI
definition source: OBI
definition source: Philly 2011 workshop

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has_participant
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
definition: 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.
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: 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
has curation status: ready for release
definition: 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has_participant
sub property of: topObjectProperty
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
has curation status: ready for release
definition: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: pdro.owl

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: ready for release
definition: 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.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: metadata complete
definition: 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.
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: obi.owl

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: metadata complete
definition: 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.
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition source: 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
imported from: obi.owl

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: ready for release
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition: 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.
definition editor: OBI
definition source: OBI
imported from: obi.owl

is member of organization
type: ObjectProperty
inverse of: has organization member
domain: Class
  union of: Homo sapiens
  union of: organization
range: organization
editor preferred label: is member of organization
has curation status: metadata complete
definition: Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
editor note: 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
editor note: JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Helen Parkinson
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred label: has organization member
has curation status: metadata incomplete
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
definition editor: Person: Jie Zheng

specifies value of
type: ObjectProperty
sub property of: is about
domain: value specification
editor preferred label: specifies value of
has curation status: metadata incomplete
definition: A relation between a value specification and an entity which the specification is about.
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: has value specification
has curation status: metadata complete
definition: A relation between an information content entity and a value specification that specifies its value.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

is genome of organism
type: ObjectProperty
sub property of: part of continuant at some time
definition: a 'part of continuant at some time' relation that incides a genome belongs to a organism.
definition editor: Yongqun He, Bin Zhao
imported from: ogg.owl

is gene of organism
type: ObjectProperty
sub property of: part of continuant at some time
domain: gene
range: organism
definition: a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
definition editor: Oliver He, Yue Liu
imported from: ogg.owl

owns
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is owned by
type: AsymmetricProperty
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
range: Class
  union of: material entity
  union of: information content entity
definition editor: Mathias Brochhausen
elucidation: This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
Source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

administrates
type: ObjectProperty
type: AsymmetricProperty
domain: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
range: Class
  union of: material entity
  union of: information content entity
definition: a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
definition editor: Mathias Brochhausen
comment: A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl

is owned by
type: ObjectProperty
type: AsymmetricProperty
domain: Class
  union of: material entity
  union of: information content entity
range: Class
  union of: Homo sapiens
  union of: organization
  union of: collection of humans
  union of: aggregate of organizations
definition: a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

is-aggregate-of
type: ObjectProperty
has obsolescence reason: BFO relation takes precedence.
imported from: The Ontology of Medically Related Social Entities
comment: 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.
deprecated: true

inheres_in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
sub property of: topObjectProperty
inverse of: bearer of
type: FunctionalProperty
domain: specifically dependent continuant
range: independent continuant
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: 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
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: 'inheres in at all times'
alternative term: inheres_in
imported from: geno.owl
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/ro.owl
temporal interpretation: axiom holds for all times
label: inheres in

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres_in
sub property of: topObjectProperty
domain: independent continuant
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: 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
editor note: 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.
alternative term: bearer of
alternative term: bearer_of
alternative term: is bearer of
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/ro.owl
temporal interpretation: axiom holds for all times
label: bearer_of
label: is bearer of

participates in
type: ObjectProperty
equivalent property:
  inverse of: has_participant
sub property of: topObjectProperty
inverse of: has_participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/ro.owl

has_participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
sub property of: topObjectProperty
domain: occurrent
range: continuant
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative term: has_participant
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
label: has participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
sub property of: topObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
editor preferred label: is concretized as
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: 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).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
alternative term: concretized by at some time
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
sub property of: topObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
editor preferred label: concretizes
example of usage: 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).
example of usage: 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).
definition: 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.
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
comment: 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.

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres_in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative term: function_of
alternative term: is function of
imported from: obi.owl

quality of
type: ObjectProperty
equivalent property:
  inverse of: has quality
sub property of: inheres_in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of
imported from: ontoneo.owl
imported from: pdro.owl

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres_in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative term: is role of
alternative term: role_of
imported from: obi.owl
imported from: ontoneo.owl
imported from: pdro.owl

has function
type: ObjectProperty
equivalent property:
  inverse of: function of
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_function
imported from: obi.owl
imported from: ro.owl

has quality
type: ObjectProperty
equivalent property:
  inverse of: quality of
sub property of: bearer of
domain: independent continuant
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_quality
imported from: ontoneo.owl
imported from: pdro.owl

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_role
imported from: obi.owl
imported from: ontoneo.owl
imported from: pdro.owl

derives from
type: ObjectProperty
equivalent property:
  inverse of: derives into
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: 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
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
curator note: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
imported from: obi.owl
imported from: ro.owl
in_subset: ro-eco

derives into
type: ObjectProperty
equivalent property:
  inverse of: derives from
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: 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
editor note: 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'.
alternative term: derives_into
imported from: obi.owl
imported from: ro.owl
in_subset: ro-eco

location of
type: ObjectProperty
equivalent property:
  inverse of: located in
inverse of: located in
type: TransitiveProperty
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: 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
alternative term: location_of
imported from: obi.owl
temporal interpretation: axiom holds for all times

located in
type: ObjectProperty
equivalent property:
  inverse of: location of
type: TransitiveProperty
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: 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
editor note: 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
alternative term: located_in
imported from: obi.owl
temporal interpretation: axiom holds for all times
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
definition editor: David Osumi-Sutherland
alternative term: starts_at_end_of
imported from: obi.owl
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
definition editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
imported from: obi.owl
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: is part of
property chain axiom: has part
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: geno.owl
imported from: ontoneo.owl
imported from: ro.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: ro-eco

in taxon
type: ObjectProperty
definition: x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
imported from: geno.owl

connected to
type: ObjectProperty
sub property of: mereotopologically related to
domain: Restriction
  on property: is part of
  some values from: system
range: Restriction
  on property: is part of
  some values from: system
property chain axiom:
  inverse of: connects
property chain axiom: connects
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
imported from: ro.owl

connects
type: ObjectProperty
sub property of: mereotopologically related to
domain: independent continuant
range: Restriction
  on property: is part of
  some values from: system
example of usage: The M8 connects Glasgow and Edinburgh
example of usage: a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
definition: c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
imported from: ro.owl

drains
type: ObjectProperty
sub property of: connected to
definition: Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
editor note: Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: ro.owl

develops from
type: ObjectProperty
inverse of: develops into
type: TransitiveProperty
domain: independent continuant
range: independent continuant
has curation status: pending final vetting
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition editor: Melissa Haendel
definition editor: Terry Meehan
imported from: ro.owl
comment: This is the transitive form of the develops from relation

develops into
type: ObjectProperty
sub property of: developmentally succeeded by
sub property of: has potential to develop into
sub property of: has potential to directly develop into
type: TransitiveProperty
has curation status: pending final vetting
definition: inverse of develops from
definition editor: Chris Mungall
definition editor: David Osumi-Sutherland
definition editor: Terry Meehan
imported from: ro.owl
in_subset: RO_0002259

has prototype
type: ObjectProperty
domain: Class
  union of: independent continuant
  union of: process
example of usage: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
has curation status: pending final vetting
definition: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
editor note: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
editor note: TODO: add homeomorphy axiom
editor note: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
definition editor: Chris Mungall
imported from: ro.owl

temporal relation
type: ObjectProperty
domain: occurrent
range: occurrent
editor preferred label: temporal relation
has curation status: pending final vetting
editor note: move to BFO?
definition editor: Chris Mungall
definition source: Allen's interval algebra
definition source: Allen
curator note: 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.
imported from: obi.owl
imported from: ro.owl
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
label: temporally related to

starts
type: ObjectProperty
sub property of: is part of
sub property of: temporal relation
domain: process boundary
range: process
editor preferred label: starts
has curation status: pending final vetting
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen

ends
type: ObjectProperty
sub property of: temporal relation
inverse of: ends with
domain: process boundary
range: process
has curation status: pending final vetting
definition: inverse of ends with
definition editor: Chris Mungall
imported from: ro.owl
in_subset: ro-eco

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporal relation
type: TransitiveProperty
has curation status: pending final vetting
definition: 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.
definition editor: Chris Mungall
alternative term: finished by
imported from: ro.owl
in_subset: ro-eco

has input
type: ObjectProperty
sub property of: has_participant
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: consumes
imported from: ro.owl

has output
type: ObjectProperty
sub property of: has_participant
definition: 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.
definition editor: Chris Mungall
alternative term: produces
imported from: ro.owl

developmentally succeeded by
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: pending final vetting
definition: Inverse of developmentally preceded by
definition editor: Chris Mungall
imported from: ro.owl

inheres in part of
type: ObjectProperty
sub property of: depends on
property chain axiom: inheres_in
property chain axiom: is part of
definition: 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.
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: ontoneo.owl
imported from: pdro.owl
temporal interpretation: axiom holds for all times

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
imported from: ontoneo.owl
imported from: ro.owl
temporal interpretation: axiom holds for all times

developmentally related to
type: ObjectProperty
definition: A relationship that holds between entities participating in some developmental process (GO:0032502)
definition editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
imported from: ro.owl

member of
type: ObjectProperty
equivalent property:
  inverse of: has member
sub property of: is part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
temporal interpretation: axiom holds for all times

has member
type: ObjectProperty
equivalent property:
  inverse of: member of
sub property of: has part
type: IrreflexiveProperty
example of usage: Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
imported from: geno.owl
imported from: ro.owl
temporal interpretation: axiom holds for all times

input of
type: ObjectProperty
sub property of: participates in
definition: inverse of has input
definition editor: Chris Mungall
imported from: ro.owl

output_of
type: ObjectProperty
sub property of: participates in
definition: inverse of has output
definition editor: Chris Mungall
imported from: pr.owl
imported from: ro.owl
database_cross_reference: RO:0002353
has_obo_namespace: protein
id: output_of
is transitive: false
shorthand: output_of
label: output of

has developmental potential involving
type: ObjectProperty
sub property of: developmentally related to
domain: anatomical entity
range: anatomical entity
has curation status: requires discussion
definition: x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
definition editor: Chris Mungall
imported from: ro.owl

has potential to develop into
type: ObjectProperty
sub property of: has developmental potential involving
has curation status: requires discussion
definition: x has the potential to develop into y iff x develops into y or if x is capable of developing into y
definition editor: Chris Mungall
imported from: ro.owl

has potential to directly develop into
type: ObjectProperty
sub property of: has potential to develop into
has curation status: requires discussion
definition: x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
definition editor: Chris Mungall
imported from: ro.owl

depends on
type: ObjectProperty
definition editor: Chris Mungall
imported from: ontoneo.owl
imported from: pdro.owl

towards
type: ObjectProperty
sub property of: depends on
definition: q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
editor note: This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: ontoneo.owl

has modifier
type: ObjectProperty
definition: A relation that holds between an attribute or a qualifier and another attribute.
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
curator note: This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
imported from: ontoneo.owl
imported from: pdro.owl
in_subset: ro-eco

disease has location
type: ObjectProperty
domain: disease
range: independent continuant
range: Class
  union of: material anatomical entity
  union of: immaterial anatomical entity
definition: A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
editor note: TODO: complete range axiom once more of CARO has been mireoted in to this ontology
curator note: This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
imported from: ro.owl
created by: cjm
creation date: 2017-11-05T04:06:02Z

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
editor note: TODO: Add homeomorphy axiom
imported from: ro.owl
is homeomorphic for: continuant
is homeomorphic for: occurrent
creator: bgee.unil.ch
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000041
database_cross_reference: SO:similar_to
alternative_term: sameness
alternative_term: similar to
has_related_synonym: correspondence
has_related_synonym: resemblance

part_of
type: ObjectProperty
type: TransitiveProperty
imported from: ontoneo.owl
has_obo_namespace: fma
id: part_of

regional_part_of
type: ObjectProperty
sub property of: part_of
imported from: ontoneo.owl
has_obo_namespace: fma
id: regional_part_of

systemic_part_of
type: ObjectProperty
sub property of: part_of
imported from: ontoneo.owl
has_obo_namespace: fma
id: systemic_part_of

is related to
type: ObjectProperty
type: SymmetricProperty
definition: A is related to B iff there is some relation between A and B.
imported from: ontoneo.owl
imported from: pdro.owl
comment: 'is related to' is the top level relation in SIO

is comparable to
type: ObjectProperty
sub property of: is related to
type: SymmetricProperty
definition: is comparable to is a relation between two entities that share at least one feature whose value can be compared.
imported from: ontoneo.owl
imported from: pdro.owl

is identical to
type: ObjectProperty
sub property of: is comparable to
type: SymmetricProperty
definition: is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes.
imported from: ontoneo.owl
imported from: pdro.owl

participates in via role
type: ObjectProperty
sub property of: participates in
domain: continuant
range: occurrent
property chain axiom: has role
property chain axiom: realized in
editor preferred label: participates in via role
definition: aa object property chain: if individual I has role R which is realized in process P, then I 'participates in via role' P
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-11T14:36:32Z
deprecated: true

linked in dataset with
type: ObjectProperty
type: SymmetricProperty
domain: information content entity
range: information content entity
editor preferred label: linked in dataset with
example of usage: In some database table about employment, my social security number appears in the same row with some employer identification number. (Alternatively, they both appear in the same XML or JSON path, etc.) Either way, a rule could be written in (or outside of) OWL interpreting that co-occurrence to mean that I am employed by the institution denoted by that employer identification number. Applications, like Drivetrain, may perform some (closed-world?) checks before instantiating the implied relationship: if there is, in reality, no institution denoted by the employer identification number, the system might refuse to instantiate any statement at all about who I work for.
definition: A relationship between two information content entities that are connected or linked by placement in the same structural subdivision of a dataset and intended to be about entities that have some relationship in reality.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Chris Stoeckert
date: 2018-01-23T15:00:15Z
comment: this is a non-owl shortcut, stating that two ICE were found on the same row of a data table. This may lead to a conclusion that the two ICEs are values borne by two things that have some relationship in reality. For example, if a patient identifier and an encounter identifier were found in the same row, one might infer that the denoted participant participated in the denoted encounter with a participation under investigation role.

born on
type: ObjectProperty
domain: Homo sapiens
range: start of neonate stage
property chain axiom: participates in
property chain axiom: neonate stage OTR NTR
property chain axiom:
  inverse of: birth instant starts NTR
property chain axiom:
  inverse of: SNS OTR birth instant
editor preferred label: has birth
definition: an object property chain 'shortcut': if human H participates in a 'neonate stage' N that is started by 'start of neonate stage' S, then H 'born on' S
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-09-20T14:07:39Z
comment: the TURBO team referent tracks births (for which each person only has one) rather than birth dates

has matching CV term
type: ObjectProperty
definition: Given that D is a data item bearing some textual value L, T is a class or instance term from some ontology or RDF linked data set, and H is this 'has matching CV term' property, D H T means that L was drawn from some controlled vocabulary containing term T, which has the same meaning as L. As a term, T will be represented by a URI, whereas L is a datatype literal (which was likely instantiated from a relational database or other non-semantic resource.) For example, if D is an instance of 'gene' (http://purl.obolibrary.org/obo/OGG_0000000002) with literal value "ENSG00000081237", <https://www.uniprot.org/uniprot/P08575> may be selected at T. In this case, the author of the triple is asserting that the value "ENSG00000081237" was drawn from the terms provided in Ensembl's RDF model. That namespace can be communicated with a 'has namespace' (TURBO_0000703) triple. D a <http://purl.obolibrary.org/obo/OGG_0000000002> D <http://transformunify.org/ontologies/TURBO_0006512> "ENSG00000081237" D <http://transformunify.org/ontologies/TURBO_0000304> <http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000000003> D <http://transformunify.org/ontologies/TURBO_0000703> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45763> This property is intended to enable rapid re-representation from literal values to URI-bearing terms, so T may come from a vocabulary with weak semantics. Statements about reality could be added in the future, like D <http://purl.obolibrary.org/obo/IAO_0000142> <http://purl.obolibrary.org/obo/HGNC_9667> Which says that allele information D mentions a particular gene modeled in the Protein Ontology. The 'mentions' property has stronger semantics than this 'has matching CV term' and the Protein Ontology has a stronger commitment to reality than the Uniprot RDF model.
definition editor: Mark A. Miller
alternative term: has matching controlled vocabulary term

has matching Ensembl term
type: ObjectProperty
sub property of: has matching CV term

has matching ICD term
type: ObjectProperty
sub property of: has matching CV term
definition: a 'has matching CV term', where the matching term is drawn from any of the versions and variants of the International Classification of Diseases. The particular ICD falvor can be communicated with a 'has namespace' (TURBO_0000703) triple taking an object like <http://purl.obolibrary.org/obo/NCIT_C71890> for ICD-9 or <http://purl.obolibrary.org/obo/NCIT_C128691> for ICD-10-CM
creator: Mark A. Miller
date: 2018-08-17T13:50:36Z
deprecated: true

has matching RxNORM term
type: ObjectProperty
sub property of: has matching CV term
deprecated: true

has namespace
type: ObjectProperty
definition editor: Mark A. Miller
definition editor: This property can be used along with 'has matching CV term' or any of its sub-properties to indicate the controlled vocabulary form which a matching terms was selected.

instantiation object shortcut
type: ObjectProperty
sub property of: topObjectProperty
domain: TURBO data model
definition editor: Mark A. Miller
date: 2019-03-01T15:16:10Z

shortcut person data model to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: person data model
definition editor: Mark A. Miller
date: 2019-03-01T15:16:33Z
comment: shortcut person data model to data

shortcut person data model to patient CRID registry
type: ObjectProperty
sub property of: shortcut person data model to entity
domain: person data model
range: patient identifier registry
definition editor: Mark A. Miller
date: 2019-03-01T15:16:59Z
deprecated: true

shortcut person data model to gender identty datum
type: ObjectProperty
sub property of: shortcut person data model to entity
domain: person data model
range: gender identity datum
definition editor: Mark A. Miller
date: 2019-03-01T16:09:01Z

shortcut person data model to racial identity datum
type: ObjectProperty
sub property of: shortcut person data model to entity
domain: person data model
range: racial identity datum
definition editor: Mark A. Miller
date: 2019-03-01T16:17:33Z

shortcut person data model to ethnic identity datum
type: ObjectProperty
sub property of: shortcut person data model to entity
domain: person data model
range: ethnic identity datum
definition editor: Mark A. Miller
date: 2019-03-01T16:19:38Z

shortcut health care encounter data model to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: health care encounter data model
definition editor: Mark A. Miller
date: 2019-03-02T18:58:36Z
deprecated: false

shortcut health care encounter data model to encounter registry
type: ObjectProperty
sub property of: shortcut health care encounter data model to entity
domain: health care encounter data model
range: health care encounter identifier registry
definition editor: Mark A. Miller
date: 2019-03-02T18:59:39Z
deprecated: true

shortcut health care encounter data model to patient registry
type: ObjectProperty
sub property of: shortcut health care encounter data model to entity
domain: health care encounter data model
range: patient identifier registry
definition editor: Mark A. Miller
date: 2019-03-02T18:59:58Z
deprecated: true

shortcut observation to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: data item
definition editor: Mark A. Miller
date: 2019-03-04T16:14:56Z

shortcut observation to patient registry
type: ObjectProperty
sub property of: shortcut observation to entity
definition editor: Mark A. Miller
date: 2019-03-04T16:19:40Z

shortcut observation to encounter registry
type: ObjectProperty
sub property of: shortcut observation to entity
definition editor: Mark A. Miller
date: 2019-03-04T16:20:00Z

shortcut observation to observation type registry
type: ObjectProperty
sub property of: shortcut observation to entity
definition editor: Mark A. Miller
date: 2019-03-04T16:22:49Z

shortcut observation to unit term
type: ObjectProperty
sub property of: shortcut observation to entity
definition editor: Mark A. Miller
date: 2019-03-04T16:26:47Z

shortcut observation to observation type term
type: ObjectProperty
sub property of: shortcut observation to entity
definition editor: Mark A. Miller
date: 2019-03-04T21:45:11Z

shortcut health care encounter data model to patient data model
type: ObjectProperty
sub property of: shortcut health care encounter data model to entity
domain: health care encounter data model
range: person data model
definition editor: Mark A. Miller
date: 2019-03-05T20:37:24Z

shortcut biobank encounter data model to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: biobank encounter data model
definition editor: Mark A. Miller
date: 2019-03-05T20:38:48Z

shortcut biobank encounter data model to person data model
type: ObjectProperty
sub property of: shortcut biobank encounter data model to entity
domain: biobank encounter data model
range: person data model
definition editor: Mark A. Miller
date: 2019-03-05T20:38:58Z

clinical datum about patient
type: ObjectProperty
sub property of: is about
domain: data item
range: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: patient role

has measurement specification
type: ObjectProperty
sub property of: has part
domain: planned process
range: value specification
alternative term: has measured value (from James Overton's 2019-04-08 proposal)

shortcut allele information data model to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: allele information data model

shortcut allele information to zygosity value specification
type: ObjectProperty
sub property of: shortcut allele information data model to entity
domain: allele information data model
range: zygosity value specification

shortcut allele information to biobank encounter data model
type: ObjectProperty
sub property of: shortcut allele information data model to entity
domain: allele information data model
range: biobank encounter data model

shortcut allele information to genotype identifier registry
type: ObjectProperty
sub property of: shortcut allele information data model to entity
domain: allele information data model
deprecated: true

shortcut allele information to biobank encounter identifier registry
type: ObjectProperty
sub property of: shortcut allele information data model to entity
deprecated: true

writes triples about
type: ObjectProperty
sub property of: mentions in RDF
definition: inserts RDF triples about this object
alternative term: createdTripleAbout
elucidation: if ?s1 'writes triples about' ?o1, then at least one triple will be submitted to some RDF model/triplestore in which ?o1 ?p ?o2

mentions in RDF
type: ObjectProperty

inserted triples into
type: ObjectProperty
sub property of: mentions in RDF
domain: semantic expansion of data model
range: named graph
alternative term: addedTriplesTo
elucidation: this predicate documents what named graph is the destination for the triples generated by the subject process.

sourced triples from
type: ObjectProperty
sub property of: mentions in RDF
domain: semantic expansion of data model
range: named graph
alternative term: sourced input from
elucidation: this predicate documents the named graph from which a process drew its input

shortcut tumor data model to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: tumor data model

shortcut tumor data model to patient registry
type: ObjectProperty
sub property of: shortcut tumor data model to entity
domain: tumor data model
range: patient identifier registry
deprecated: true

DOB about SNS
type: ObjectProperty
sub property of: is about
domain: date of birth
range: start of neonate stage
property chain axiom: participates in
property chain axiom: neonate stage OTR NTR
property chain axiom:
  inverse of: birth instant starts NTR
property chain axiom:
  inverse of: SNS OTR birth instant
property chain axiom: DOB about day of birth
property chain axiom:
  inverse of: birth instant TPO birth day
property chain axiom:
  inverse of: SNS OTR birth instant
comment: 'is about' o inverse ('birth instance TPO birth day') o inverse ('SNS OTR birth instant')

DOB about day of birth
type: ObjectProperty
sub property of: is about
domain: date of birth
range: day of birth

birth instant TPO birth day
type: ObjectProperty
sub property of: temporal part of
domain: birth instant
range: day of birth

SNS OTR birth instant
type: ObjectProperty
sub property of: occupies temporal region
domain: start of neonate stage
range: birth instant

SNS starts neonate stage
type: ObjectProperty
sub property of: starts
domain: start of neonate stage
range: neonate stage
property chain axiom: SNS OTR birth instant
property chain axiom: birth instant starts NTR
property chain axiom:
  inverse of: neonate stage OTR NTR

neonate stage OTR NTR
type: ObjectProperty
sub property of: occupies temporal region
domain: neonate stage
range: neonate temporal region

birth instant TPO NTR
type: ObjectProperty
sub property of: temporal part of
domain: birth instant
range: neonate temporal region

birth instant starts NTR
type: ObjectProperty
sub property of: starts
domain: birth instant
range: neonate temporal region

shortcut person CRID model to entity
type: ObjectProperty
sub property of: instantiation object shortcut
domain: person CRID data model

shortcut person CRID model to singleton registry denoter
type: ObjectProperty
sub property of: shortcut person CRID model to entity
domain: person CRID data model
range: patient registry denoter

shortcut health care encounter data model to encounter id source
type: ObjectProperty
sub property of: shortcut health care encounter data model to entity
domain: health care encounter data model
range: health care encounter identifier source denoter
deprecated: true

shortcut health care encounter data model to singleton health care encounter identifier source dentoer
type: ObjectProperty
sub property of: shortcut health care encounter data model to entity
domain: health care encounter data model
range: health care encounter identifier source denoter

shortcut tumor data model to singleton tumor registry denoter
type: ObjectProperty
sub property of: shortcut tumor data model to entity
domain: tumor data model
range: tumor registry denoter

shortcut tumor data model to singleton patient registry denoter
type: ObjectProperty
sub property of: shortcut tumor data model to entity
domain: tumor data model
range: patient registry denoter

shortcut person data model to singleton patient CRID registry denoter
type: ObjectProperty
sub property of: shortcut person data model to entity
domain: person data model
range: patient registry denoter

shortcut health care encounter data model to singleton patient registry denoter
type: ObjectProperty
sub property of: shortcut health care encounter data model to entity
domain: health care encounter data model
range: patient registry denoter

shortcut allele information to singleton biobank encounter identifier registry denoter
type: ObjectProperty
sub property of: shortcut allele information data model to entity
domain: allele information data model
range: biobank encounter registry denoter

shortcut allele information to singleton genotype identifier registry denoter
type: ObjectProperty
sub property of: shortcut allele information data model to entity
domain: allele information data model
range: genotype identifier registry denoter

shortcut biobank encounter data model to singleton biobank encounter registry denoter
type: ObjectProperty
sub property of: shortcut biobank encounter data model to entity
domain: biobank encounter data model

shortcut biobank encounter data model to singleton patient registry denoter
type: ObjectProperty
sub property of: shortcut biobank encounter data model to entity
domain: biobank encounter data model
range: patient registry denoter

has specified allele information output
type: ObjectProperty

code
type: DatatypeProperty
comment: double check property type in NCIT download

has_string
type: DatatypeProperty
domain: biological sequence
range: string
definition: Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').
imported from: geno.owl

has_member_count
type: DatatypeProperty
definition: Describes the number of members in some set.
alternative term: has_count
imported from: geno.owl
comment: In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'.

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
imported from: obi.owl

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
editor preferred label: has specified numeric value
has curation status: metadata complete
definition: A relation between a value specification and a number that quantifies it.
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

has specified value
type: DatatypeProperty
domain: value specification
editor preferred label: has specified value
has curation status: metadata incomplete
definition: A relation between a value specification and a literal.
editor note: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
definition source: OBI
imported from: obi.owl

shortcut biobank consenter to data shortcut
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: biobank consenter
editor preferred label: shortcut biobank consenter to data shortcut
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter to a/n to data shortcut
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T13:48:27Z
deprecated: true

shortcut biobank consenter to biological sex URI string
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: anyURI
editor preferred label: shortcut biobank consenter to biological sex URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biological sex URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T13:52:22Z
deprecated: true

shortcut biobank consenter to data set title
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
editor preferred label: shortcut biobank consenter to dataset title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a dataset title
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T13:54:45Z
deprecated: true

shortcut biobank consenter to textual date of birth text
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
editor preferred label: shortcut biobank consenter to textual date of birth text
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a textual date of birth text
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T13:55:40Z
deprecated: true

shortcut biobank consenter to xsd-formatted date of birth
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: date
editor preferred label: shortcut biobank consenter to xsd-formatted date of birth
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a xsd-formatted date of birth
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T13:56:37Z
deprecated: true

shortcut biobank consenter to gender identity datum text
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
editor preferred label: shortcut biobank consenter to gender identity datum text
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a gender identity datum text
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T13:57:40Z
deprecated: true

shortcut biobank consenter to gender identity datum URI string
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: anyURI
editor preferred label: shortcut biobank consenter to gender identity datum URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a gender identity datum URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T14:03:37Z
deprecated: true

shortcut biobank consenter to biobank consenter CRID symbol
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
editor preferred label: shortcut biobank consenter to biobank consenter CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biobank consenter CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-22T14:05:09Z
deprecated: true

shortcut biobank consenter to biobank consenter registry denoter
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
editor preferred label: shortcut biobank consenter to biobank consenter registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biobank consenter registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-24T17:46:48Z
deprecated: true

shortcut biobank consenter to biobank consenter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
editor preferred label: shortcut biobank consenter to biobank consenter identifier registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biobank consenter identifier registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-24T17:47:54Z
deprecated: true

shortcut biobank consenter to racial identity registry URI string
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: anyURI
creator: Mark Miller
date: 2018-07-25T14:57:55Z
deprecated: true

shortcut biobank consenter to racial identity registry denoter
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
creator: Mark Miller
date: 2018-07-25T14:59:42Z
deprecated: true

shortcut biobank consenter to racial identity CRID symbol
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: string
creator: Mark Miller
date: 2018-07-25T15:00:20Z
deprecated: true

shortcut biobank consenter to racial identity datum URI string
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: anyURI
creator: Mark Miller
date: 2018-07-25T15:01:01Z
deprecated: true

shortcut biobank consenter to racial identity datum veracity
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
domain: biobank consenter
range: boolean
creator: Mark Miller
date: 2018-07-25T15:18:51Z
deprecated: true

shortcut biobank consenter to racial identity text
type: DatatypeProperty
sub property of: shortcut biobank consenter to data shortcut
creator: Mark Miller
date: 2018-07-27T22:08:20Z
deprecated: true

shortcut biobank encounter to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: biobank encounter
editor preferred label: shortcut biobank encounter to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: still working out the relationships between biobank encounters and health care encounters. use separate properties due to domain constraint? or make a parent class?

shortcut biobank encounter to data set title
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
editor preferred label: shortcut biobank encounter to data set title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a data set title
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

shortcut biobank encounter to textual encounter date
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
editor preferred label: shortcut biobank encounter to textual encounter date
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a textual encounter date
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: the textual representation of a date isn't technically interdependent with anything else. However, if it was present in tabular data, it should be passed on with this shortcut, to provide provenance for the xsd representation of the date

shortcut biobank encounter to xsd-formatted encounter date
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: date
editor preferred label: shortcut biobank encounter to xsd-formatted encounter date
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a xsd-formatted encounter date
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

shortcut biobank encounter to height in cm
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: float
editor preferred label: shortcut biobank encounter to height in cm
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a height in cm
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-09T15:17:05Z

shortcut biobank encounter to weight in kg
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: float
editor preferred label: shortcut biobank encounter to weight in kg
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a weight in kg
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-09T15:17:25Z

shortcut biobank encounter to encounter CRID symbol
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
editor preferred label: shortcut biobank encounter to encounter CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a encounter CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

shortcut biobank encounter to encounter registry denoter
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
editor preferred label: shortcut biobank encounter to encounter registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a encounter registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-26T16:09:56Z

shortcut biobank encounter to encounter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
editor preferred label: shortcut biobank encounter to encounter identifier registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a encounter identifier registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-26T16:10:39Z

shortcut biobank encounter to BMI
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: float
editor preferred label: shortcut biobank encounter to BMI
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a BMI
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-10-24T13:05:28Z

shortcut health care encounter data model to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: health care encounter data model
editor preferred label: shortcut health care encounter data model to data
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter to a/n to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-09-05T16:21:09Z
comment: This property and any of its sub properties link an instance of "biobank study participant" with some literal value. See comments on parent class.

shortcut health care encounter data model to data set title
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: string
editor preferred label: shortcut health care encounter data model to data to data set title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a data set title
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: This shortcut links a health care encounter ?e (OGMS_0000097) to a textual title for a dataset ?t (IAO_0000100). Expansion involve creating a dataset instance, which will be the input into an R2R instantiation process ?i. ?e rdf:type obo:OGMS_0000097 . ?d rdf:type obo:IAO_0000100 ; obo:BFO_0000051 ?p ; dc11:title ?dsTitle . ?i rdf:type :R2RInstantiation ; obo:OBI_0000293 ?d . Note that the encounter and the dataset are still not bound above. The expander must find paths (in either orientation) between the encounter and the data set, via some information content entities Here's an illustration of "any path" in sparql, but only going in one orientation. ?e rdf:type <http://purl.obolibrary.org/obo/OGMS_0000097> . ?e (:|!:)* ?o . ?o ?p ?v That is, ?v could be the value of an identifier ?o that denotes the encounter, or it could be the value of diagnosis code that is part of a diagnosis CRID that was the output of the encounter. --- TODO: what should the dataset contain as parts in our encounter only shortcut expansion? encounter id instance encounter date instance (is the fact that the text value and mapped xsd value are both values of the same instance enough to explain the conversion? i.e., which value is actually in the data set and which is derived? is the fact that a data owner made the conversion in Karma enough justification? as in the data owner is saying that they are identical values like 2 and two? is this another process?) diagnosis (the whole CRID? ** the code symbol and the registry denoter separately?** what about the mapped registry URI?... No, that's not an ice in a data set. But we might want to explain the conversion processes from string to URI, like I suggested for string to xsd date.) registry and date conversions could be rule sin the instantiation process?

shortcut health care encounter data model to textual encounter date
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: string
editor preferred label: shortcut health care encounter data model to textual encounter date
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a textual encounter date
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: This shortcut links a health care encounter ?e (OGMS_0000097) to the textual representation ?tv of the date ?d (turbo:ProcStartTimeMeas) on which the encounter took place . Furthermore, date ?d is about the temporal boundary ?es (turbo:HealthcareEncStart) that starts encounter ?e. ?tv will typically part of some dataset (see ScEnc2DataSet.) ?e rdf:type obo:OGMS_0000097 . ?d rdf:type :ProcStartTimeMeas ; :hasTextualValue ?tv ; obo:IAO_0000136 ?es . ?es rdf:type :HealthcareEncStart ; obo:RO_0002223 ?e . Although not constrained at this point (?) the ?tv's type would reasonably be an xsd:string. Note that TURBO will typically expect an xsd:date literal bound to date instances like ?d. As of the end of August 2017, that means that the textual date value will need to be converted to an xsd:date within a python transformation, in Karma. --- the textual representation of a date isn't technically interdependent with anything else. However, if it was present in tabular data, it should be passed on with this shortcut, to provide provenance for the xsd representation of the date

shortcut health care encounter data model to xsd-formatted encounter date
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: date
editor preferred label: shortcut health care encounter data model to xsd-formatted encounter date
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a xsd-formatted encounter date
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: definition "This shortcut links a health care encounter ?e (OGMS_0000097) to and xsd:date literal ?xv, which is the measurement value* of date ?d (turbo:ProcStartTimeMeas) on which the encounter took place . Furthermore, date ?d is about the temporal boundary ?es (turbo:HealthcareEncStart) that starts encounter ?e ?xv will typcally part of some dataset (see ScEnc2DataSet.) In semi-turtle syntax, It means that ?d rdf:type :ProcStartTimeMeas ; obo:IAO_0000004 ?xv ; obo:IAO_0000136 ?es . ?e rdf:type obo:OGMS_0000097 . ?es rdf:type :HealthcareEncStart ; obo:RO_0002223 ?e . As of the end of August 2017, that means that a textual date value will need to be converted to an xsd:date within a python transformation, in Karma. *oops, this violates the xsd:float range expectation of has measurement value (IAO_0000004) as defined in the IAO owl file. I added xsd:date to that range definition within turbo.owl and turbo_merged.owl. Some applications seem to accept the dual range, but some (like top braid composer) only seem to consider one of the datatype ranges… first found in the file??? I have also created turbo:hasDateValue"

shortcut health care encounter data model to height in cm
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: float
editor preferred label: shortcut health care encounter data model to height in cm
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a height in cm
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-09T15:17:05Z

shortcut health care encounter data model to weight in kg
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: float
editor preferred label: shortcut health care encounter data model to weight in kg
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a weight in kg
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-09T15:17:25Z

shortcut health care encounter data model to encounter ID symbol
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: string
editor preferred label: shortcut health care encounter data model to encounter ID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a encounter ID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: this shortcut links a health care encounter ?e (OGMS_0000097) to the value ?iv of its identifier ?i. (turbo:EncounterID). ?i denotes ?e. ?e rdf:type obo:OGMS_0000097 . ?i rdf:type :EncounterID ; obo:IAO_0000219 ?e ; :thingLiteralValue ? iv.

shortcut health care encounter data model to encounter registry denoter
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: string
editor preferred label: shortcut health care encounter data model to encounter registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a encounter registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: no example of use yet... we may end up saying that encounter identifiers don't really come from registries

shortcut health care encounter data model to encounter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: string
editor preferred label: shortcut health care encounter data model to encounter identifier registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a encounter identifier registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-26T16:07:06Z

shortcut health care encounter data model to BMI
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: float
editor preferred label: shortcut health care encounter data model to BMI
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a BMI
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-10-24T13:05:28Z
comment: Used when instantiating tabular/relational data about health care encounters that includes a BMI column. Upon expansion, :e a :healthCareEncounter ; :hasSpecifiedOutput ?BMI. :BMI a :bmiDataItem ; :hasLiteralValue "25"^^xsd:float upon participant-to-encounter joining: :BMI :isAbout :adipose . :adipose a :adiposeTissue ; :partOf :studyParticipant .

shortcut health care encounter data model to diagnosis code symbol
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: string
editor preferred label: shortcut health care encounter data model to diagnosis code symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a diagnosis code symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: this shortcut links a health care encounter ?e (OGMS_0000097) to the value ?dcv of a diagnosis code symbol ?dcs. (turbo:EncounterDiagCodeSymbol). ?dcs is part of a diagnosis CRID ?dcrid (turbo:DiagCodeRegitryID) and is typically part of some dataset (see ScEnc2DataSet.) ?dcrid is the output of the encounter ?e. ?e rdf:type obo:OGMS_0000097 ; obo:OBI_0000299 ?dcrid . ?dcrid rdf:type :DiagCrid ; obo:BFO_0000051 ?dcs . ?dcs rdf:type :EncounterDiagCodeSymbol ; :thingLiteralValue ?dcv .

shortcut health care encounter to diagnosis code registry denoter
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: string
editor preferred label: shortcut health care encounter data model to diagnosis code registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a diagnosis code registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: this shortcut links a health care encounter ?e (OGMS_0000097) to the value ?drnv of a diagnosis code registry denoter ?dcrn (turbo:DiagCodeRegitryID), which denotes a registry instance ?dcru like <http://purl.obolibrary.org/obo/NCIT_C71892> for ICD-10. The mapping from denoters of registries to URIs that already exist in some ontology like NCIT will be the responsibility of the data owner and will be executed with a python transformation in Karma. ?dcrn is part of a diagnosis CRID ?dcrid (turbo:DiagCrid) and ?drnv is typically part of some dataset (see ScEnc2DataSet.) ?dcrid is the output of the encounter ?e. ?e rdf:type obo:OGMS_0000097 ; obo:OBI_0000299 ?dcrid . ?dcrid rdf:type :DiagCrid ; obo:BFO_0000051 ?dcrn . ?dcrn rdf:type :DiagCodeRegitryID ; obo:IAO_0000219 ?dcru ; :hasTextualValue ?drnv . --- the textual representation of a diagnosis code registry isn't technically interdependent with anything else. However, if it was present in tabular data, it should be passed on with this shortcut as provenance for the diagnosis code registry URI, which is interdependent with the diagnosis code symbol.

shortcut health care encounter to diagnosis code registry URI string
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: anyURI
editor preferred label: shortcut health care encounter to diagnosis code registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a diagnosis code registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: this shortcut links a health care encounter ?e (OGMS_0000097) to the URI of an instance of a diagnosis code registry ?dcru. the value ?drnv of a diagnosis code registry denoter ?dcrn (turbo:DiagCodeRegitryID) denotes a registry instance ?dcru like <http://purl.obolibrary.org/obo/NCIT_C71892> for ICD-10. The mapping from denoters of registries to URIs that already exist in some ontology like NCIT will be the responsibility of the data owner and will be executed with a python transformation in Karma. ?dcrn is part of a diagnosis CRID ?dcrid (turbo:DiagCrid) and ?drnv is typically part of some dataset (see ScEnc2DataSet.) ?dcrid is the output of the encounter ?e. ?e rdf:type obo:OGMS_0000097 ; obo:OBI_0000299 ?dcrid . ?dcrid rdf:type :DiagCrid ; obo:BFO_0000051 ?dcrn . ?dcrn rdf:type :DiagCodeRegitryID ; obo:IAO_0000219 ?dcru ; :hasTextualValue ?drnv . --- failed parse rules for Karma? assumes the tabular data being instantiated by Karma has a column of strings denoting diagnosis code registries. Ideally a Karma python transformation will convert the strings into URIs for diagnosis code registry instances from some ontology like NCIT

instantiation hybrid shortcut
type: DatatypeProperty
editor preferred label: instantiation hybrid shortcut
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: this property and any sub properties are used to simplify the experience of using Karma or related relational to RDF instantiation software. They link instances/individuals to data literals, even (or especially!) when the literal is about an instance of some other class, not the subject of the shortcut triple. It is the responsibility of TURBO’s Drivetrain application to expand shortcut triples into realism based semantic triples using BFO classes, based on the shortcut predicate and the class of the instance in the subject position

shortcut biobank encounter CRID to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: biobank encounter CRID
editor preferred label: shortcut biobank encounter CRID to data
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-29T21:44:08Z

shortcut health care encounter CRID to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: health care encounter CRID
editor preferred label: shortcut health care encounter CRID to data
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-29T21:45:02Z

shortcut biobank encounter CRID to data set title
type: DatatypeProperty
sub property of: shortcut biobank encounter CRID to data
domain: biobank encounter CRID
range: string
editor preferred label: shortcut biobank encounter CRID to dataset title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to dataset title
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T14:21:07Z

shortcut biobank encounter CRID to biobank encounter CRID symbol
type: DatatypeProperty
sub property of: shortcut biobank encounter CRID to data
domain: biobank encounter CRID
range: string
editor preferred label: shortcut biobank encounter CRID to biobank encounter CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to biobank encounter CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T15:54:17Z

shortcut biobank encounter CRID to biobank encounter registry denoter
type: DatatypeProperty
sub property of: shortcut biobank encounter CRID to data
domain: biobank encounter CRID
range: string
editor preferred label: shortcut biobank encounter CRID to biobank encounter registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to biobank encounter registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T14:19:17Z

shortcut biobank encounter CRID to biobank encounter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut biobank encounter CRID to data
domain: biobank encounter CRID
range: anyURI
editor preferred label: shortcut biobank encounter CRID to biobank encounter identifier registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to biobank encounter identifier registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T14:17:41Z

shortcut health care encounter to drug prescription text
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: string
editor preferred label: shortcut health care encounter to drug prescription text
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter to a/n to drug prescription text
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-14T15:05:57Z

shortcut health care encounter to drug prescription CRID symbol
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: string
editor preferred label: shortcut health care encounter to drug prescription CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter to a/n to drug prescription CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-27T21:47:38Z

shortcut health care encounter CRID to data set title
type: DatatypeProperty
sub property of: shortcut health care encounter CRID to data
domain: health care encounter CRID
range: string
editor preferred label: shortcut health care encounter CRID to dataset title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to dataset title
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T14:22:32Z

shortcut health care encounter CRID to health care encounter CRID symbol
type: DatatypeProperty
sub property of: shortcut health care encounter CRID to data
domain: health care encounter CRID
range: string
editor preferred label: shortcut health care encounter CRID to health care encounter CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to health care encounter CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T15:55:51Z

shortcut health care encounter CRID to health care encounter registry denoter
type: DatatypeProperty
sub property of: shortcut health care encounter CRID to data
domain: health care encounter CRID
range: anyURI
editor preferred label: shortcut health care encounter CRID to health care encounter registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to health care encounter registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T14:23:25Z

shortcut health care encounter CRID to health care encounter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut health care encounter CRID to data
domain: health care encounter CRID
range: string
editor preferred label: shortcut health care encounter CRID to health care encounter identifier registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to health care encounter identifier registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T14:24:07Z

shortcut biobank consenter CRID to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: biobank consenter CRID
editor preferred label: shortcut biobank consenter CRID to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T16:20:12Z
deprecated: true

shortcut biobank consenter CRID to data set title
type: DatatypeProperty
sub property of: shortcut biobank consenter CRID to data
domain: biobank consenter CRID
range: string
editor preferred label: shortcut biobank consenter CRID to dataset title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to dataset title
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T16:29:11Z
deprecated: true

shortcut biobank consenter CRID to biobank consenter CRID symbol
type: DatatypeProperty
sub property of: shortcut biobank consenter CRID to data
domain: biobank consenter CRID
range: string
editor preferred label: shortcut biobank consenter CRID to biobank consenter CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to biobank consenter CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T16:30:55Z
deprecated: true

shortcut biobank consenter CRID to biobank consenter registry denoter
type: DatatypeProperty
sub property of: shortcut biobank consenter CRID to data
domain: biobank consenter CRID
range: string
editor preferred label: shortcut biobank consenter CRID to biobank consenter registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to biobank consenter registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T16:31:40Z
deprecated: true

shortcut biobank consenter CRID to biobank consenter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut biobank consenter CRID to data
domain: biobank consenter CRID
range: anyURI
editor preferred label: shortcut biobank consenter CRID to biobank consenter identifier registry URI string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to biobank consenter identifier registry URI string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T16:30:02Z
deprecated: true

shortcut diagnosis to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: diagnosis
editor preferred label: shortcut diagnosis to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-07T22:07:58Z

shortcut diagnosis to diagnosis code symbol
type: DatatypeProperty
sub property of: shortcut diagnosis to data
domain: diagnosis
range: string
editor preferred label: shortcut diagnosis to diagnosis code symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n diagnosis to a/n to diagnosis code symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-07T22:08:58Z

shortcut diagnosis to diagnosis code registry denoter
type: DatatypeProperty
sub property of: shortcut diagnosis to data
domain: diagnosis
range: string
editor preferred label: shortcut diagnosis to diagnosis code registry denoter
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n diagnosis to a/n to diagnosis code registry denoter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-07T22:09:53Z

shortcut diagnosis to diagnosis code registry
type: DatatypeProperty
sub property of: shortcut diagnosis to data
domain: diagnosis
range: anyURI
editor preferred label: shortcut diagnosis to diagnosis code registry
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n diagnosis to a/n to diagnosis code registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-07T22:11:30Z

shortcut diagnosis to data set title
type: DatatypeProperty
sub property of: shortcut diagnosis to data
domain: diagnosis
range: string

shortcut prescription to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: drug prescription
editor preferred label: shortcut prescription to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-28T17:27:03Z

shortcut prescription to prescription CRID symbol
type: DatatypeProperty
sub property of: shortcut prescription to data
domain: drug prescription
range: string
editor preferred label: shortcut prescription to prescription CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n prescription to a/n to prescription CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-28T17:27:53Z

shortcut prescription to data set title
type: DatatypeProperty
sub property of: shortcut prescription to data
domain: drug prescription
range: string

shortcut prescription to prescription fullname/order_name
type: DatatypeProperty
sub property of: shortcut prescription to data
domain: drug prescription
range: string
editor preferred label: shortcut prescription to prescription fullname/order_name
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n prescription to a/n to prescription fullname/order_name
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-28T17:32:40Z

shortcut prescription to drug uri string
type: DatatypeProperty
sub property of: shortcut prescription to data
domain: drug prescription
range: anyURI
editor preferred label: shortcut prescription to drug uri string
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n prescription to a/n to drug uri string
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-28T17:34:33Z

has literal value
type: DatatypeProperty
domain: information content entity
range: Literal
editor preferred label: has literal value
example of usage: If X is a gender identity datum in a data set (and is therefore a from a subclass of owl:Thing), then it's literal value might be 'M' or 'male' or '0', or any other value provided by the author of the data set.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
term tracker item: https://github.com/obi-ontology/obi/issues/818
date: 2017-04-12T14:00:00-05:00
comment: analogous to has specified value, but not limited to numerical ranges. links a datum to a literal.
comment: the creation of this data property was motivated by the observation that there was no general-purpose data property in any OBO foundry ontology that took a string range. Previous label was 'literal value of any owl:Thing'
deprecated: true

has date value
type: DatatypeProperty
sub property of: has literal value
domain: information content entity
range: date
editor preferred label: has date value
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: I have seen "has measurement value" used for dates, but it has a plain numerical range in (OBI? OBIB?) I had added date as a second range for hmv, but Top Braid Composer only seems to consider the “first” range when determining what relationships can be drawn between two instances in graph mode.
deprecated: true

has textual value
type: DatatypeProperty
sub property of: has literal value
domain: information content entity
range: string
editor preferred label: has textual value
definition: has a literal value that can be mapped to an ontology term
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: true
deprecated: true

has boolean value
type: DatatypeProperty
sub property of: has literal value
domain: information content entity
range: boolean
creator: Mark Miller
date: 2018-07-25T15:18:05Z
deprecated: true

has LOF style gene hybrid identifier
type: DatatypeProperty
sub property of: has representation
domain: allele information
range: string
creator: Mark A. Miller
comment: This predicate may be of narrow applicability to modeling loss-of-function reports created by Scott Damrauer (https://www.pennmedicine.org/providers/profile/scott-damrauer) and colleagues. It is used to link from an allele information instance to the gene identifier used in the source loss of function matrix file, such as eve.UPENN_Freeze_One.L2.M3.lofMatrix.txt These identifiers have had a format like "CAPG(ENSG00000042493)"

has namespace textual value
type: DatatypeProperty
sub property of: has representation

shortcut allele info to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: allele information
editor preferred label: shortcut allele info to data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:31:20Z

shortcut allele info to biobank encounter CRID symbol
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
editor preferred label: shortcut allele info to biobank encounter CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a biobank encounter CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:33:06Z

shortcut allele info to geno_id CRID symbol
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
editor preferred label: shortcut allele info to geno_id CRID symbol
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a genotype identifier CRID symbol
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:34:07Z

shortcut allele info to geno_id CRID registry URI string
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: anyURI
editor preferred label: shortcut allele info to geno_id registry
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a genotype identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:35:37Z

shortcut allele info to protein term URI string
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: anyURI
editor preferred label: shortcut allele info to protein
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to protein
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:36:34Z

shortcut allele info to gene concatenated text
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
editor preferred label: shortcut allele info to gene text
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a gene identiifer and a zygosity level
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:37:21Z
comment: Scott Damraurer's team identifies genes like this: SYMBOL(ENSGENEID) For a while, TURBO was constructing shortcuts like gene:SYMBOL(ENSGENEID);zygosity:N

shortcut allele info to zygosity value text
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
editor preferred label: shortcut allele info to zygosity value text
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to zygosity value text
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:37:54Z

shortcut allele info to zygosity value specification
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: anyURI
editor preferred label: shortcut allele info to zygosity value specification
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to zygosity value specification
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:38:37Z

shortcut allele info to LOF data set title
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
editor preferred label: shortcut allele info to dataset title
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to the title of the dataset containing (at least) sample identifiers, gene identifiers, and zygosity values
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-17T11:23:59Z

shortcut allele info to biobank encounter CRID registry URI string
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: anyURI
editor preferred label: shortcut allele info to biobank encounter CRID registry
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to biobank encounter CRID registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-22T19:16:25Z

shortcut allele info to gene term URI string
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: anyURI
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a gene term

shortcut racial identity datum to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: racial identity datum

shortcut racial identity datum to biobank consenter CRID symbol
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: string

shortcut racial identity datum to biobank consenter registry denoter
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: string

shortcut racial identity datum to biobank consenter identifier registry URI string
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: anyURI

shortcut racial identity datum to racial identity CRID symbol
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: string

shortcut racial identity datum to racial identity registry denoter
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: string

shortcut racial identity datum to racial identity registry URI string
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: anyURI

shortcut racial identity datum to boolean
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: boolean
comment: have not yet decided if this is necessary... if there is a white racial identity datum about me, is it necessary to say that that datum is true?

shortcut racial identity datum to data set title
type: DatatypeProperty
sub property of: shortcut racial identity datum to data
domain: racial identity datum
range: string

shortcut tumor grading datum to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: tumor grading datum

shortcut tumor grading datum to grading process end date
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: date

shortcut tumor grading datum to biobank consenter CRID symbol
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: string

shortcut tumor grading datum to patient identifier registry text
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: string

shortcut tumor grading datum to tissue text
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: string

shortcut tumor grading datum to patient identifier registry URI string
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: anyURI

shortcut tumor grading datum to grade text
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: string

shortcut tumor grading datum to grade URI string
type: DatatypeProperty
sub property of: shortcut tumor grading datum to data
domain: tumor grading datum
range: anyURI
comment: 'who' is responsible for converting a grade text (like "G3") into a URI (like http://purl.obolibrary.org/obo/OBI_0002208)? Carnival should take responsibility for converting the patient registry text (like "HUP") into a URI, but some post-Drivetrain process will probably be responsible for converting tissue text into a FMA or Uberon URI.

shortcut health care encounter to patient identifier symbol
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: string
creator: Mark Miller
date: 2018-10-04T14:27:28Z

shortcut health care encounter to patient identifier registry denoter
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: string
creator: Mark Miller
date: 2018-10-04T14:29:07Z

shortcut health care encounter to patient identifier registry URI string
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter
range: anyURI
creator: Mark Miller
date: 2018-10-04T14:29:28Z

shortcut biobank encounter to patient identifier symbol
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
creator: Mark Miller
date: 2018-10-04T14:49:04Z

shortcut biobank encounter to patient identifier registry denoter
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: string
creator: Mark Miller
date: 2018-10-04T14:50:58Z

shortcut biobank encounter to patient identifier registry URI string
type: DatatypeProperty
sub property of: shortcut biobank encounter to data
domain: biobank encounter
range: anyURI
range: string
creator: Mark Miller
date: 2018-10-04T14:51:55Z

primary diagnoisis
type: DatatypeProperty
sub property of: topDataProperty
domain: diagnosis
range: boolean
definition: https://www.health.ny.gov/statistics/sparcs/sysdoc/elements_837/principal_diagnosis_code.htm

order in diagnosis sequence
type: DatatypeProperty
domain: diagnosis
range: positiveInteger
comment: https://www.molinahealthcare.com/providers/wa/medicaid/comm/PDF/education-sheet-icd-10-diagnosis-code-sequencing.pdf

has ensembl gene ID
type: DatatypeProperty
sub property of: has representation
creator: Mark Miller
date: 2018-12-05T14:19:57Z
comment: do we need to specify version?

has gene symbol
type: DatatypeProperty
sub property of: has representation
creator: Mark Miller
date: 2018-12-05T14:20:08Z
comment: Do we need to specify authority? As in, Ensembl gets human symbols from HGNC?

shortcut PSA datum to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: prostate specific antigen concentration datum
creator: Mark Miller
date: 2019-01-16T15:44:31Z

shortcut PSA datum to PSA value
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: decimal
creator: Mark Miller
date: 2019-01-16T15:44:53Z

shortcut PSA datum to patient CRID regisry denoter text
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: string
creator: Mark Miller
date: 2019-01-16T15:45:28Z

shortcut PSA datum to patient CRID symbol
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: string
creator: Mark Miller
date: 2019-01-16T15:45:47Z

shortcut PSA datum to blood draw date
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: date
creator: Mark Miller
date: 2019-01-16T15:46:11Z

shortcut PSA datum to patient CRID registry denoter URI as string
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: anyURI
creator: Mark Miller
date: 2019-01-16T17:34:45Z

shortcut PSA valspec to concentration unit URI as string
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: anyURI
creator: Mark Miller
date: 2019-01-16T18:04:01Z

shortcut Gleason datum to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: prostate Gleason grading datum
creator: Mark Miller
date: 2019-01-17T21:14:52Z

shortcut Gleason datum to Gleason score textual value
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: string
creator: Mark Miller
date: 2019-01-17T21:16:18Z

shortcut Gleason datum to Gleason group/profile textual value
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: string
creator: Mark Miller
date: 2019-01-17T21:17:15Z

shortcut Gleason datum to Gleason score URI as string
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: string
creator: Mark Miller
date: 2019-01-17T21:18:56Z

shortcut Gleason datum to Gleason group/profile URI as string
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: anyURI
creator: Mark Miller
date: 2019-01-17T21:19:13Z

shortcut Gleason datum to biopsy date
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: date
creator: Mark Miller
date: 2019-01-17T21:19:42Z

shortcut Gleason datum to histology date
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: date
creator: Mark Miller
date: 2019-01-17T21:20:10Z

shortcut Gleason datum to patient CRID registry denoter text
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: string
creator: Mark Miller
date: 2019-01-17T21:20:50Z

shortcut Gleason datum to patient CRID registry denoter URI as string
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: anyURI
creator: Mark Miller
date: 2019-01-17T21:21:01Z

shortcut Gleason datum to patient CRID symbol
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: string
creator: Mark Miller
date: 2019-01-17T21:21:19Z

shortcut summary staging datum to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: summarized stage of cancer progression
creator: Mark Miller
date: 2019-01-29T15:03:33Z
comment: add some date boundary shortcut? what date would be meaningful within summary staging shortcuts? the date of the staging process, or some upstream assay or sample collection?

shortcut summary staging datum to stage string
type: DatatypeProperty
sub property of: shortcut summary staging datum to data
domain: summarized stage of cancer progression
range: string
creator: Mark Miller
date: 2019-01-29T15:04:35Z

shortcut summary staging datum to patient CRID registry denoter text
type: DatatypeProperty
sub property of: shortcut summary staging datum to data
domain: summarized stage of cancer progression
range: string
creator: Mark Miller
date: 2019-01-29T15:36:03Z

shortcut summary staging datum to regden uri string
type: DatatypeProperty
sub property of: shortcut summary staging datum to data
domain: summarized stage of cancer progression
range: anyURI
creator: Mark Miller
date: 2019-01-29T15:36:23Z

shortcut summary staging datum to patient CRID symbol
type: DatatypeProperty
sub property of: shortcut summary staging datum to data
domain: summarized stage of cancer progression
range: string
creator: Mark Miller
date: 2019-01-29T15:36:40Z

shortcut summary staging datum to data set title
type: DatatypeProperty
sub property of: shortcut summary staging datum to data
domain: summarized stage of cancer progression
range: string
creator: Mark Miller
date: 2019-01-31T16:29:47Z

shortcut PSA datum to data set title
type: DatatypeProperty
sub property of: shortcut PSA datum to data
domain: prostate specific antigen concentration datum
range: string
definition editor: Mark A. Miller
date: 2019-02-06T14:57:29Z

shortcut Gleason datum to data set title
type: DatatypeProperty
sub property of: shortcut Gleason datum to data
domain: prostate Gleason grading datum
range: string
definition editor: Mark A. Miller
date: 2019-02-06T14:58:12Z

shortcut allele info to biobank encounter CRID registry text
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
definition editor: Mark A. Miller
date: 2019-02-12T15:27:17Z

shortcut allele info to geno_id CRID registry text
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
definition editor: Mark A. Miller
date: 2019-02-12T15:28:23Z

shortcut allele info to gene symbol text
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
definition editor: Mark A. Miller
date: 2019-02-12T15:30:33Z

shortcut allele info to Ensembl gene identifier text
type: DatatypeProperty
sub property of: shortcut allele info to data
domain: allele information
range: string
definition editor: Mark A. Miller
date: 2019-02-12T16:02:20Z

shortcut allele info to sample/encounter key
type: DatatypeProperty
sub property of: shortcut allele info to data
definition: an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a exome sequencing sample identifier to the identifier of the encounter in which the sample was colelcted
definition editor: Mark A. Miller
date: 2019-02-12T17:50:00Z

shortcut person data model to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: person data model
definition editor: Mark A. Miller
date: 2019-03-01T15:13:18Z
comment: shortcut person data model to entity

shortcut person data model to patient CRID symbol value
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T15:14:03Z

shortcut person data model to dataset title
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T15:43:31Z

shortcut person data model to DOB (textual)
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T15:57:02Z

shortcut person data model to DOB (xsd compliant)
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: date
definition editor: Mark A. Miller
date: 2019-03-01T15:59:16Z

shortcut person data model to first name
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T16:03:48Z

shortcut person data model to last name
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T16:04:45Z

has representation
type: DatatypeProperty
domain: information content entity
range: Literal
example of usage: ?x a 'data item' ; 'has representation' 'It was the best of times, it was the worst of times.' .
example of usage: ?x a 'data item'; 'has representation' '20 grams' .
has curation status: requires discussion
definition editor: Mark A. Miller
date: 2019-03-01T17:00:04Z
comment: Subject of active discussion by OBI, with similar proposals from Damion Dooley and others. Intended to bind literals to data items, in a way that is more general and succincter than has value specification -> has specified value. DD would give has parsed/atomic/literal value and has textual/raw value separate parents, so that classes could be cardinality constrained to take a single parsed/atomic/literal values but any number of textual/raw values. These properties can take any kind of literal as their object. (Previous discussions had considered separate data properties for different types of literals) James: broaden domain? remove costraint?

has raw literal representation
type: DatatypeProperty
sub property of: has representation
domain: data item
range: Literal
definition: has a value asserted directly by some external authority, like a CSV files or database table.
definition editor: Mark A. Miller
date: 2019-03-01T17:00:27Z

has parsed/transformed literal representation
type: DatatypeProperty
sub property of: has representation
domain: data item
range: Literal
definition: has a value that can be parsed or transformed from an authoritatively asserted raw values. For example, the string "9/10/71" might be transformed to "1971-09-10"^^xsd:date OR "1971-10-09"^^xsd:date depending on the cultural origin of the raw data.
definition editor: Mark A. Miller
date: 2019-03-01T17:00:50Z
see also: 'has raw literal represenation'

shortcut person data model to gender identity datum text
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T18:16:29Z
comment: also allow OMOP IDs?

shortcut person data model to ethnic identity datum text
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T18:16:37Z
comment: also allow OMOP IDs?

shortcut person data model to racial identity datum text
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string
definition editor: Mark A. Miller
date: 2019-03-01T18:16:46Z
comment: also allow OMOP IDs?

SPARQL run time in seconds
type: DatatypeProperty
sub property of: has representation
definition editor: Mark A. Miller
alternative term: completionTimeInSeconds
date: 2019-03-02T14:40:23Z

Inserted triples count
type: DatatypeProperty
sub property of: has representation
definition editor: Mark A. Miller
date: 2019-03-02T14:40:35Z

shortcut observation to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
definition editor: Mark A. Miller
date: 2019-03-04T16:13:05Z

shortcut observation to textual observation date
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:18:03Z

shortcut observation to xsd formatted observation date
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:18:30Z

shortcut observation to patient symbol value
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:19:12Z

shortcut observation to encounter symbol value
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:20:31Z

shortcut observation to observation type code
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:22:19Z

shortcut observation to observation value
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:26:07Z

shortcut observation to textual units label
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T16:26:25Z

shortcut observation to data set title
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T21:17:41Z

shortcut observation to units type term
type: DatatypeProperty
sub property of: shortcut observation to data
definition editor: Mark A. Miller
date: 2019-03-04T21:29:44Z

has database primary key vaue
type: DatatypeProperty

shortcut person data model to person PK value
type: DatatypeProperty
sub property of: shortcut person data model to data
domain: person data model
range: string

shortcut observation to patient PK value
type: DatatypeProperty
sub property of: shortcut observation to data

shortcut observation to encounter PK value
type: DatatypeProperty
sub property of: shortcut observation to data

shortcut observation to units type code
type: DatatypeProperty
sub property of: shortcut observation to data

shortcut health care encounter to previous PK
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data

shortcut allele info to encounter PK value
type: DatatypeProperty
sub property of: shortcut allele info to data

shortcut tumor data model to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut

shortcut tumor data model to patient CRID symbol value
type: DatatypeProperty
sub property of: shortcut tumor data model to data

shortcut tumor data model to tumor CRID symbol value
type: DatatypeProperty
sub property of: shortcut tumor data model to data

shortcut health care encounter data model to systolic BP in mmHg
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: float

shortcut health care encounter data model to diastolic BP in mmHg
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data
domain: health care encounter data model
range: float

shortcut person CRID data model to data
type: DatatypeProperty
sub property of: instantiation hybrid shortcut
domain: person CRID data model

shortcut person CRID data model to symbol value
type: DatatypeProperty
sub property of: shortcut person CRID data model to data
domain: person CRID data model
range: string

shortcut health care encounter data model to patient identifier PK
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data

shortcut health care encounter data model to encounter identifier PK
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data

shortcut health care encounter data model to omop encounter type concept code
type: DatatypeProperty
sub property of: shortcut health care encounter data model to data

International Classification of Diseases
type: Class
subclass of: diagnosis code registry

Systematized Nomenclature of Medicine
type: Class
subclass of: centrally registered identifier registry
definition: A multiaxial, hierarchical classification system for diseases in man developed by the College of American Pathologists.
editor note: A multiaxial, hierarchical classification system for diseases in man developed by the College of American Pathologists. (NCI)
editor note: A structured nomenclature and classification of the terminology used in human and veterinary medicine developed by the College of Pathologists and American Veterinary Medical Association. Terms are applied to one of eleven independent systematized modules.
ICO_0000091: C1136257
ICO_0000092: C53489
alternative_term: SNOMED
alternative_term: SNOMED (Systematized Nomenclature of Medicine)
alternative_term: Systematized Nomenclature of Medicine

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
editor preferred label: entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
imported from: bfo.owl
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: mondo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

continuant
type: Class
subclass of: entity
subclass of: Restriction
  on property: is part of
  all values from: continuant
subclass of: Restriction
  on property: has prototype
  all values from: continuant
subclass of: Restriction
  on property: in similarity relationship with
  all values from: continuant
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor preferred label: continuant
definition: 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.
editor note: 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
editor note: 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
imported from: bfo.owl
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: mondo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: is part of
  all values from: occurrent
subclass of: Restriction
  on property: in similarity relationship with
  all values from: occurrent
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor preferred label: occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
imported from: bfo.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
elucidation: 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])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: is part of
  all values from: independent continuant
subclass of: Restriction
  on property: specifically depends on at some time
  all values from: Nothing
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
imported from: bfo.owl
imported from: geno.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (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]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

spatial region
type: Class
subclass of: immaterial entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: spatial region
subclass of: Restriction
  on property: has continuant part at some time
  all values from: spatial region
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: spatial region
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: spatial region
subclass of: Restriction
  on property: occupies spatial region at some time
  has self: true
subclass of: Restriction
  on property: has spatial occupant at some time
  has self: true
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
imported from: ogg.owl
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

temporal region
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has occurrent part
  all values from: temporal region
subclass of: Restriction
  on property: part of occurrent
  all values from: temporal region
subclass of: Restriction
  on property: occupies temporal region
  has self: true
subclass of: Restriction
  on property: has temporal occupant
  has self: true
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: 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
imported from: bfo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ontoneo.owl
imported from: pdro.owl
elucidation: 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])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

spatiotemporal region
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: projects onto spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: projects onto temporal region
  some values from: temporal region
subclass of: Restriction
  on property: has occurrent part
  all values from: spatiotemporal region
subclass of: Restriction
  on property: part of occurrent
  all values from: spatiotemporal region
subclass of: Restriction
  on property: has spatiotemporal occupant
  has self: true
subclass of: Restriction
  on property: occupies spatiotemporal region
  has self: true
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
imported from: ogg.owl
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: specifically depends on at some time
  some values from: material entity
subclass of: Restriction
  on property: has occurrent part
  all values from: Class
    union of: process
    union of: process boundary
subclass of: Restriction
  on property: part of occurrent
  all values from: process
subclass of: Restriction
  on property: has prototype
  all values from: process
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
imported from: bfo.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: pr.owl
imported from: ro.owl
has associated axiom(fol): (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]
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: bfo
id: BFO:0000015
label: processo @pt

disposition
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: role
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocitosis and exocitosis
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89
editor note: 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.
imported from: ido.owl
imported from: mondo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ro.owl
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (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]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: is part of
  all values from: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: quality
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
editor preferred label: realizable entity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
imported from: ico.owl
imported from: ido.owl
imported from: mondo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: pdro.owl
imported from: ro.owl
elucidation: 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])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (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]
has associated axiom(fol): (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]

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: is part of
  all values from: quality
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: realizable entity
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: realizable entity
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: bfo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (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]
translated to Portuguese by: PERSON: Fernanda Farinelli
label: qualidade @pt

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: inheres in at all times
  some values from: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
subclass of: Restriction
  on property: is part of
  all values from: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
editor preferred label: specifically dependent continuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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.
definition: 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])
definition: 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])
editor note: 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.
imported from: bfo.owl
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: mondo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
has associated axiom(fol): (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]
has associated axiom(fol): (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]

role
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: disposition
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: disposition
BFO OWL specification label: role
BFO CLIF specification label: Role
editor preferred label: role
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
editor note: 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.
imported from: bfo.owl
imported from: ico.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

fiat object part
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
imported from: bfo.owl
imported from: ontoneo.owl
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: 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)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: 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).
definition source: 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.
imported from: bfo.owl
imported from: ontoneo.owl
imported from: pdro.owl
elucidation: 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])
has associated axiom(fol): (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]

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
imported from: ogg.owl
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: 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.
editor note: 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).
editor note: 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
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
imported from: bfo.owl
imported from: ontoneo.owl
imported from: pdro.owl
elucidation: 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])

generically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: concretized by at some time
  some values from: specifically dependent continuant
subclass of: Restriction
  on property: is part of
  all values from: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: specifically dependent continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
editor preferred label: generically dependent continuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: 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])
imported from: bfo.owl
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: 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.
imported from: obi.owl
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

process boundary
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: exists at
  all values from: zero-dimensional temporal region
subclass of: Restriction
  on property: has occurrent part
  all values from: process boundary
subclass of: Restriction
  on property: occupies spatiotemporal region
  all values from: Class
    intersection of: spatiotemporal region
    intersection of: Restriction
      on property: temporal part of
      some values from: spatiotemporal region
subclass of: Restriction
  on property: part of occurrent
  all values from: Class
    union of: process
    union of: process boundary
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
imported from: ogg.owl
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

one-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: 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).
imported from: obi.owl
imported from: pdro.owl
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

material entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  all values from: three-dimensional spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: material entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    union of: material entity
    union of: immaterial entity
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    union of: material entity
    union of: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
imported from: bfo.owl
imported from: geno.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
imported from: ro.owl
elucidation: 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])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (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]
has associated axiom(fol): (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]

immaterial entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: has continuant part at some time
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    complement of: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    complement of: material entity
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: 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
imported from: ogg.owl
imported from: ro.owl

zero-dimensional temporal region
type: Class
subclass of: temporal region
subclass of: Restriction
  on property: has proper occurrent part
  all values from: Nothing
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
imported from: ogg.owl
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

anatomical entity
type: Class
subclass of: biological entity
imported from: caro.owl
imported from: ro.owl

connected anatomical structure
type: Class
subclass of: material anatomical entity
imported from: caro.owl
imported from: ro.owl

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
subclass of: Restriction
  on property: drains
  all values from: connected anatomical structure
imported from: caro.owl
imported from: ro.owl

immaterial anatomical entity
type: Class
subclass of: immaterial entity
imported from: ro.owl

biological entity
type: Class
subclass of: independent continuant
imported from: ro.owl

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
definition: 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.
imported from: chebi.owl
imported from: obi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl
imported from: obi.owl

glucose
type: Class
subclass of: molecular entity
editor preferred label: glucose
definition: An aldohexose used as a source of energy and metabolic intermediate.
imported from: chebi.owl
imported from: obi.owl

benzodiazepine
type: Class
subclass of: molecular entity
definition: A group of heterocyclic compounds with a core structure containing a benzene ring fused to a diazepine ring.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: benzodiazepines
id: CHEBI:22720
in_subset: 3 STAR

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: 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
alternative term: molecular entity
imported from: chebi.owl
imported from: obi.owl
imported from: pr.owl
alternative_term: molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: entidad molecular
has_related_synonym: entidades moleculares
has_related_synonym: entite moleculaire
has_related_synonym: molecular entities
has_related_synonym: molekulare Entitaet
id: CHEBI:23367
in_subset: 3 STAR

chemical entity
type: Class
subclass of: material entity
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
imported from: pr.owl
has_obo_namespace: chebi_ontology
id: CHEBI:24431

alprazolam
type: Class
subclass of: benzodiazepine
definition: A member of the class of triazolobenzodiazepines that is 4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine carrying methyl, phenyl and chloro substituents at positions 1, 6 and 8 respectively. Alprazolam is only found in individuals that have taken this drug.
imported from: chebi.owl
charge: 0
formula: C17H13ClN4
inchi: InChI=1S/C17H13ClN4/c1-11-20-21-16-10-19-17(12-5-3-2-4-6-12)14-9-13(18)7-8-15(14)22(11)16/h2-9H,10H2,1H3
inchikey: VREFGVBLTWBCJP-UHFFFAOYSA-N
mass: 308.76478
monoisotopicmass: 308.08287
smiles: Cc1nnc2CN=C(c3ccccc3)c3cc(Cl)ccc3-n12
database_cross_reference: CAS:28981-97-7
database_cross_reference: DrugBank:DB00404
database_cross_reference: Drug_Central:136
database_cross_reference: HMDB:HMDB0014548
database_cross_reference: KEGG:C06817
database_cross_reference: KEGG:D00225
database_cross_reference: LINCS:LSM-5460
database_cross_reference: PMID:10350361
database_cross_reference: PMID:10443648
database_cross_reference: PMID:10631626
database_cross_reference: PMID:10963939
database_cross_reference: PMID:10997633
database_cross_reference: PMID:11304902
database_cross_reference: PMID:11824768
database_cross_reference: PMID:12035937
database_cross_reference: PMID:15647704
database_cross_reference: PMID:15725773
database_cross_reference: PMID:15830221
database_cross_reference: PMID:16103667
database_cross_reference: PMID:16139113
database_cross_reference: PMID:16572266
database_cross_reference: PMID:17631455
database_cross_reference: PMID:24361783
database_cross_reference: PMID:24464531
database_cross_reference: PMID:24629629
database_cross_reference: PMID:24840273
database_cross_reference: PMID:24977401
database_cross_reference: PMID:25032127
database_cross_reference: PMID:25139178
database_cross_reference: PMID:25199955
database_cross_reference: PMID:25300043
database_cross_reference: PMID:25427652
database_cross_reference: PMID:25581490
database_cross_reference: PMID:25620535
database_cross_reference: PMID:7907366
database_cross_reference: PMID:9050091
database_cross_reference: Reaxys:1223125
database_cross_reference: VSDB:2960
database_cross_reference: Wikipedia:Alprazolam
alternative_term: 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine
alternative_term: Alprazolam
has_obo_namespace: chebi_ontology
has_related_synonym: 8-Chloro-1-methyl-6-phenyl-4H-s-triazolo(4,3-a)(1,4)benzodiazepine
has_related_synonym: Xanax
id: CHEBI:2611
in_subset: 3 STAR

urobilinogen
type: Class
subclass of: molecular entity
definition: A member of the class of bilanes that is a colourless product formed in the intestine by the reduction of bilirubin.
imported from: chebi.owl
charge: 0
formula: C33H44N4O6
inchi: InChI=1S/C33H44N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h26-27,34-35H,7-15H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)
inchikey: OBHRVMZSZIDDEK-UHFFFAOYSA-N
mass: 592.72582
monoisotopicmass: 592.32609
has_alternative_id: CHEBI:27246
has_alternative_id: CHEBI:5844
database_cross_reference: Beilstein:75461
database_cross_reference: CAS:14684-37-8
database_cross_reference: HMDB:HMDB0004158
database_cross_reference: KEGG:C05790
database_cross_reference: PMID:21614935
database_cross_reference: PMID:24709296
database_cross_reference: PMID:24714521
database_cross_reference: Reaxys:75461
alternative_term: 2,17-diethyl-3,7,13,18-tetramethyl-1,19-dioxo-1,4,5,10,15,16,19,22,23,24-decahydro-21H-biline-8,12-dipropanoic acid
alternative_term: Urobilinogen
has_obo_namespace: chebi_ontology
has_related_synonym: 2,17-diethyl-1,4,5,10,15,16,19,22,23,24-decahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid
has_related_synonym: 8,12-bis(2-carboxyethyl)-3,18-diethyl-2,7,13,17-tetramethylbilane-1,19(4H,16H)-dione
has_related_synonym: I-Urobilinogen
has_related_synonym: Mesobilirubinogen
has_related_synonym: mesobilirubinogen IXalpha
has_related_synonym: urobilinogen IXalpha
id: CHEBI:29026
in_subset: 3 STAR

organic group
type: Class
subclass of: molecular entity
definition: Any substituent group or skeleton containing carbon.
imported from: pr.owl
has_obo_namespace: chebi_ontology
id: CHEBI:33247

atom
type: Class
subclass of: material entity
editor preferred label: atom
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl
imported from: obi.owl

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
definition: 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.
imported from: chebi.owl
imported from: obi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: ribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl

amino-acid residue
type: Class
subclass of: organic group
definition: When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
imported from: pr.owl
alternative_term: amino acid residue
has_narrow_synonym: protein residue
has_obo_namespace: chebi_ontology
id: CHEBI:33708

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
definition: 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.
alternative term: polymer
imported from: chebi.owl
imported from: obi.owl

hemoglobin
type: Class
subclass of: macromolecule
imported from: chebi.owl
database_cross_reference: COMe:PRX000321
alternative_term: hemoglobin
has_obo_namespace: chebi_ontology
has_related_synonym: haemoglobin
has_related_synonym: vertebrate haemoglobin
id: CHEBI:35143
in_subset: 3 STAR

organic amino compound
type: Class
subclass of: molecular entity
definition: A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
imported from: pr.owl
has_obo_namespace: chebi_ontology
id: CHEBI:50047

cell
type: Class
subclass of: material entity
subclass of: material anatomical entity
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
definition: 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.
imported from: cl.owl
imported from: obi.owl
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
has_obo_namespace: cell
in_subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

native cell
type: Class
subclass of: cell
definition: A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
imported from: cl.owl
database_cross_reference: CARO:0000013
has_narrow_synonym: cell in vivo
has_obo_namespace: cell
in_subset: upper level
comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl
imported from: obi.owl

erythrocyte
type: Class
subclass of: cell
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
imported from: cl.owl
database_cross_reference: BTO:0000424
database_cross_reference: CALOHA:TS-0290
database_cross_reference: FMA:81100
alternative_term: RBC
alternative_term: red blood cell
has_obo_namespace: cell

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl
imported from: obi.owl

neutrophil
type: Class
subclass of: cell
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
imported from: cl.owl
has_broad_synonym: PMN
has_broad_synonym: poly
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
has_broad_synonym: polymorphonuclear neutrophil
has_broad_synonym: polynuclear neutrophilic leucocyte
has_broad_synonym: polynuclear neutrophilic leukocyte
database_cross_reference: BTO:0000130
database_cross_reference: CALOHA:TS-0688
database_cross_reference: FMA:62860
alternative_term: neutrocyte
alternative_term: neutrophil leucocyte
alternative_term: neutrophil leukocyte
alternative_term: neutrophilic leucocyte
alternative_term: neutrophilic leukocyte
has_obo_namespace: cell

abnormal cell
type: Class
subclass of: cell
subclass of: Restriction
  on property: derives from
  some values from: native cell
definition: A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.
imported from: cl.owl
creator: http://orcid.org/0000-0001-9990-8331
date: 2017-01-30T18:53:32Z
database_cross_reference: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
has_obo_namespace: cell
comment: https://github.com/obophenotype/cell-ontology/issues/448

neoplastic cell
type: Class
subclass of: abnormal cell
definition: An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.
imported from: cl.owl
creator: http://orcid.org/0000-0001-9990-8331
date: 2017-01-30T19:16:26Z
database_cross_reference: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
has_obo_namespace: cell
has_related_synonym: tumor cell
has_related_synonym: tumour cell
comment: https://github.com/obophenotype/cell-ontology/issues/448

malignant cell
type: Class
subclass of: neoplastic cell
definition: A neoplastic cell that is capable of entering a surrounding tissue
imported from: cl.owl
creator: http://orcid.org/0000-0001-9990-8331
date: 2017-01-30T19:39:12Z
database_cross_reference: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
has_obo_namespace: cell
has_related_synonym: cancer cell
comment: https://github.com/obophenotype/cell-ontology/issues/448

body weight
type: Class
subclass of: weight
definition: O peso corporal de um organismo. @pt
definition: The heaviness or degree to which an entire organism's body is drawn to the earth by gravity.
alternative term: peso corporal @pt
imported from: ontoneo.owl
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/cmo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0000012
label: peso do corpo @pt

body height
type: Class
subclass of: height
definition: Altura corporal de um organismo. @pt
definition: The vertical measurement of a body.
imported from: ontoneo.owl
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/cmo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0000106
label: altura corporal @pt

complete personal name
type: Class
subclass of: personal name
subclass of: Restriction
  on property: has part
  some values from: given name
subclass of: Restriction
  on property: has part
  some values from: family name
definition: A personal name composed of one given name, one family name, and sometimes of one or several middle names.
imported from: pdro.owl

African
type: Class
subclass of: ethnic group
definition: An ethnic group comprised of persons with African ancestral origins who self identify, or are identified, as African.
definition source: NCIt:C42331
imported from: ero.owl

Latino, Carribean
type: Class
subclass of: Latino
definition editor: PERSON:Matthew Brush
imported from: ero.owl

Latino, South American
type: Class
subclass of: Latino
definition editor: PERSON:Matthew Brush
imported from: ero.owl

Human body
type: Class
subclass of: Body of vertebrate
subclass of: Class
  intersection of: Restriction
    on property: has quality
    some values from: body weight
  intersection of: Restriction
    on property: has quality
    some values from: body height
  intersection of: Restriction
    on property: has quality
    some values from: genotypic sex
  intersection of: Restriction
    on property: is identical to
    some values from: Homo sapiens
definition: Anatomical structure which is the aggregate material substance of an individual member of the Homo sapiens species. Examples: There is only one human body.
definition: TO DO @pt
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: fma
id: FMA:20394
label: corpo humano @pt

Body of vertebrate
type: Class
subclass of: Body
imported from: ontoneo.owl
imported from: pdro.owl
has_obo_namespace: fma
id: FMA:256133

Body
type: Class
subclass of: object aggregate
definition: Anatomical structure which is the aggregate material substance of an individual member of a species.
definition: TO DO @pt
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: fma
id: FMA:256135
label: corpo @pt

Wall of blood vessel
type: Class
subclass of: Region of organ component
imported from: ontoneo.owl
alternative_term: Blood vessel wall
has_obo_namespace: fma
id: FMA:67473
label: parede do vaso sanguíneo @pt

Region of organ component
type: Class
subclass of: fiat object part
definition: Cardinal organ part which is a fiat subdivision of an organ component. Examples: cervical part of wall of esophagus, mucosa of body of stomach.
imported from: ontoneo.owl
alternative_term: Organ component region
has_obo_namespace: fma
id: FMA:86103

Hematopoietic system
type: Class
subclass of: object aggregate
imported from: ontoneo.owl
alternative_term: Hemopoietic system
alternative_term: Organa haemopoietica
has_obo_namespace: fma
id: FMA:9667

Portion of body substance
type: Class
subclass of: object
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures. Examples: saliva, semen, cerebrospinal fluid, respiratory air, urine, feces, blood, plasma, lymph.
definition: TO DO @pt
alternative term: substância corporal @pt
imported from: ontoneo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
alternative_term: Body substance
has_obo_namespace: fma
id: FMA:9669
label: porção de substância corporal @pt

Portion of blood
type: Class
subclass of: Portion of body substance
subclass of: Restriction
  on property: regional_part_of
  some values from: Hematopoietic system
subclass of: Restriction
  on property: systemic_part_of
  some values from: Hematopoietic system
definition: Body substance which consists of plasma and blood cells
definition: Uma porção de substância corporal em estado líquido, produzido na medula óssea, constituído pelo plasma e alguns componentes celulares denominados de eritrócitos, leucócitos e plaquetas, que circula pelo sistema vascular, e tem como função o transporte de nutrientes, oxigênio, toxinas e gás carbônico pelo corpo. @pt
alternative term: sangue @pt
imported from: ontoneo.owl
alternative_term: Blood
has_obo_namespace: fma
id: FMA:9670
comment: NEW DEFINITION PROPOSAL: A portion of body substance in a liquid state, produced by the bone marrow, made up of plasma and some cellular components called erythrocytes, leukocytes, and platelets, which circulates through the vascular system, and has the function of transporting nutrients, oxygen, toxins and carbon dioxide through the body.
label: porção de sangue @pt

zygosity
type: Class
subclass of: allelic state
subclass of: Restriction
  on property: inheres_in
  some values from: single locus complement
definition: An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).
alternative term: allelic state
definition source: derived from https://en.wikipedia.org/wiki/Zygosity
imported from: geno.owl
database_cross_reference: http://semanticscience.org/resource/SIO_001263

heterozygous
type: Class
subclass of: disomic zygosity
imported from: geno.owl

homozygous
type: Class
subclass of: disomic zygosity
imported from: geno.owl

disomic zygosity
type: Class
subclass of: zygosity
imported from: geno.owl

genomic feature
type: Class
equivalent class: Class
  intersection of: sequence_feature
  intersection of: Restriction
    on property: has_location
    some values from: genomic feature location
subclass of: Restriction
  on property: is part of
  some values from: genome
subclass of: Restriction
  on property: has_sequence
  some values from: genomic sequence
subclass of: Restriction
  on property: in taxon
  some values from: organism
definition: A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)
editor note: This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology.
imported from: geno.owl
comment: 1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. 2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). 3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.

wild-type allele
type: Class
subclass of: allele
subclass of: Restriction
  on property: varies_with
  some values from: genomic feature
definition: An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.
alternative term: wild-type allele
imported from: geno.owl
comment: 'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.

allele
type: Class
equivalent class: Class
  intersection of: genomic feature
  intersection of: Restriction
    on property: varies_with
    some values from: genomic feature
definition: One of a set of sequence features known to exist at a particular genomic location.
editor note: A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. [1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) [2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) [3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) [4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) [5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) [6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) [6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 [7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) [8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) [9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) [10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) [11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)
alternative term: variable feature
imported from: geno.owl
comment: An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).

single locus complement
type: Class
subclass of: genomic feature set
example of usage: The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome.
definition: A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism.
editor note: TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label.
alternative term: allelic complement
alternative term: homologous allele complement
alternative term: single locus feature complement
imported from: geno.owl
comment: A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.

sequence feature set
type: Class
subclass of: sequence feature or set
subclass of: Restriction
  on property: has member
  some values from: sequence_feature
subclass of: Restriction
  on property: has_member_count
  some values from: int
example of usage: 1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus 2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. 3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}
definition: A set of sequence features.
imported from: geno.owl
comment: 'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. [1] https://www.snpedia.com/index.php/APOE-%CE%B54 [2] https://www.snpedia.com/index.php/APOE-%CE%B52 [3] https://www.snpedia.com/index.php/Gs270

genomic feature set
type: Class
subclass of: sequence feature set
subclass of: Restriction
  on property: in taxon
  some values from: organism
subclass of: Restriction
  on property: has member
  some values from: genomic feature
definition: A set of genomic features (i.e. sequence features that are of genomic origin).
editor note: In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member.
alternative term: genomic locus complement
imported from: geno.owl
comment: A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.

sequence feature or set
type: Class
equivalent class: Class
  union of: sequence feature or set
  union of: sequence_feature
subclass of: generically dependent continuant
definition: A sequence feature or a set of such features.
alternative term: sequence feature or collection
imported from: geno.owl
comment: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.

biological sequence
type: Class
subclass of: biological sequence or set
subclass of: Restriction
  on property: has_string
  some values from: string
definition: A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).
editor note: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
alternative term: biomacromolecular sequence
alternative term: state
imported from: geno.owl
database_cross_reference: VMC:State
comment: 'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.

sequence feature attribute
type: Class
subclass of: specifically dependent continuant
definition: An attribute, quality, or state of a sequence feature or collection.
imported from: geno.owl
database_cross_reference: http://purl.oboInOwllibrary.org/oboInOwl/SO_0000400
comment: Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity.

sequence feature location
type: Class
subclass of: generically dependent continuant
definition: The location of a sequence feature as defined by its start and end position on some reference coordinate system.
imported from: geno.owl
comment: 1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.

allelic state
type: Class
subclass of: sequence feature attribute
definition: A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism
imported from: geno.owl

genomic feature location
type: Class
subclass of: sequence feature location
definition: The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system
editor note: In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.
editor note: In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).
alternative term: genomic location
alternative term: genomic locus
imported from: geno.owl
database_cross_reference: VMC:Location
comment: 1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.

biological sequence or set
type: Class
subclass of: generically dependent continuant
definition: A biolocical sequence, or set of such sequences.
alternative term: biological sequence or collection
imported from: geno.owl

genomic sequence
type: Class
equivalent class: Restriction
  on property: is_sequence_of
  some values from: genomic feature
subclass of: biological sequence
definition: A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).
imported from: geno.owl
comment: A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.

cell
type: Class
subclass of: material entity
subclass of: cell
definition: The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
imported from: cl.owl
OBO foundry unique label: cell and encapsulating structures
database_cross_reference: NIF_Subcellular:sao1813327414
database_cross_reference: Wikipedia:Cell_(biology)
has_obo_namespace: cellular_component
id: GO:0005623
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim plant

translation
type: Class
subclass of: biological_process
definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
imported from: pr.owl
alternative_term: protein anabolism
has_obo_namespace: biological_process
id: GO:0006412

blood circulation
type: Class
subclass of: biological_process
definition: The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
imported from: ontoneo.owl
imported from: http://purl.obolibrary.org/obo/go.owl
label: circulação sanguínea @pt

biological_process
type: Class
subclass of: process
editor preferred label: biological_process
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
imported from: go.owl
imported from: ido.owl
imported from: obi.owl
imported from: ontoneo.owl
imported from: pr.owl
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
database_cross_reference: Wikipedia:Biological_process
alternative_term: biological process
alternative_term: physiological process
has_obo_namespace: biological_process
id: GO:0008150
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.

health insurance identifier
type: Class
subclass of: individual organism identifier
subclass of: Restriction
  on property: denotes
  qualified cardinality: 1
  on class: Homo sapiens
imported from: pdro.owl
comment: An individual organism identifier that is used to identify a beneficiary of some health insurance.

medical record identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  qualified cardinality: 1
  on class: Class
    intersection of: medical record
    intersection of: Restriction
      on property: is about
      some values from: patient
definition: A CRID symbol that is sufficent to look up a patient file in a medical record registry.
imported from: pdro.owl

patient
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: patient role
imported from: pdro.owl

Phenotypic abnormality
type: Class
equivalent class: Restriction
  on property: has part
  some values from: Class
    intersection of: quality
    intersection of: Restriction
      on property: inheres in part of
      some values from: Body
    intersection of: Restriction
      on property: has modifier
      some values from: abnormal
subclass of: quality
definition: A phenotypic abnormality.
imported from: ontoneo.owl
imported from: pdro.owl
alternative_term: Organ abnormality
has_obo_namespace: human_phenotype
id: HP:0000118
comment: PERSON: Fernanda Farinelli OntONeo development prioritizes the reuse of classes and entities from FMA ontology to deal with human anatomy approaches. Originally this class has reference to UBERON:0000468. UBERON ontology has cross-reference annotation (database_cross_reference) of UBERON: 0000468 to FMA_256135. Due this cross-reference annotation we opted to replace the UBERON:0000468 by FMA_256135.
comment: This is the root of the phenotypic abnormality subontology of the HPO.

diastolic blood pressure measurement datum
type: Class
subclass of: blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: diastolic blood pressure
definition editor: Amanda Hicks
has OMOP concept ID: 3012888
comment: A blood pressure measurement datum that is a quality measure of some diastolic blood pressure

systolic blood pressure measurement datum
type: Class
subclass of: blood pressure measurement datum
subclass of: Restriction
  on property: is about
  some values from: systolic blood pressure
definition: A blood pressure measurement datum that is a quality measure of some systolic blood pressure
creator: Amanda Hicks
has OMOP concept ID: 3004249
comment: cut and pasted int turbo.owl with text editor

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: pending final vetting
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 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.
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

objective specification
type: Class
subclass of: directive information content entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: 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.
editor note: 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."
editor note: 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.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: obi.owl
imported from: pdro.owl

action specification
type: Class
subclass of: directive information content entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
definition: a directive information entity that describes an action the bearer will take
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: obi.owl
imported from: pdro.owl

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: metadata incomplete
definition: 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
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
definition editor: GROUP: IAO
curator note: 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.
imported from: obi.owl

software
type: Class
subclass of: plan specification
editor preferred label: software
has curation status: metadata complete
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI
imported from: obi.owl

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: 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.
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: geno.owl
imported from: iao.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
has curation status: pending final vetting
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 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).
editor note: 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).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
imported from: pdro.owl

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
has curation status: pending final vetting
definition: A generically dependent continuant that is about some thing.
definition: An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor note: 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).
editor note: 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.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: geno.owl
imported from: iao.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
has curation status: metadata complete
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

directive information content entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 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.
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: iao.owl
imported from: obi.owl
imported from: pdro.owl
label: directive information entity

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: metadata complete
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: pending final vetting
definition: 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.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: pdro.owl

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: 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.
editor note: 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
editor note: 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.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
imported from: pdro.owl

image
type: Class
subclass of: figure
editor preferred label: image
has curation status: ready for release
definition: 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.
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI
imported from: obi.owl

data about an ontology part
type: Class
subclass of: data item
subclass of: information content entity
editor preferred label: data about an ontology part
definition: data about an ontology part is a data item about a part of an ontology, for example a term
definition editor: Person:Alan Ruttenberg
alternative term: ontology metadata
imported from: geno.owl
imported from: ico.owl
imported from: ido.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: pdro.owl

plan specification
type: Class
subclass of: directive information content entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: 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.
editor note: 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.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: obi.owl
imported from: pdro.owl
comment: 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
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred label: measurement datum
example of usage: 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,}.
has curation status: pending final vetting
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
definition: Um dado de medição é uma entidade de conteúdo de informação que é uma gravação da saída de uma medida tal como produzida por um dispositivo. @pt
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
alternative term: dado de medida @pt
alternative term: dado medido @pt
alternative term: valor medido @pt
definition source: OBI_0000305
definition source: group:OBI
imported from: iao.owl
imported from: obi.owl
imported from: ontoneo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has OMOP concept ID: 3000285
has OMOP concept ID: 3000905
has OMOP concept ID: 3000963
has OMOP concept ID: 3001802
has OMOP concept ID: 3002736
has OMOP concept ID: 3004295
has OMOP concept ID: 3005456
has OMOP concept ID: 3005897
has OMOP concept ID: 3006322
has OMOP concept ID: 3006513
has OMOP concept ID: 3006923
has OMOP concept ID: 3007070
has OMOP concept ID: 3009201
has OMOP concept ID: 3009542
has OMOP concept ID: 3009744
has OMOP concept ID: 3009966
has OMOP concept ID: 3011505
has OMOP concept ID: 3012030
has OMOP concept ID: 3012494
has OMOP concept ID: 3013603
has OMOP concept ID: 3013721
has OMOP concept ID: 3014094
has OMOP concept ID: 3015182
has OMOP concept ID: 3018572
has OMOP concept ID: 3020416
has OMOP concept ID: 3020630
has OMOP concept ID: 3022192
has OMOP concept ID: 3022621
has OMOP concept ID: 3023314
has OMOP concept ID: 3023539
has OMOP concept ID: 3023599
has OMOP concept ID: 3024128
has OMOP concept ID: 3024561
has OMOP concept ID: 3024629
has OMOP concept ID: 3024929
has OMOP concept ID: 3027114
has OMOP concept ID: 3027172
has OMOP concept ID: 3027970
has OMOP concept ID: 3029187
has OMOP concept ID: 3030315
has OMOP concept ID: 3030354
has OMOP concept ID: 3032503
has OMOP concept ID: 3035995
has OMOP concept ID: 3043111
has OMOP concept ID: 3051825
has OMOP concept ID: 40761014
has OMOP concept ID: 40769179
has OMOP concept ID: 40769184
has OMOP concept ID: 40769189
has OMOP concept ID: 40769194
has OMOP concept ID: 44786664
label: dado de medição @pt

version number
type: Class
subclass of: symbol
editor preferred label: version number
has curation status: metadata incomplete
definition: 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.
editor note: 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
definition editor: GROUP: IAO

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: conclusion based on data
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion textual entity
example of usage: 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
has curation status: metadata complete
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
definition editor: Person:Alan Ruttenberg

material information bearer
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
editor preferred label: material information bearer
example of usage: A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
example of usage: a brain
example of usage: a hard drive
has curation status: ready for release
definition: A material entity in which a concretization of an information content entity inheres.
definition editor: GROUP: IAO

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
subclass of: data about an ontology part
editor preferred label: obsolescence reason specification
has curation status: pending final vetting
definition: The reason for which a term has been deprecated. 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.
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

textual entity
type: Class
subclass of: information content entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: metadata incomplete
definition: 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.
editor note: 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.
editor note: 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.
definition editor: PERSON: Lawrence Hunter
alternative term: text
imported from: obi.owl
imported from: pdro.owl

author identification
type: Class
subclass of: written name
editor preferred label: author identification
example of usage: L. Hunter
has curation status: pending final vetting
definition: A textual entity intended to identify a particular author
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl
imported from: pdro.owl

figure
type: Class
subclass of: information content entity
editor preferred label: figure
example of usage: Any picture, diagram or table
has curation status: metadata complete
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
definition editor: PERSON: Lawrence Hunter
imported from: obi.owl

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: metadata complete
definition: A collection of information content entities intended to be understood together as a whole
definition editor: PERSON: Lawrence Hunter
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is part of
  some values from: document
editor preferred label: document part
example of usage: An abstract, introduction, method or results section.
has curation status: metadata complete
definition: an information content entity that is part of a document
definition editor: PERSON: Lawrence Hunter
imported from: iao.owl
imported from: ontoneo.owl
imported from: pdro.owl

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: has measurement unit label
  some values from: length unit
subclass of: Restriction
  on property: is quality measurement of
  some values from: length
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of length quality
definition editor: Alan Ruttenberg
has OMOP concept ID: 3036277

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: mass unit
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: obi.owl
has OMOP concept ID: 3025315

time measurement datum
type: Class
equivalent class: Restriction
  on property: DOB about day of birth
  some values from: day of birth
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: process
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: pending final vetting
definition: a planned process in which a document is created or added to by including the specified input in it.
editor note: 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
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has OMOP concept ID: 4187458
has OMOP concept ID: 4210433
has OMOP concept ID: 4326177
has OMOP concept ID: 765467

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: is part of
  some values from: CRID
example of usage: 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.
has curation status: metadata complete
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: pdro.owl

CRID
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
example of usage: Entries in a Column of which the header is "Pubmed ID"
example of usage: PMID:12345
example of usage: The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
example of usage: The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
example of usage: 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.
has curation status: metadata complete
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
editor note: 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').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID
alternative term: Centrally Registered IDentifier
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: pdro.owl
imported from: http://purl.obolibrary.org/obo/iao.owl
label: centrally registered identifier

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: pdro.owl

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: metadata incomplete

written name
type: Class
subclass of: textual entity
editor preferred label: written name
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
has curation status: pending final vetting
definition: A textual entity that denotes a particular in reality.
definition editor: PERSON: Bill Hogan
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
definition source: https://github.com/information-artifact-ontology/IAO/issues/114
curator note: 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.
imported from: obi.owl
imported from: pdro.owl

software application
type: Class
subclass of: software
has curation status: metadata incomplete
definition: A software application is software that can be directly executed by some processing unit.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: https://github.com/information-artifact-ontology/IAO/issues/80
imported from: obi.owl

identifier
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: designates
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: dubbing process
subclass of: information content entity
definition: A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
definition: An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
definition: Uma entidade de conteúdo de informação que é o resultado de um processo de identificação e é usada para se referir a uma instância de entidade compartilhada por um grupo de pessoas para se referir a essa entidade individual. @pt
definition: Une entité de contenu informationnel qui est le résultat d'un processus de dénomination d'une entité et dont l'usage est partagé par un groupe d'individus qui s'en servent pour référer à cette entité. @fr
definition editor: Mathias Brochhausen
alternative term: proper name
imported from: omiabis.owl
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
creator: Mathias Brochhausen
comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
label: nom propre @fr
label: nome próprio @pt
label: proper name

dubbing process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: identifier
subclass of: planned process
definition: A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
definition editor: Mathias Brochhausen
imported from: pdro.owl
creator: Mathias Brochhausen

personal name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: designates
    all values from: Homo sapiens
subclass of: identifier
definition: A personal name is a proper name identifying an individual person.
definition: Um nome próprio que identifica uma pessoa específica. @pt
definition: Un nom propre qui identifie une personne. @fr
definition editor: Mathias Brochhausen
alternative term: nome completo @pt
alternative term: nome da pessoa @pt
definition source: http://en.wikipedia.org/wiki/Personal_name
imported from: omiabis.owl
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
label: nom personnel @fr
label: nome pessoal @pt

given name
type: Class
subclass of: personal name
subclass of: Restriction
  on property: is part of
  some values from: personal name
definition: A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
definition: Un nom personnel qui différencie un individu au sein des membres d'un groupe qui partagent le même nom de famille. Un prénom est choisi et attribué volontairement à un individu plutôt que transmis. @fr
definition editor: Mathias Brochhausen
alternative term: first name
alternative term: nome @pt
definition source: http://en.wikipedia.org/wiki/Given_name
imported from: ontoneo.owl
imported from: pdro.owl
imported from: pno.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: primeiro nome @pt
label: prénom @fr

family name
type: Class
subclass of: personal name
subclass of: Restriction
  on property: is part of
  some values from: personal name
definition: A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
definition: Un nom de famille est typiquement une partie du nom d'une personne qui a été transmis, selon la loi ou la coutume, d'un des parents ou des deux parents à leurs enfants. @fr
definition editor: Mathias Brochhausen
alternative term: last name
alternative term: sobrenome @pt
alternative term: último nome @pt
alternative term: último sobrenome @pt
definition source: http://en.wikipedia.org/wiki/Family_name
imported from: ontoneo.owl
imported from: pdro.owl
imported from: pno.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: nom de famille @fr
label: nome de família @pt

identity document
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is about
    some values from: documented identity
  intersection of: Restriction
    on property: is concretized as
    some values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: inheres_in
        some values from: Restriction
  intersection of: Restriction
    on property: is concretized as
    all values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: inheres_in
        some values from: Restriction
subclass of: document
definition: a document that denotes some identity and is concretized by the bearer of some credential role
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

documented identity
type: Class
subclass of: information content entity
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: information content entity
  intersection of: Restriction
    on property:
      inverse of: is about
    some values from: identity document
  intersection of: Restriction
    on property: has part
    all values from: information content entity
definition: a documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
comment: is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities?

authentication
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: realizes
    some values from: credential role
  intersection of: Restriction
    on property: has_participant
    some values from: data item
  intersection of: Restriction
    on property: has_participant
    some values from: Restriction
      on property:
        inverse of: is about
      some values from: data item
example of usage: I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
definition: Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

credential role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: authentication
  intersection of: Restriction
    on property: inheres_in
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: identity document
subclass of: role
definition: a role that inheres in a concretization of an identity document and is realized by an authentication process
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

social act
type: Class
subclass of: process
example of usage: Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
definition: 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.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
comment: 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.

informed consent form
type: Class
subclass of: document
definition: 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.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte
alternative term: informed consent document
definition source: NCIt C16468
imported from: ico.owl

completely filled informed consent form
type: Class
subclass of: informed consent form
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: form filling
    intersection of: Restriction
      on property: has_specified_input
      some values from: data confirm questionnaire
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: Homo sapiens
        intersection of: Restriction
definition: An informed consent form that has been filled with all required contents.
definition editor: Yongqun He
imported from: ico.owl

consenter role
type: Class
subclass of: role
definition: A role that inheres in a patient or the legal guadian when he/she participates the consenting process.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.
imported from: ico.owl

disease or disorder
type: Class
subclass of: disposition
definition: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
imported from: mondo.owl
database_cross_reference: DOID:4
database_cross_reference: EFO:0000408
database_cross_reference: ICD10:N18
database_cross_reference: ICD9:799.9
database_cross_reference: MESH:D004194
database_cross_reference: NCIT:C2991
database_cross_reference: OGMS:0000031
database_cross_reference: Orphanet:377788
database_cross_reference: SCTID:64572001
database_cross_reference: UMLS:C0012634
alternative_term: condition
alternative_term: disease
alternative_term: disease or disorder
alternative_term: disease or disorder, non-neoplastic
alternative_term: diseases
alternative_term: diseases and disorders
alternative_term: disorder
alternative_term: disorders
alternative_term: medical condition
alternative_term: other disease
id: MONDO:0000001

cancer
type: Class
subclass of: neoplasm (disease)
subclass of: Restriction
  on property: has material basis in
  some values from: malignant neoplasm (material entity)
definition: A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
imported from: mondo.owl
database_cross_reference: COHD:443392
database_cross_reference: DOID:0050686
database_cross_reference: DOID:0050687
database_cross_reference: DOID:162
database_cross_reference: EFO:0000311
database_cross_reference: GARD:0011960
database_cross_reference: ICD10:C80
database_cross_reference: ICD10:C80.1
database_cross_reference: ICD9:195.8
database_cross_reference: ICD9:199
database_cross_reference: ICD9:199.1
database_cross_reference: ICDO:8000/3
database_cross_reference: NCIT:C9305
database_cross_reference: NIFSTD:birnlex_406
database_cross_reference: ONCOTREE:MT
database_cross_reference: SCTID:363346000
database_cross_reference: UMLS:C0006826
alternative_term: CA
alternative_term: cancer
alternative_term: cell type cancer
alternative_term: malignancy
alternative_term: malignant Growth
alternative_term: malignant neoplasm
alternative_term: malignant neoplasm (disease)
alternative_term: malignant neoplastic disease
alternative_term: malignant tumor
alternative_term: neoplasm (disease), malignant
alternative_term: neoplasm, malignant
alternative_term: organ system cancer
alternative_term: primary cancer
has_related_synonym: MT
id: MONDO:0004992

neoplasm (disease)
type: Class
subclass of: neoplastic disease or syndrome
definition: A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
imported from: mondo.owl
has_broad_synonym: cell process disease
database_cross_reference: COHD:438112
database_cross_reference: DOID:14566
database_cross_reference: EFO:0000616
database_cross_reference: HP:0002664
database_cross_reference: ICD10:C00.D48
database_cross_reference: ICD9:140-239.99
database_cross_reference: ICD9:239.8
database_cross_reference: ICD9:239.9
database_cross_reference: MESH:D009369
database_cross_reference: NCIT:C3262
database_cross_reference: ONCOTREE:OTHER
database_cross_reference: SCTID:55342001
database_cross_reference: UMLS:CN236628
alternative_term: disease of cellular proliferation
alternative_term: neoplasia
alternative_term: neoplasm
alternative_term: neoplastic disease
alternative_term: neoplastic growth
alternative_term: tumor
alternative_term: tumor disease
has_narrow_synonym: other neoplasm
id: MONDO:0005070

neoplastic disease or syndrome
type: Class
subclass of: cell proliferation disorder
definition: Either an isolated neoplasm or a syndrome with neoplasm as a major feature.
imported from: mondo.owl
has_related_synonym: neoplastic disease
has_related_synonym: neoplastic disorder
id: MONDO:0023370

cell proliferation disorder
type: Class
subclass of: disease or disorder
subclass of: Restriction
  on property: realized in
  some values from: dysregulation of cell proliferation
definition: Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions.
imported from: mondo.owl
id: MONDO:0045024

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ido.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: pdro.owl

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ido.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: pdro.owl

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ido.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: pdro.owl

Eukaryota
type: Class
subclass of: organism
subclass of: Restriction
  on property: has part
  some values from: genome of Eukaryota
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ido.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: ogg.owl
imported from: pdro.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
alternative_term: eucaryotes
alternative_term: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred label: Bilateria
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Eukaryota
subclass of: Euarchontoglires
subclass of: organism
subclass of: Class
  intersection of: Restriction
    on property: is designated by
    some values from: personal name
  intersection of: Restriction
    on property: is identical to
    some values from: Human body
subclass of: Restriction
  on property: has part
  some values from: genome of Homo sapiens
editor preferred label: Homo sapiens
definition: TO DO @pt
alternative term: human
alternative term: human being
alternative term: humano, ser humano @pt
alternative term: man
imported from: ncbitaxon.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
has_rank: NCBITaxon species
translated to Portuguese by: PERSON: Fernanda Farinelli
commented SPARQL query for expansion: PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX sm: <tag:stardog:api:mapping:> PREFIX turbo: <http://transformunify.org/ontologies/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX ontologies: <http://transformunify.org/ontologies/> insert { graph turbo:expanedUnlinkedPeople { ?person a obo:NCBITaxon_9606 ; turbo:TURBO_0000303 ?sns ; ontologies:TURBO_0010390 ?race_concept_id ; ontologies:TURBO_0010391 ?ethnicity_concept_id ; ontologies:TURBO_0010392 ?gender_concept_id ; ontologies:TURBO_0010393 ?person_id . ?sns a obo:UBERON_0035946 . ?birthdate a <http://www.ebi.ac.uk/efo/EFO_0004950> ; obo:IAO_0000136 ?sns ; obo:IAO_0000004 ?birth_datetime ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . turbo:expanedUnlinkedPeople a obo:IAO_0000100 ; <http://purl.org/dc/elements/1.1/title> ?dataSetTitle . ?crid a obo:IAO_0000578 ; obo:IAO_0000219 ?person . ?cridSymb a obo:IAO_0000577 ; obo:BFO_0000050 ?crid ; turbo:TURBO_0010094 ?person_source_value ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . ?encRegDen obo:BFO_0000050 ?crid . } } where { service <http://localhost:5820/forvg/query> { graph <virtual://synthea_omop_rds> { ?subject <http://transformunify.org/ontologies/TURBO_0010086> ?birth_datetime . ?subject <http://transformunify.org/ontologies/TURBO_0010282> ?regden . ?subject <http://transformunify.org/ontologies/TURBO_0010079> ?person_source_value . ?subject rdf:type <http://transformunify.org/ontologies/TURBO_0010161> . ?subject <http://transformunify.org/ontologies/TURBO_0010100> ?race_concept_id . ?subject <http://transformunify.org/ontologies/TURBO_0010099> ?ethnicity_concept_id . ?subject <http://transformunify.org/ontologies/TURBO_0010098> ?gender_concept_id . ?subject <http://transformunify.org/ontologies/TURBO_0010170> ?person_id . bind(uuid() as ?person) bind(uuid() as ?sns) bind(uuid() as ?birthdate) # bind(sha1(concat("dataset", ?data…
database_cross_reference: GC_ID:1
alternative_term: human
alternative_term: man
has_obo_namespace: ncbi_taxonomy

Central African
type: Class
subclass of: population
definition: 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.
alternative term: Central African
imported from: ncit.owl

North African
type: Class
subclass of: population
definition: 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.
alternative term: North African
imported from: ncit.owl

South African
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the country of South Africa.
alternative term: South African
imported from: ncit.owl

Southeast Asian
type: Class
subclass of: population
definition: 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.
alternative term: Southeast Asian
imported from: ncit.owl

Central Asian
type: Class
subclass of: population
definition: 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.
alternative term: Central Asian
imported from: ncit.owl

Australian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the country or continent of Australia.
alternative term: Australian
imported from: ncit.owl

New Zealander
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the country of New Zealand.
alternative term: New Zealander
imported from: ncit.owl

Scandinavian
type: Class
subclass of: population
definition: 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.
alternative term: Scandinavian
imported from: ncit.owl

Australian/New Zealand Ethnicity
type: Class
subclass of: ethnic group
definition: A collection of ethnic geographical categories including Australian and New Zealander.
alternative term: Australian/New Zealand
alternative term: Australian/New Zealand Ethnicity
imported from: ncit.owl

Gleason Score for Prostate Cancer
type: Class
subclass of: categorical value specification
definition: The score derived from universally embraced prostate cancer grading system developed by Dr. Donald F. Gleason in 1977. The system provides a reproducible description of the glandular architecture of prostate tissue to which a pathologist assigns a score depending primarily on the microscopic patterns of cancerous glands and cell morphology. The system correlates well with behavior at the extremes: Gleason 1+1 tumors are the most well differentiated, slowly growing and rarely spread; Gleason 4+5 tumors are the most poorly differentiated, often widely metastatic at the time of diagnosis. In the commoner intermediate grade tumors, however, behavior is extremely variable.
alternative_term: Gleason Score
alternative_term: Gleason Score for Prostate Cancer
alternative_term: Gleason Sum
alternative_term: Gleason score

Gleason Grading System
type: Class
subclass of: categorical value specification
definition: A grading system for prostatic carcinoma based on the microscopic glandular architectural patterns of the malignant epithelial cells. Nuclear atypia is not evaluated. It defines five patterns or grades which reflect decreasing differentiation.
alternative_term: Gleason Grade
alternative_term: Gleason Grade for Prostate Cancer
alternative_term: Gleason Grading System

South Asian
type: Class
subclass of: population
definition: Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka.
alternative term: South Asian
alternative term: South Asians
imported from: ncit.owl

European
type: Class
subclass of: population
definition: Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere.
alternative term: EUROPEAN
alternative term: European
imported from: ncit.owl

Mediterranean
type: Class
subclass of: population
definition: Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe.
alternative term: MEDITERRANEAN
alternative term: Mediterranean
imported from: ncit.owl

Western European
type: Class
subclass of: European
definition: Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France.
alternative term: WESTERN EUROPEAN
alternative term: Western European
imported from: ncit.owl

Eastern European
type: Class
subclass of: European
definition: 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.
alternative term: EASTERN EUROPEAN
alternative term: Eastern European
imported from: ncit.owl

Middle Eastern
type: Class
subclass of: population
definition: 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.
alternative term: MIDDLE EASTERN
alternative term: Middle Eastern
imported from: ncit.owl

human subject recuiter role
type: Class
subclass of: worker role
definition: A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

data confirm questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire that comprises a set of questions about patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by a recruiter based on an Electronic Medical Record (EMR).
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

form filling
type: Class
subclass of: document editing
definition: A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group

medication role
type: Class
subclass of: role
definition: A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group

medication material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: medication role
subclass of: material entity
definition: A material entity that is bearer of a medication role.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Penn Group

blood draw time
type: Class
subclass of: data item
definition: A data item that reports the time of day when a blood specimen was collected.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
definition source: OBIB
ontology term requester: NCI BBRB

blood specimen collection
type: Class
subclass of: collecting specimen from organism
definition: A collecting specimen from organism that results in a blood specimen.
definition editor: Person: Chris Stoeckert, Helena Ellis, Jie Zheng
alternative term: blood draw
definition source: OBIB
ontology term requester: NCI BBRB

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
definition: TO DO @pt
editor note: '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.)
editor note: 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.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: 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)
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: processo planejado @pt

regulator role
type: Class
subclass of: regulatory role
editor preferred label: regulator role
example of usage: Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
has curation status: metadata complete
definition: a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
definition editor: Person:Jennifer Fostel
alternative term: regulator
definition source: OBI

biological feature identification objective
type: Class
subclass of: objective specification
editor preferred label: biological feature identification objective
has curation status: metadata incomplete
definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
definition editor: Jennifer Fostel
imported from: obi.owl

regulatory role
type: Class
subclass of: role
editor preferred label: regulatory role
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
has curation status: metadata complete
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
definition editor: GROUP: Role branch
definition source: OBI, CDISC
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent

material supplier role
type: Class
subclass of: service provider role
editor preferred label: material supplier role
example of usage: Jackson Labs is an organization which provide mice as experimental material
has curation status: metadata complete
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor note: Supplier role is a special kind of service, e.g. biobank
definition editor: PERSON:Jennifer Fostel
alternative term: material provider role
alternative term: supplier

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
definition editor: PERSON: Alan Ruttenberg
imported from: obi.owl

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
definition editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: 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
imported from: obi.owl
ISA alternative term: study

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred label: evaluant role
example of usage: 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.
has curation status: ready for release
definition: 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
editor note: 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)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 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.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method
has OMOP concept ID: 37393315
has OMOP concept ID: 4014117
has OMOP concept ID: 4015052
has OMOP concept ID: 4018595
has OMOP concept ID: 4018603
has OMOP concept ID: 4024509
has OMOP concept ID: 4041881
has OMOP concept ID: 40481948
has OMOP concept ID: 4060266
has OMOP concept ID: 4060626
has OMOP concept ID: 4061811
has OMOP concept ID: 4078285
has OMOP concept ID: 4091461
has OMOP concept ID: 4102154
has OMOP concept ID: 4134565
has OMOP concept ID: 4136494
has OMOP concept ID: 4149386
has OMOP concept ID: 4149631
has OMOP concept ID: 4151408
has OMOP concept ID: 4168615
has OMOP concept ID: 4181917
has OMOP concept ID: 4191851
has OMOP concept ID: 4191853
has OMOP concept ID: 4195803
has OMOP concept ID: 4258677
has OMOP concept ID: 4304821
has OMOP concept ID: 44784284

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: 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.
definition editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: obi.owl

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
definition: 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.
definition editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: 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.
imported from: obi.owl
comment: (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 t…

patient role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Homo sapiens
editor preferred label: patient role
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has curation status: metadata complete
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
definition editor: GROUP:Role Branch
alternative term: patient
definition source: OBI, CDISC
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
imported from: pdro.owl

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: ready for release
definition: A planned process which results in physical changes in a specified input material
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived
imported from: obi.owl

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
editor preferred label: study subject role
example of usage: 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.
has curation status: ready for release
definition: 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.
editor note: 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.
definition editor: GROUP: Role Branch
definition source: OBI
curator note: 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

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: 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.
has curation status: ready for release
definition: 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
editor note: 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.
editor note: 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.
editor note: 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.
editor note: 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.
definition editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: sequence feature identification objective
has curation status: metadata incomplete
definition: Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
definition editor: Jennifer Fostel
imported from: obi.owl

worker role
type: Class
subclass of: investigation agent role
editor preferred label: worker role
example of usage: 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
has curation status: metadata complete
definition: 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
editor note: "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
definition editor: Person:Jennifer Fostel
alternative term: worker
definition source: OBI

filter paper
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
editor preferred label: filter paper
has curation status: metadata complete
definition: a device manufacture with the intent to provide a porous unsized paper used for filtering.
definition editor: Frank Gibson
definition source: sep:00107
imported from: obi.owl

population
type: Class
subclass of: material entity
editor preferred label: population
example of usage: 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.
has curation status: pending final vetting
definition: 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
editor note: 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/
definition editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
editor preferred label: imaging assay
has curation status: pending final vetting
definition: An assay that produces a picture of an entity.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl
has OMOP concept ID: 4024289
has OMOP concept ID: 4047491
has OMOP concept ID: 4058899
has OMOP concept ID: 4145310
has OMOP concept ID: 4163872
has OMOP concept ID: 4243062
has OMOP concept ID: 4252419

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres_in
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: Restriction
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: investigation
editor preferred label: investigation agent role
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: ready for release
definition: 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.
editor note: 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.
editor note: 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)
definition editor: GROUP: Role Branch
alternative term: investigator
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
ISA alternative term: study person role
comment: 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)

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: 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.
has curation status: ready for release
definition: 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.
definition: 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.
editor note: 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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl

DNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: deoxyribonucleic acid
editor preferred label: DNA extraction
has curation status: metadata incomplete
definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

plan
type: Class
subclass of: realizable entity
editor preferred label: plan
example of usage: The plan of researcher X to perform an experiment according to a protocol.
has curation status: pending final vetting
definition: A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
editor note: This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
definition editor: AR, BP, JM, MC, PRS
definition source: branch derived

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: 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.
has curation status: ready for release
definition: 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.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
ISA alternative term: study protocol

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: adding a material entity into a target
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
has curation status: ready for release
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
definition editor: BP
definition source: branch derived
imported from: obi.owl

analyte role
type: Class
subclass of: measurand role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
editor preferred label: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: ready for release
definition: 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.
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

material to be added role
type: Class
subclass of: role
editor preferred label: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: metadata complete
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
definition editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch
imported from: obi.owl

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred label: interpreting data
example of usage: 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.
has curation status: ready for release
definition: 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
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has_participant
    some values from: plan specification
editor preferred label: planning
example of usage: 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.
has curation status: ready for release
definition: a process of creating or modifying a plan specification
editor note: 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'.
definition editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch

histological sample preparation
type: Class
subclass of: material processing
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: organ section
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
subclass of: Restriction
  on property: has_participant
  some values from: microtome
editor preferred label: histological sample preparation
has curation status: pending final vetting
definition: histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
definition editor: PERSON:Bjoern Peters
definition source: OBI branch derived
imported from: obi.owl

contain function
type: Class
subclass of: function
editor preferred label: contain function
example of usage: A syringe, a beaker
has curation status: ready for release
definition: A contain function is a function to constrain a material entities location in space
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot
imported from: obi.owl

material separation function
type: Class
subclass of: function
editor preferred label: material separation function
has curation status: ready for release
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot
imported from: obi.owl

filter function
type: Class
subclass of: material separation function
editor preferred label: filter function
has curation status: ready for release
definition: A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
definition editor: Frank Gibson
imported from: obi.owl

mechanical function
type: Class
subclass of: function
editor preferred label: mechanical function
has curation status: ready for release
definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot
definition source: http://en.wikipedia.org/wiki/Mechanical_work
imported from: obi.owl

transfer function
type: Class
subclass of: function
editor preferred label: transfer function
has curation status: ready for release
definition: A transfer function is a function to displace a material from one location to another.
definition editor: Bill Bug
definition editor: Daniel Schober
definition editor: Frank Gibson
definition editor: Melanie Courtot
imported from: obi.owl

measuring glucose concentration in blood serum assay
type: Class
subclass of: analyte assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: blood serum specimen
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: blood serum specimen
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: inheres_in
        some values from: glucose
  intersection of: Restriction
    on property: has_specified_input
    some values from: glucose
editor preferred label: measuring glucose concentration in blood serum assay
example of usage: Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319.
has curation status: metadata incomplete
definition: An assay that determines the concentration of glucose molecules in a blood serum sample
definition editor: Bjoern Peters
definition source: OBI
imported from: obi.owl

syringe
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: transfer function
editor preferred label: syringe
example of usage: Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
has curation status: ready for release
definition: a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
definition editor: Philippe Rocca-Serra
definition source: OBI Instrument adapted from Wikipedia
imported from: obi.owl

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: extraction
editor preferred label: extract
example of usage: 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
has curation status: metadata complete
definition: an extract is a material entity which results from an extraction process
definition editor: PERSON: Philippe Rocca-Serra
alternative term: extracted material
definition source: GROUP: OBI Biomatrial Branch
imported from: obi.owl

injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres_in
        some values from: syringe
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred label: injection
example of usage: Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
has curation status: metadata complete
definition: injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
definition editor: Philippe Rocca-Serra
definition source: OBI Biomaterial
imported from: obi.owl

DNA sequence feature detection assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: DNA extract
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: DNA extract
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
editor preferred label: DNA sequence feature detection assay
example of usage: genotyping using an Affymetrix chip
has curation status: metadata incomplete
definition: An assay with the objective to determine a sequence feature of DNA
definition editor: Bjoern Peters
definition editor: Philippe Rocca-Serra
definition source: OBI
imported from: obi.owl

adding material objective
type: Class
subclass of: material combination objective
editor preferred label: adding material objective
example of usage: creating a mouse infected with LCM virus
has curation status: ready for release
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
definition editor: BP
imported from: obi.owl

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred label: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: ready for release
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
definition editor: PERSON: Bjoern Peters
definition source: PPPB branch
imported from: obi.owl

DNA sequence variation detection assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: DNA extract
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
editor preferred label: DNA sequence variation detection assay
example of usage: Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
has curation status: ready for release
definition: An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule.
definition editor: Philippe Rocca-Serra
definition source: OBI Biomaterial
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: ready for release
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
definition editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

analyte assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
editor preferred label: analyte assay
example of usage: 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
has curation status: ready for release
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
definition editor: Alan Ruttenberg
definition editor: Bjoern Peters
definition editor: Helen Parkinson
definition editor: Philippe Rocca-Serra
definition source: Alan Ruttenberg
definition source: Bjoern Peters
definition source: Helen Parkinson
definition source: OBI Planned process branch
definition source: Philippe Rocca-Serra
imported from: obi.owl

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
editor preferred label: target of material addition role
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has curation status: metadata complete
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
definition editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

mass measurement assay
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: evaluant role
      intersection of: Restriction
        on property: role of
        some values from: material entity
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: mass measurement datum
editor preferred label: mass measurement assay
example of usage: The patients was weighed and mass was determined to be 47 kilograms
has curation status: metadata complete
definition: An assay that determines the mass of an evaluant
definition editor: Helen Parkinson
definition source: OBI
imported from: obi.owl

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: ready for release
definition: 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.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Frank Gibson
imported from: obi.owl

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
definition: an objective specifiction that creates an specific output object from input materials.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

manufacturing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: manufacturing objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
editor preferred label: manufacturing
has curation status: ready for release
definition: Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
editor note: Manufacturing implies reproducibility and responsibility AR
editor note: This includes a single scientist making a processed material for personal use.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

manufacturing objective
type: Class
subclass of: material transformation objective
editor preferred label: manufacturing objective
has curation status: ready for release
definition: is the objective to manufacture a material of a certain function (device)
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI PlanAndPlannedProcess Branch

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
editor preferred label: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: ready for release
definition: a planned process that carries out a study design
editor note: 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.
definition source: branch derived
curator note: 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.
imported from: obi.owl

manufacturer role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: manufacturing
editor preferred label: manufacturer role
example of usage: With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
has curation status: metadata incomplete
definition: Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
definition editor: GROUP: Role Branch
definition source: OBI

DNA sequencing assay
type: Class
equivalent class: Class
  intersection of: sequencing assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: DNA sequencer
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: DNA extract
        intersection of: Restriction
  intersection of: Restriction
    on property: has_specified_output
    some values from: DNA sequence data
subclass of: sequencing assay
editor preferred label: DNA sequencing assay
example of usage: Illumina (Solexa) sequencing is an example of DNA sequencing
has curation status: metadata incomplete
definition: A sequencing assay which determines information on the sequence of a DNA molecule.
definition editor: Philippe Rocca-Serra
alternative term: nucleotide sequencing
definition source: url:https://en.wikipedia.org/wiki/DNA_sequencing
imported from: obi.owl

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: ready for release
definition: is an objective to transform a material entity into spatially separated components.
definition editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
has curation status: ready for release
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
definition editor: bp
definition source: bp
imported from: obi.owl

blood specimen
type: Class
subclass of: specimen from organism
subclass of: Restriction
  on property: is_specified_output_of
  some values from: collecting specimen from organism
subclass of: Restriction
  on property: has role
  some values from: specimen role
subclass of: Restriction
  on property: derives from
  some values from: blood
editor preferred label: blood specimen
example of usage: blood drawn from a human for glucose assay
has curation status: ready for release
definition: a material entity derived from a portion of blood collected from an organism
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

data representational model
type: Class
subclass of: directive information content entity
editor preferred label: data representational model
example of usage: gene regulatory graph model
example of usage: phylogenetic tree
example of usage: protein interaction network
has curation status: metadata complete
definition: Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
definition editor: Melanie Courtot
alternative term: data structure
alternative term: data structure specification
definition source: GROUP: OBI
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
imported from: obi.owl

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
editor preferred label: specimen collection process
example of usage: 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
has curation status: ready for release
definition: A planned process with the objective of collecting a specimen.
editor note: 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.
editor note: 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.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
definition editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
imported from: obi.owl

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred label: sample from organism
has curation status: example to be eventually removed
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: 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.
imported from: obi.owl

portioning objective
type: Class
subclass of: material separation objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: metadata incomplete
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
imported from: obi.owl

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: metadata complete
definition: 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).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: obi.owl

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

material combination objective
type: Class
subclass of: material transformation objective
editor preferred label: material combination objective
has curation status: ready for release
definition: is an objective to obtain an output material that contains several input materials.
definition editor: PPPB branch
definition source: bp
imported from: obi.owl

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: 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.
has curation status: pending final vetting
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 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.
imported from: obi.owl

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
editor preferred label: material sample
example of usage: 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.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
definition editor: OBI: workshop
alternative term: sample population
imported from: obi.owl
ISA alternative term: sample

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: ready for release
definition: An objective specification maintains some or all of the qualities of a material over time.
definition editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: obi.owl

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Homo sapiens
subclass of: Restriction
  on property: has_participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
editor preferred label: informed consent process
has curation status: ready for release
definition: 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.
editor note: 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.
definition editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres_in
    some values from: deoxyribonucleic acid
subclass of: region
editor preferred label: primary structure of DNA macromolecule
has curation status: metadata incomplete
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
definition editor: BP et al
imported from: obi.owl

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
editor preferred label: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: ready for release
definition: A device in which a measure function inheres.
definition editor: GROUP:OBI Philly workshop
definition source: OBI
imported from: obi.owl

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred label: material maintenance
has curation status: metadata incomplete
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
imported from: obi.owl

record of missing knowledge
type: Class
subclass of: information content entity
editor preferred label: record of missing knowledge
example of usage: A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
has curation status: metadata complete
definition: a information content entity created to indicate that information about something is not available to the person recording it.
editor note: This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
definition editor: Bjoern Peters

material separation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: material separation function
subclass of: device
editor preferred label: material separation device
example of usage: flow cytometer
has curation status: metadata incomplete
definition: A device with a separation function realized in a planed process
imported from: obi.owl

intramuscular injection
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres_in
        some values from: syringe
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: skeletal muscle tissue
subclass of: injection
subclass of: administering substance in vivo
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
editor preferred label: intramuscular injection
has curation status: metadata incomplete
definition: is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
imported from: obi.owl
has OMOP concept ID: 4295880

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: categorical value specification
editor preferred label: categorical measurement datum
has curation status: metadata complete
definition: A measurement datum that is reported on a categorical scale
definition editor: Bjoern Peters
alternative term: nominal mesurement datum
definition source: Bjoern Peters
imported from: obi.owl

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    union of: Homo sapiens
    union of: organization
subclass of: Restriction
  on property: realized in
  all values from: planned process
editor preferred label: service provider role
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has curation status: metadata incomplete
definition: 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
definition editor: PERSON:Helen Parkinson

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: 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.
has curation status: ready for release
definition: A specimen that has been intentionally physically modified.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl
comment: A tissue sample that has been sliced and stained for a histology study.

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 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…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: metadata complete
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition editor: Person:Chris Stoeckert
definition source: GROUP: OBI
imported from: obi.owl

questionnaire
type: Class
subclass of: document
editor preferred label: questionnaire
has curation status: metadata complete
definition: A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
editor note: JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
editor note: Need to clarify if this is a document or a directive information entity (or what their connection is))
definition editor: PERSON: Jessica Turner
definition source: Merriam-Webster

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: nucleic acid extraction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
editor preferred label: nucleic acid extract
has curation status: metadata complete
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: obi.owl

DNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA extraction
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
editor preferred label: DNA extract
has curation status: metadata complete
definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
definition editor: Person: Jie Zheng
definition source: Group: UPenn group
imported from: obi.owl

nucleic acid sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: nucleic acid sequencer
has curation status: metadata complete
definition: An device that is used to determine the order of nucleotides in nucleic acid sequences.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
imported from: obi.owl

protein sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: protein sequencer
has curation status: metadata complete
definition: An device that is used to determine the order of amino acids in protein sequences.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
imported from: obi.owl

individual organism identifier
type: Class
subclass of: centrally registered identifier symbol
subclass of: Restriction
  on property: denotes
  all values from: organism
editor preferred label: individual organism identifier
has curation status: metadata complete
definition: a CRID symbol used to distinguish one individual organism from another.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_169 Individual
imported from: pdro.owl

age measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: age
editor preferred label: age measurement datum
has curation status: metadata complete
definition: A time measurement datum that is the result of measurement of age of an organism
editor note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage
definition editor: PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
definition source: MO_178 Age
curator note: In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
curator note: discussed on Nov 15, dev call All subtype will be defined by textual definition now.

age since birth measurement datum
type: Class
subclass of: age measurement datum
editor preferred label: age since birth measurement datum
has curation status: metadata complete
definition: An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
definition editor: PERSON:Chris Stoeckert, Jie Zheng
definition source: MO_710 birth

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: is part of
  some values from: genotype information
editor preferred label: genetic population background information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
has curation status: metadata complete
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
editor note: proposed and discussed on San Diego OBI workshop, March 2011
definition editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

genotype information
type: Class
subclass of: genetic characteristics information
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: genetic population background information
  intersection of: Restriction
    on property: has part
    some values from: genetic alteration information
editor preferred label: genotype information
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
has curation status: metadata complete
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
definition editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

allele information
type: Class
subclass of: genetic alteration information
subclass of: Class
  intersection of: Restriction
    on property: is part of
    some values from: genotype information
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: allele information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: metadata complete
definition: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
editor note: discussed on San Diego OBI workshop, March 2011
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_58 Allele
imported from: obi.owl

genetic alteration information
type: Class
subclass of: genetic characteristics information
editor preferred label: genetic alteration information
has curation status: metadata complete
definition: a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
definition editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

genetic characteristics information
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: region
    intersection of: Restriction
      on property: is concretized as
      some values from: Restriction
        on property: inheres_in
        some values from: Class
editor preferred label: genetic characteristics information
has curation status: metadata complete
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_66 IndividualGeneticCharacteristics
curator note: MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
imported from: obi.owl

specimen from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: Class
      union of: material anatomical entity
      union of: anatomical cluster
subclass of: specimen
editor preferred label: specimen from organism
has curation status: ready for release
definition: 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).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
alternative term: tissue specimen
definition source: MO_954 organism_part
imported from: obi.owl

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
editor preferred label: DNA sequence data
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: metadata complete
definition: A sequence data item that is about the primary structure of DNA
definition editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
curator note: 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
imported from: obi.owl

genetic material
type: Class
subclass of: nucleic acid
subclass of: Restriction
  on property: is part of
  some values from: Class
    union of: cell
    union of: Viruses
editor preferred label: genetic material
has curation status: requires discussion
definition: A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants.
editor note: MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion).
alternative term: genomic material
alternative term: hereditary genetic material
definition source: OBI developer calls, March 4 2013 and March 11 2013
imported from: obi.owl
comment: Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells).

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: 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".
has curation status: ready for release
definition: An information content entity that is inferred from data.
editor note: 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.
definition editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: metadata complete
definition: 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.
definition editor: PERSON: Matthew Brush
imported from: obi.owl

mass value specification
type: Class
subclass of: scalar value specification
subclass of: Restriction
  on property: specifies value of
  some values from: mass
subclass of: Restriction
  on property: has measurement unit label
  all values from: mass unit
editor preferred label: mass value specification
has curation status: metadata incomplete
definition: A value specification that specifies the mass of some thing.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

categorical value specification
type: Class
subclass of: value specification
editor preferred label: categorical value specification
has curation status: metadata incomplete
definition: A value specification that is specifies one category out of a fixed number of nominal categories
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
editor preferred label: scalar value specification
has curation status: metadata incomplete
definition: A value specification that consists of two parts: a numeral and a unit label
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: 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.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

exome sequencing assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: exome sequencing assay
example of usage: DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
has curation status: metadata complete
definition: A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
definition editor: ImmPort
alternative term: WES
definition source: PMID:25827230
imported from: obi.owl

volume value specification
type: Class
subclass of: value specification
subclass of: Class
  intersection of: Restriction
    on property: specifies value of
    some values from: volume
  intersection of: Restriction
    on property: has measurement unit label
    all values from: volume unit
editor preferred label: volume value specification
has curation status: ready for release
definition: A value specification that specifies the volume of some thing.
definition editor: Chris Stoeckert
definition source: OBI

volume measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: has value specification
      some values from: volume value specification
editor preferred label: volume measurement assay
has curation status: ready for release
definition: An assay to determine the volume of an evaluant.
definition editor: Bjoern Peters
definition editor: Chris Stoeckert
definition source: OBI

reason for lack of data item
type: Class
subclass of: information content entity
editor preferred label: reason for lack of data item
example of usage: cannot be assessed", "not applicable", "unknown
has curation status: metadata complete
definition: An information content entity that provides an explanation why a data item is not provided.
definition editor: Chris Stoeckert, Helena Ellis
definition source: OBI
ontology term requester: NCI BBRB

histologic grade according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to AJCC 7th edition
example of usage: G4: Undifferentiated
example of usage: G1:Well differentiated
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade according to the Fuhrman Nuclear Grading System
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade according to the Fuhrman Nuclear Grading System
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Histologic Grade (Fuhrman Nuclear Grading System)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor
type: Class
subclass of: categorical value specification
editor preferred label: histologic grade for ovarian tumor
has curation status: metadata complete
definition: A categorical value specification that is a histologic grade assigned to a ovarian tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor according to a two-tier grading system
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to a two-tier grading system
has curation status: metadata complete
definition: A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

histologic grade for ovarian tumor according to the World Health Organization
type: Class
subclass of: histologic grade for ovarian tumor
editor preferred label: histologic grade for ovarian tumor according to the World Health Organization
has curation status: metadata complete
definition: A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic primary tumor stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic primary tumor stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for colon and rectum according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic lymph node stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic lymph node stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for colon according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for colon according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: colon distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for lung according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for lung according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: lung distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for kidney according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for kidney according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: kidney distant Metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pathologic distant metastases stage for ovary according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: pathologic distant metastases stage for ovary according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: M: ovarian distant metastases (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

clinical tumor stage group according to AJCC 7th edition
type: Class
subclass of: categorical value specification
editor preferred label: clinical tumor stage group according to AJCC 7th edition
has curation status: metadata complete
definition: A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical tumor stage group (AJCC 7th Edition)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

International Federation of Gynecology and Obstetrics cervical cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
has curation status: metadata complete
definition: A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Clinical FIGO stage
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
type: Class
subclass of: categorical value specification
editor preferred label: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
has curation status: metadata complete
definition: A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

measurand role
type: Class
subclass of: role
subclass of: Restriction
  on property: role of
  some values from: material entity
editor preferred label: measurand role
has curation status: metadata complete
definition: 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.
definition editor: Person: Alan Ruttenberg, Jie Zheng
definition source: https://en.wiktionary.org/wiki/measurand
term tracker item: https://github.com/obi-ontology/obi/issues/778
imported from: obi.owl

prostate gland specimen
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: specimen
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: collecting specimen from organism
    intersection of: Restriction
      on property: derives from
      some values from: prostate gland
subclass of: specimen from organism
editor preferred label: prostate gland specimen
has curation status: ready for release
definition: A specimen that is derived from prostate gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB

blood serum specimen
type: Class
subclass of: processed specimen
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: Class
      union of: filtration
      union of: centrifugation
      union of: dialysis
    intersection of: Restriction
      on property: has_specified_input
      some values from: blood specimen
subclass of: Restriction
  on property: has role
  some values from: specimen role
editor preferred label: blood serum specimen
example of usage: PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
has curation status: metadata complete
definition: A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
definition editor: PERSON: Maura Gasparetto
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
imported from: obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: object
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: genome
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: organizational term
has curation status: ready for release
definition: 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.
definition: TO DO @pt
editor note: 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')
editor note: 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.
editor note: Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: geno.owl
imported from: ido.owl
imported from: obi.owl
imported from: ogg.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
database_cross_reference: NCIT:C14250
database_cross_reference: SNOMEDID:R-005B2
database_cross_reference: ns2:SIO_010000
label: organismo @pt

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: ready for release
definition: A material entity that has the specimen role.
editor note: 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.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: 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).
has curation status: metadata complete
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 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.
definition editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: 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.

organ section
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    union of: histological sample preparation
    union of: collecting specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred label: organ section
example of usage: A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
has curation status: pending final vetting
definition: A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: CEBS
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: differential expression analysis objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
editor preferred label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: ready for release
definition: A planned process that produces output data from input data.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Philippe Rocca-Serra
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors

differential expression analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: differential expression analysis objective
example of usage: Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
has curation status: ready for release
definition: A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
definition editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
definition editor: James Malone
definition source: PERSON: James Malone

edited document
type: Class
subclass of: document
subclass of: Restriction
  on property: is_specified_output_of
  some values from: document editing
editor preferred label: edited document
example of usage: The OBI manuscript is (much) edited imformation
has curation status: ready for release
definition: A document which is the output of a document editing process
definition editor: Person:Bjoern Peters
definition editor: Philippe Rocca-Serra

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: metadata incomplete
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: 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.
definition editor: Person:Bjoern Peters
definition editor: Philippe Rocca-Serra
imported from: obi.owl

filtration
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has_participant
  some values from: filter paper
editor preferred label: filtration
example of usage: PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
has curation status: metadata complete
definition: filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
definition editor: Philippe Rocca-Serra
definition source: OBI-Branch: adapted from wikipedia and wordnet
imported from: obi.owl

centrifugation
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
subclass of: Restriction
  on property: has_participant
  some values from: centrifuge
editor preferred label: centrifugation
example of usage: PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
has curation status: metadata complete
definition: centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
definition editor: Philippe Rocca-Serra
definition source: adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
imported from: obi.owl

staining
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: staining
example of usage: PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
has curation status: pending final vetting
definition: Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
definition editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining

storage
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: storage
example of usage: PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
has curation status: metadata complete
definition: 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
definition editor: Philippe Rocca-Serra
definition source: OBI-Branch

document editing
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: document
subclass of: Restriction
  on property: has_specified_output
  some values from: edited document
editor preferred label: document editing
example of usage: Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
has curation status: metadata complete
definition: is a planned process with specified input original document and specified output edited document
definition editor: Philippe Rocca-Serra and OBI consortium
definition source: adapted from wikipedia

digital curation
type: Class
subclass of: documenting
editor preferred label: digital curation
example of usage: PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
has curation status: metadata complete
definition: Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
definition editor: Philippe Rocca-Serra
definition source: wikipedia

DNA sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: DNA sequencer
example of usage: ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
has curation status: ready for release
definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
definition editor: Trish Whetzel
definition source: MO
imported from: obi.owl

centrifuge
type: Class
subclass of: measurement device
subclass of: material separation device
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: has function
    some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: measure function
subclass of: Restriction
  on property: has function
  some values from: Class
    intersection of: material separation function
    intersection of: Restriction
      on property: realized in
      all values from: centrifugation
editor preferred label: centrifuge
has curation status: ready for release
definition: A device with a rapidly rotating container that applies centrifugal force to its contents
definition editor: Melanie Courtot
definition editor: Person: Jennifer Fostel
definition editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Centrifuge
imported from: obi.owl

microtome
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: material separation function
subclass of: Restriction
  on property: has function
  some values from: mechanical function
editor preferred label: microtome
example of usage: PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
has curation status: pending final vetting
definition: A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
definition editor: PERSON: Phillippe Rocca-Serra
definition source: PERSON: Daniel Schober
imported from: obi.owl

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred label: study design
example of usage: 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.
has curation status: ready for release
definition: 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: 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.
definition editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

tumor grading
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: specimen
subclass of: Restriction
  on property: has_specified_output
  some values from: Restriction
    on property: is about
    some values from: disease course
editor preferred label: tumor grading
has curation status: pending final vetting
definition: An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
definition editor: Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
alternative term: grading of tumor
definition source: OBI branch derived; submitted by MO
imported from: obi.owl

collecting specimen from organism
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
definition editor: PERSON:Bjoern Peters
definition source: IEDB
imported from: obi.owl
has OMOP concept ID: 4234541
has OMOP concept ID: 4278515
has OMOP concept ID: 4294513
has OMOP concept ID: 4331248

administering substance in vivo
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: material to be added role
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: Class
subclass of: adding a material entity into a target
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: organism
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: Restriction
  on property: has_specified_output
  max cardinality: 1
editor preferred label: administering substance in vivo
example of usage: Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
example of usage: injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
has curation status: pending final vetting
definition: A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
editor note: Different routes and means of administration should go as children underneath this
editor note: Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
editor note: needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
definition editor: Bjoern Peters
definition editor: Person:Bjoern Peters
definition source: IEDB
imported from: obi.owl

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material component separation
example of usage: 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
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
definition editor: Bjoern Peters
definition source: IEDB
imported from: obi.owl

histological assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has part
  some values from: imaging assay
subclass of: Restriction
  on property: has part
  some values from: histological sample preparation
subclass of: Restriction
  on property: has_specified_output
  some values from: Restriction
    on property: is about
    some values from: Class
      union of: cell
      union of: organ section
editor preferred label: histological assay
example of usage: the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
has curation status: pending final vetting
definition: An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement.
definition editor: Adam Witney
definition editor: Helen Parkinson
alternative term: histology
alternative term: histopathology
definition source: OBI branch derived
imported from: obi.owl

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: maintaining cell culture
example of usage: 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
has curation status: pending final vetting
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: 'establishing cell culture'
has curation status: metadata complete
definition: 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).
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: 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.

sequencing assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        union of: nucleic acid sequencer
        union of: protein sequencer
        union of: DNA sequencer
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: Class
        intersection of: Restriction
  intersection of: Restriction
    on property: has_specified_output
    some values from: sequence data
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: region
subclass of: assay
editor preferred label: sequencing assay
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has curation status: pending final vetting
definition: An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

dialysis
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: dialysis
example of usage: the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
has curation status: pending final vetting
definition: a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
definition editor: PERSON:Kevin Clancy
definition source: OBI branch derived
imported from: obi.owl

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: nucleic acid
editor preferred label: nucleic acid extraction
example of usage: 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.
has curation status: pending final vetting
definition: a material separation to recover the nucleic acid fraction of an input material
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO. Could be defined class
imported from: obi.owl

donor
type: Class
subclass of: role
editor preferred label: donor
example of usage: A T cell line from a PPD(+) donor.
has curation status: metadata complete
definition: A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
definition editor: IEDB
alternative term: donor role
definition source: IEDB
curator note: Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.

genome
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: gene
definition: A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
definition editor: Oliver He
definition source: Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
definition source: WEB: http://en.wikipedia.org/wiki/Genome
imported from: ogg.owl

gene
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has disposition at all times
  some values from: gene disposition
definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
definition editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
imported from: ogg.owl
comment: In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.

gene disposition
type: Class
subclass of: disposition
definition: a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
definition editor: Yongqun He
definition source: WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
imported from: ogg.owl
comment: YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition".

protein-coding gene disposition
type: Class
subclass of: gene disposition
definition: a gene disposition that a gene can be used as a blueprint for generating a protein (i.e., a gene encodes for a protein).
definition editor: Yongqun He
definition source: WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
imported from: ogg.owl

genome of Eukaryota
type: Class
subclass of: genome
subclass of: Restriction
  on property: has part
  some values from: gene of Eukaryota
subclass of: Restriction
  on property: is genome of organism
  some values from: Eukaryota
definition: The genome of an organism of Eukaryota
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 2759

genome of Homo sapiens
type: Class
subclass of: genome of Eukaryota
subclass of: Restriction
  on property: has part
  some values from: gene of Homo sapiens
subclass of: Restriction
  on property: is genome of organism
  some values from: Homo sapiens
definition: The genome of an organism of Homo sapiens
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

gene of Eukaryota
type: Class
subclass of: gene
subclass of: Restriction
  on property: is gene of organism
  some values from: Eukaryota
definition: A gene of an organism of Eukaryota
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 2759

gene of Homo sapiens
type: Class
subclass of: gene of Eukaryota
subclass of: Restriction
  on property: is gene of organism
  some values from: Homo sapiens
definition: A gene of an organism of Homo sapiens
definition editor: Yue Liu, Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

protein-coding gene of Homo sapiens
type: Class
subclass of: gene of Homo sapiens
subclass of: Restriction
  on property: has disposition at all times
  some values from: protein-coding gene disposition
definition: A gene of Homo sapiens that has a protein-coding gene disposition
definition editor: Bin Zhao, Oliver He
imported from: ogg.owl
organism NCBITaxon ID: 9606

FAS
type: Class
subclass of: protein-coding gene of Homo sapiens
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: ALPS1A
alternative term: APO-1
alternative term: APT1
alternative term: CD95
alternative term: FAS1
alternative term: FASTM
alternative term: TNFRSF6
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: FAS
full name from nomenclature authority: Fas cell surface death receptor
NCBI GeneID: 355
NCBI LocusTag: RP11-399O19.7
gene map location: 10q24.1
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 10
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0002377 (EC: IEA); GO_0003014 (EC: IEA); GO_0004871 (EC: TAS, PMID: 10875918); GO_0004872 (EC: NAS, PMID: 7533181); GO_0004888 (EC: IEA); GO_0005515 (EC: IPI, PMID: 10918185); GO_0005634 (EC: IDA); GO_0005737 (EC: IDA); GO_0005829 (EC: NAS, PMID: 7533181); GO_0005886 (EC: IDA); GO_0005886 (EC: IMP); GO_0005886 (EC: TAS); GO_0006461 (EC: TAS, PMID: 10875918); GO_0006915 (EC: IDA, PMID: 9681877); GO_0006915 (EC: TAS); GO_0006919 (EC: TAS); GO_0006924 (EC: IEA); GO_0006925 (EC: IEA); GO_0006927 (EC: IEA); GO_0007165 (EC: TAS, PMID: 9360929); GO_0008625 (EC: IEA); GO_0009636 (EC: IEA); GO_0009897 (EC: IEA); GO_0009986 (EC: IDA); GO_0016021 (EC: IEA); GO_0019724 (EC: IEA); GO_0019900 (EC: IPI, PMID: 7538908); GO_0031264 (EC: IDA, PMID: 11101870); GO_0031265 (EC: IDA); GO_0032464 (EC: IEA); GO_0042802 (EC: IPI); GO_0042981 (EC: NAS, PMID: 7533181); GO_0043065 (EC: IDA); GO_0043065 (EC: IMP); GO_0043066 (EC: IEA); GO_0045060 (EC: IEA); GO_0045121 (EC: IDA); GO_0045619 (EC: IEA); GO_0045637 (EC: IEA); GO_0048536 (EC: IEA); GO_0050869 (EC: IEA); GO_0051260 (EC: IEA); GO_0051384 (EC: IEA); GO_0070062 (EC: IDA); GO_0071260 (EC: IEP, PMID: 19593445); GO_0071285 (EC: IEA); GO_0071455 (EC: IMP); GO_0097049 (EC: IEA); GO_0097190 (EC: TAS); GO_0097191 (EC: IMP); GO_0097192 (EC: IEA); GO_0097527 (EC: IMP, PMID: 16507998); GO_2001239 (EC: TAS); GO_2001241 (EC: IEA)
has PubMed association: PMID: 1375228; 1385299; 1385309; 1713127; 2469768; 2787530; 7510905; 7514572; 7529798; 7530336; 7533181; 7536190; 7536343; 7538907; 7538908; 7539892; 7540117; 7542559; 7543095; 7575433; 7859281; 8521815; 8524870; 8598453; 8626376; 8648105; 8681376; 8780394; 8864141; 8906799; 8929361; 8940097; 8967952; 8976184; 9002959; 9028321; 9028957; 9039262; 9045686; 9079683; 9082980; 9126929; 9159204; 9199966; 9208847; 9215629; 9223324; 9226175; 9228058; 9247148; 9257699; 9263011; 9267021; 9268734; 9322534; 9325248; 9360929; 9427646; 9475352; 9560245; 9681877; 9721089; 9727492; 9740801; 9751072; 9787134; 9821419; 9835052; 9847311; 9857224; 9920849; 9927496; 9971775; 10068040; 10072505; 10090885; 10200300; 10235259; 10340403; 10462485; 10505674; 10506221; 10535980; 10542291; 10620127; 10625668; 10630977; 10671224; 10706119; 10709732; 10713117; 10799864; 10871852; 10875918; 10918185; 10978533; 11003656; 11034606; 11035039; 11036836; 11048727; 11048730; 11101867; 11101870; 11112409; 11129341; 11177389; 11193028; 11208609; 11298454; 11323689; 11418480; 11436125; 11483955; 11495919; 11550967; 11606059; 11692157; 11733515; 11771526; 11773067; 11779855; 11782802; 11786482; 11786908; 11788891; 11790791; 11809905; 11824955; 11830507; 11836578; 11857317; 11861273; 11864613; 11867183; 11877055; 11891278; 11895550; 11909874; 11920253; 11941452; 11949822; 11961305; 11965496; 11975981; 11986289; 11994542; 12021072; 12032668; 12034188; 12037669; 12040174; 12049185; 12060388; 12060768; 12064832; 12067476; 12096347; 12096925; 12098516; 12107169; 12131184; 12137598; 12139945; 12140383; 12150947; 12163388; 12169207; 12177303; 12185583; 12188927; 12196516; 12198154; 12207331; 12207908; 12220552; 12221075; 12234263; 12244143; 12270344; 12324452; 12372427; 12388693; 12393468; 12393649; 12393889; 12397013; 12414525; 12415011; 12419941; 12452031; 12455036; 12466128; 12477932; 12482410; 12482505; 12485855; 12497631; 12507389; 12513829; 12515395; 12515623; 12516573; 12557947; 12581154; 12583439; 1258673…
description: Fas cell surface death receptor
database_cross_reference: Ensembl:ENSG00000026103
database_cross_reference: HGNC:11920
database_cross_reference: HPRD:00609
database_cross_reference: MIM:134637
database_cross_reference: Vega:OTTHUMG00000018701
comment: Other designations: APO-1 cell surface antigen|CD95 antigen|Delta Fas/APO-1/CD95|FAS 827dupA|FAS receptor variant 9|FASLG receptor|Fas (TNF receptor superfamily, member 6)|Fas AMA|TNF receptor superfamily member 6|apoptosis antigen 1|apoptosis-mediating surface antigen FAS|tumor necrosis factor receptor superfamily member 6|tumor necrosis factor receptor superfamily, member 6

PTPRC
type: Class
subclass of: protein-coding gene of Homo sapiens
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: B220
alternative term: CD45
alternative term: CD45R
alternative term: GP180
alternative term: L-CA
alternative term: LCA
alternative term: LY5
alternative term: T200
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: PTPRC
full name from nomenclature authority: protein tyrosine phosphatase, receptor type, C
NCBI GeneID: 5788
NCBI LocusTag: RP11-553K8.4
gene map location: 1q31-q32
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 1
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0001915 (EC: ISS); GO_0001960 (EC: ISS); GO_0002244 (EC: IMP); GO_0002378 (EC: IMP, PMID: 1793833); GO_0004725 (EC: IDA, PMID: 2853967); GO_0005001 (EC: TAS, PMID: 2845400); GO_0005515 (EC: IPI, PMID: 10369126); GO_0005886 (EC: TAS); GO_0005887 (EC: ISS); GO_0005925 (EC: ISS); GO_0006469 (EC: IDA, PMID: 9197241); GO_0006469 (EC: ISS); GO_0006470 (EC: ISS); GO_0006933 (EC: IMP); GO_0007166 (EC: TAS, PMID: 2845400); GO_0007411 (EC: TAS); GO_0009897 (EC: IDA, PMID: 17213291); GO_0016311 (EC: ISS); GO_0019901 (EC: IPI, PMID: 14625311); GO_0030217 (EC: ISS); GO_0030890 (EC: IMP, PMID: 1793833); GO_0035335 (EC: IDA, PMID: 2853967); GO_0035335 (EC: TAS, PMID: 2845400); GO_0042100 (EC: ISS); GO_0042102 (EC: ISS); GO_0044770 (EC: IMP, PMID: 1793833); GO_0045121 (EC: IEA); GO_0045860 (EC: NAS, PMID: 15275963); GO_0048539 (EC: IMP); GO_0048864 (EC: IMP); GO_0050852 (EC: IDA, PMID: 10358156); GO_0050852 (EC: TAS); GO_0050853 (EC: ISS); GO_0050857 (EC: ISS); GO_0051209 (EC: ISS); GO_0051607 (EC: ISS); GO_0051726 (EC: ISS); GO_0070062 (EC: IDA, PMID: 12519789); GO_2000473 (EC: IMP); GO_2000648 (EC: IMP)
has PubMed association: PMID: 1355979; 1373652; 1648262; 1655467; 1680916; 1695146; 1793833; 1834739; 1970422; 1976695; 2169617; 2524382; 2531281; 2550143; 2824653; 2845400; 2853967; 2956090; 2971730; 7516335; 7526385; 7537381; 7539755; 7737297; 7961877; 8157290; 8473339; 8537410; 8557683; 8570203; 8576115; 8663450; 8703037; 8955171; 8980254; 9148925; 9197241; 9368621; 9403695; 9535845; 9573028; 9624153; 9973453; 10066810; 10228003; 10229804; 10330160; 10358156; 10369126; 10415030; 10473580; 10490978; 10683443; 10700239; 10702677; 10921916; 11101853; 11145714; 11201744; 11254687; 11369760; 11528386; 11548742; 11551930; 11564800; 11778694; 11804554; 11827988; 11841494; 11862398; 11877294; 11909961; 11975983; 11994288; 12008046; 12022705; 12028593; 12073144; 12100025; 12147336; 12354383; 12376545; 12386161; 12393728; 12430875; 12477932; 12499376; 12519755; 12519789; 12556471; 12560083; 12574355; 12589038; 12589045; 12595907; 12618866; 12626536; 12633939; 12716971; 12820694; 12864992; 12880639; 14525771; 14565647; 14625311; 14631169; 14636588; 14641523; 14684825; 14726805; 14979481; 14983037; 15014144; 15018649; 15057492; 15085197; 15214936; 15231748; 15240561; 15275963; 15302935; 15314282; 15333587; 15548260; 15584483; 15603882; 15624328; 15626731; 15684325; 15687496; 15808544; 15946252; 15960938; 15963758; 16172127; 16247487; 16269626; 16332974; 16341674; 16344560; 16360841; 16378074; 16393978; 16503409; 16505159; 16524887; 16538473; 16857986; 16955142; 16998493; 16999868; 17122895; 17172930; 17213291; 17242371; 17378731; 17524482; 17591854; 17635802; 17656643; 17692374; 17803443; 17823079; 17897956; 18029348; 18157742; 18174230; 18292296; 18312479; 18511809; 18634151; 18669861; 18680516; 18719244; 18840711; 18992193; 19059880; 19111528; 19167335; 19246294; 19332764; 19454697; 19481264; 19546439; 19585516; 19635795; 19850743; 19879912; 19898481; 20093141; 20119835; 20139978; 20156100; 20164196; 20191119; 20231690; 20309874; 20505149; 20932480; 21054833; 21067564; 21106704; 21179414; 2127823…
description: protein tyrosine phosphatase, receptor type, C
database_cross_reference: Ensembl:ENSG00000081237
database_cross_reference: HGNC:9666
database_cross_reference: HPRD:01050
database_cross_reference: MIM:151460
database_cross_reference: Vega:OTTHUMG00000035702
comment: Other designations: CD45 antigen|T200 glycoprotein|T200 leukocyte common antigen|protein tyrosine phosphatase, receptor type, c polypeptide|receptor-type tyrosine-protein phosphatase C

phenotype
type: Class
subclass of: quality
editor preferred label: phenotype
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
imported from: ogms.owl

sign
type: Class
subclass of: entity
definition: A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance.
definition: TO DO @pt
editor note: note: defined class
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:14:36Z
imported from: ontoneo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: sinal @pt

vital sign
type: Class
subclass of: sign
definition: A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
definition: TO DO @pt
definition editor: Albert Goldfain
alternative term: SSVV @pt
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:19:17Z
imported from: ontoneo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: sinal vital @pt

disease
type: Class
subclass of: disposition
subclass of: Restriction
  on property: has material basis in
  some values from: disorder
editor preferred label: disease
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: obi.owl
imported from: ogms.owl
imported from: ro.owl

disorder
type: Class
subclass of: material entity
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
imported from: ido.owl
imported from: ogms.owl

physical examination
type: Class
subclass of: health care process assay
definition: A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T11:50:18Z
imported from: ogms.owl
has OMOP concept ID: 4240345

bodily process
type: Class
subclass of: process
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:53:49Z
imported from: ogms.owl

pathological bodily process
type: Class
subclass of: bodily process
definition: A bodily process that is clinically abnormal.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:54:29Z
imported from: ogms.owl

disease course
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: disease
subclass of: biological_process
editor preferred label: disease course
definition: The totality of all processes through which a given disease instance is realized.
curator note: replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role'
imported from: obi.owl
imported from: ogms.owl

diagnosis
type: Class
subclass of: data item
editor preferred label: diagnosis
definition: The representation of a conclusion of a diagnostic process.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
imported from: ogms.owl

pathological anatomical structure
type: Class
subclass of: material entity
subclass of: Restriction
  on property: develops from
  some values from: anatomical structure
definition: An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
curator note: creation date: 2009-07-13T02:14:05Z
imported from: ogms.owl

treatment
type: Class
subclass of: planned process
definition: A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z
imported from: ogms.owl
has OMOP concept ID: 4035793
has OMOP concept ID: 4043071
has OMOP concept ID: 40492359
has OMOP concept ID: 40493226
has OMOP concept ID: 4057420
has OMOP concept ID: 4078793
has OMOP concept ID: 4107731
has OMOP concept ID: 4108705
has OMOP concept ID: 4125906
has OMOP concept ID: 4127235
has OMOP concept ID: 4146536
has OMOP concept ID: 4163708
has OMOP concept ID: 4163971
has OMOP concept ID: 4170947
has OMOP concept ID: 4181781
has OMOP concept ID: 4198190
has OMOP concept ID: 4199458
has OMOP concept ID: 4202451
has OMOP concept ID: 4216130
has OMOP concept ID: 4235738
has OMOP concept ID: 4240305
has OMOP concept ID: 4276519
has OMOP concept ID: 4293740
has OMOP concept ID: 4301346
has OMOP concept ID: 4323902
has OMOP concept ID: 4336464
has OMOP concept ID: 4337138
has OMOP concept ID: 44783196
has OMOP concept ID: 45766298

health care process
type: Class
subclass of: process
subclass of: planned process
definition: 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
definition: A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process
definition editor: Albert Goldfain
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
curator note: creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18
imported from: ogms.owl
imported from: ontoneo.owl
imported from: pdro.owl
has OMOP concept ID: 37018340
has OMOP concept ID: 4015590
has OMOP concept ID: 4015701
has OMOP concept ID: 4059978
has OMOP concept ID: 40619801
has OMOP concept ID: 40623280
has OMOP concept ID: 4073422
has OMOP concept ID: 4078199
has OMOP concept ID: 4084216
has OMOP concept ID: 4117038
has OMOP concept ID: 4127260
has OMOP concept ID: 4128031
has OMOP concept ID: 4128597
has OMOP concept ID: 4139064
has OMOP concept ID: 4139065
has OMOP concept ID: 4150970
has OMOP concept ID: 4166761
has OMOP concept ID: 4186930
has OMOP concept ID: 4197460
has OMOP concept ID: 4199276
has OMOP concept ID: 4202832
has OMOP concept ID: 4238715
has OMOP concept ID: 4275113
has OMOP concept ID: 43020419
has OMOP concept ID: 43021839
has OMOP concept ID: 4302270
has OMOP concept ID: 4311671
has OMOP concept ID: 4330583
has OMOP concept ID: 44805732

health care encounter
type: Class
subclass of: process
subclass of: planned process
subclass of: health care process
definition: 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
definition: TO DO @pt
definition editor: Albert Goldfain
alternative term: atendimento médico @pt
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
commented SPARQL query for expansion: PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX sm: <tag:stardog:api:mapping:> PREFIX turbo: <http://transformunify.org/ontologies/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> #delete { # ?hce1 a obo:OGMS_0000097 ; # turbo:TURBO_0010385 ?linkingPk ; # turbo:TURBO_0010386 ?patientPk ; # turbo:TURBO_0010388 ?omopVisitConcept1 . # ?hce2 a obo:OGMS_0000097 ; # turbo:TURBO_0010387 ?linkingPk ; # turbo:TURBO_0010388 ?omopVisitConcept2 . #} insert { graph turbo:encounterTypesLinksParticipation { ?role a obo:OBI_0000093 ; obo:RO_0000052 ?person . ?hce1 a ?encType1 ; obo:BFO_0000055 ?role . ?hce2 a ?encType2 ; obo:BFO_0000055 ?role ; obo:RO_0002090 ?hce1 . } } where { graph turbo:expanedUnlinkedEncounters { ?hce1 a obo:OGMS_0000097 ; turbo:TURBO_0010385 ?linkingPk ; turbo:TURBO_0010386 ?patientPk ; turbo:TURBO_0010388 ?omopVisitConcept1 . ?hce2 a obo:OGMS_0000097 ; turbo:TURBO_0010387 ?linkingPk ; turbo:TURBO_0010388 ?omopVisitConcept2 . } graph turbo:expanedUnlinkedPeople { ?person a obo:NCBITaxon_9606 ; turbo:TURBO_0010393 ?patientPk . } graph <https://raw.githubusercontent.com/PennTURBO/Turbo-Ontology/master/ontologies/turbo_merged.owl> { ?encType1 rdfs:subClassOf obo:OGMS_0000097 ; turbo:TURBO_0010147 ?omopVisitConcept1 . ?encType2 rdfs:subClassOf obo:OGMS_0000097 ; turbo:TURBO_0010147 ?omopVisitConcept2 . } bind(uri(concat("http://transformunify.org/ontologies/", sha1(concat(str(?person), "patient role", year(now()), month(now()), day(now()))))) as ?role) }
commented SPARQL query for expansion: PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX sm: <tag:stardog:api:mapping:> PREFIX turbo: <http://transformunify.org/ontologies/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> insert { graph turbo:expanedUnlinkedEncounters { ?hce a obo:OGMS_0000097 ; turbo:TURBO_0010385 ?prevPk ; turbo:TURBO_0010387 ?encounterPk ; turbo:TURBO_0010386 ?patientPk ; turbo:TURBO_0010388 ?omopVisitConcept . ?hceStart a obo:BFO_0000035 ; obo:RO_0002223 ?hce . ?hceStartDate a obo:IAO_0000416 ; obo:IAO_0000136 ?hceStart ; obo:IAO_0000004 ?encStartDateVal ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . turbo:expanedUnlinkedEncounters a obo:IAO_0000100 ; <http://purl.org/dc/elements/1.1/title> ?dataSetTitle . ?crid a obo:IAO_0000578 ; obo:IAO_0000219 ?hce . ?cridSymb a obo:IAO_0000577 ; obo:BFO_0000050 ?crid ; turbo:TURBO_0010094 ?syntheaVisitId ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . ?encRegDen obo:BFO_0000050 ?crid . } } where { service <http://localhost:5820/forvg/query> { graph <virtual://synthea_omop_rds> { ?subject turbo:TURBO_0000643 ?dataSetTitle . ?subject turbo:TURBO_0000645 ?encStartDateVal . ?subject turbo:TURBO_0010270 ?encRegDen . ?subject turbo:TURBO_0000648 ?syntheaVisitId . ?subject rdf:type turbo:TURBO_0010158 . ?subject turbo:TURBO_0010174 ?prevPk . ?subject turbo:TURBO_0010380 ?patientPk . ?subject turbo:TURBO_0010381 ?encounterPk . ?subject turbo:TURBO_0010382 ?omopVisitConcept . bind(uuid() as ?hce) bind(uuid() as ?hceStart) bind(uuid() as ?hceStartDate) # bind(sha1(concat("dataset", ?dataSetTitle, year(now()), month(now()), day(now()))) as ?dataset) bind(uuid() as ?crid) bind(uuid() as ?cridSymb) } } }
commented SPARQL query for expansion: PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> delete { ?hce a obo:OGMS_0000097 ; ?p ?o . } where { ?hce a obo:OGMS_0000097 ; ?p ?o . ?p rdfs:subPropertyOf <http://transformunify.org/ontologies/TURBO_0010384> }
label: consulta médica @pt

outpatient encounter
type: Class
subclass of: health care encounter
definition: TODO
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: ogms.owl
has OMOP concept ID: 9202

inpatient encounter
type: Class
subclass of: health care encounter
definition: TODO
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: ogms.owl
has OMOP concept ID: 9201

ED encounter
type: Class
subclass of: health care encounter
definition: TODO
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: ogms.owl
has OMOP concept ID: 9203

diagnostic process
type: Class
subclass of: health care process
definition: 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).
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
curator note: creation date: 2011-09-20T09:57:44Z
imported from: ogms.owl
has OMOP concept ID: 4010253
has OMOP concept ID: 4024958
has OMOP concept ID: 4037675
has OMOP concept ID: 4052083
has OMOP concept ID: 4055982
has OMOP concept ID: 4062501
has OMOP concept ID: 4064377
has OMOP concept ID: 4068785
has OMOP concept ID: 4075363
has OMOP concept ID: 4133840
has OMOP concept ID: 4150653
has OMOP concept ID: 4151422
has OMOP concept ID: 4163951
has OMOP concept ID: 4168236
has OMOP concept ID: 4240345
has OMOP concept ID: 4249893
has OMOP concept ID: 42535580
has OMOP concept ID: 4254766
has OMOP concept ID: 4302356
has OMOP concept ID: 4335825

health care process assay
type: Class
subclass of: health care process
definition: A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
imported from: ogms.owl
date: creation: 16MAY2017

prophylactic treatment
type: Class
subclass of: treatment
definition: A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.
curator note: Creation date: 2018-11-27
imported from: ogms.owl

biobank
type: Class
equivalent class: Class
  intersection of: object aggregate
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: object aggregate
      intersection of: Restriction
        on property: has part
        all values from: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: material information bearer
      intersection of: Restriction
        on property: participates in
        some values from: Class
  intersection of: Restriction
    on property: is owned by
    some values from: biobank organization
subclass of: object aggregate
definition: A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition editor: Mathias Brochhausen
definition source: definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf

biobank proper name
type: Class
equivalent class: Restriction
  on property: designates
  some values from: biobank
subclass of: identifier
definition: An identifier in natural language referring to a biobank.
definition editor: Mathias Brochhausen
alternative term: Name of biobank

biobank organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Class
    union of: Restriction
      on property: owns
      some values from: biobank
    union of: Restriction
      on property: administrates
      some values from: biobank
  intersection of: Restriction
    on property: bearer of
    some values from: legal person role
subclass of: organization
subclass of: Restriction
  on property: has organization member
  some values from: biobank contact person
definition: An organization bearing legal personality that ownes or adminstrates a biobank.
definition editor: Mathias Brochhausen
alternative term: biobank juristic person

contacting
type: Class
subclass of: planned process
definition: A planned process that involves a human being and is intended to initiate a communication with another human being.
definition: Contacting is the process of one human being starting a communication process with another human being. Contacting can be done using all modes of communication used by humans.
definition editor: Mathias Brochhausen

contact role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: contacting
subclass of: Restriction
  on property: realized in
  all values from: contacting
subclass of: Restriction
  on property: inheres_in
  all values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: is member of organization
      some values from: organization
definition: A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
definition editor: Mathias Brochhausen

biobank contact person
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: is member of organization
    some values from: biobank organization
  intersection of: Restriction
    on property: bearer of
    some values from: biobank contact role
subclass of: Homo sapiens
definition: A human being that is member of a biobank organization and bears the organization contact role.
definition editor: Mathias Brochhausen

sample collection or study aim description
type: Class
equivalent class: Class
  intersection of: textual entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: Class
        intersection of: object aggregate
        intersection of: Restriction
      union of: Restriction
        on property: is about
        some values from: Class
subclass of: textual entity
definition: A textual entity describing a study aim or a sample collection.
definition editor: Mathias Brochhausen
alternative term: Sample collection or study description

biobank contact role
type: Class
subclass of: contact role
definition: A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
definition: A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.

primary diagnosis
type: Class
subclass of: diagnosis
definition: A diagnosis that is the main reason for the inducement of medical care.
definition editor: Alice Nzinga
alternative term: main diagnosis
definition source: Hint: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

medical record
type: Class
subclass of: document
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: medical record part
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: health care encounter
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: quality
      intersection of: Restriction
        on property: quality of
        some values from: Class
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: information content entity
      intersection of: Restriction
        on property: is about
        some values from: Class
definition: A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting.
definition: TO DO @pt
definition editor: Martin Fransson
alternative term: prontuário do paciente, registro do paciente, registro médico @pt
imported from: omiabis.owl
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
comment: It is a chronological written account of examination, treatment, medical history or complaints.
comment: It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record
label: prontuário médico @pt

specimen ID
type: Class
subclass of: identifier
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: centrally registered identifier symbol
  intersection of: Restriction
    on property: is about
    some values from: specimen
definition: A proper name that identifies a specimen and is usually in form of a label included in the specimen cassette.
definition editor: Alice Nzinga
definition source: http://biospecimens.cancer.gov/resources/sops/GTEx_SOPs/II/A/GTEx%20Tissue%20Procurement%20SOP%20%28PR-0004%20v1.2.1%29.pdf

specimen donor
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: role
      intersection of: Restriction
        on property: realized in
        some values from: specimen collection process
subclass of: Homo sapiens
definition editor: Alice Nzinga
definition editor: Mathias Brochhausen
alternative term: sample donor
comment: A Homo sapiens who contributes specimen.

human health care role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: realized in
  some values from: health care encounter
definition: 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.
definition editor: William R. Hogan
alternative term: health care role
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
comment: Mathias Brochhausen

patient role
type: Class
subclass of: human health care role
subclass of: Restriction
  on property: inheres_in
  some values from: organism
definition: A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
definition: TO DO @pt
definition editor: Amanda Hicks
definition editor: Mathias Brochhausen
alternative term: patient
definition source: CAFE domain expert working group.
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
comment: 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.
label: papel de paciente @pt

health care provider role
type: Class
subclass of: human health care role
subclass of: Class
  intersection of: Restriction
    on property: inheres_in
    some values from: Class
      union of: Homo sapiens
      union of: organization
  intersection of: Restriction
    on property: inheres_in
    all values from: Class
      union of: Homo sapiens
      union of: organization
definition: 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.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
comment: William R. Hogan

collection of organisms
type: Class
subclass of: material entity
definition: An object aggregate of organisms.
imported from: The Ontology of Medically Related Social Entities
comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class.

collection of humans
type: Class
subclass of: collection of organisms
imported from: The Ontology of Medically Related Social Entities
comment: An object aggregate all of whose components are human beings.

role in human social processes
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres_in
  some values from: Class
    union of: organization
    union of: organism
subclass of: Restriction
  on property: inheres_in
  all values from: Class
    union of: organization
    union of: organism
definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
comment: Previous definition: A role played by an entity in human social processes.

human patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: inheres_in
    some values from: Homo sapiens
definition: A patient role that inheres in a human being.
definition: TO DO @pt
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: papel de paciente humano @pt

aggregate of organizations
type: Class
equivalent class: Class
  intersection of: Class
    complement of: organization
  intersection of: Restriction
    on property: is-aggregate-of
    all values from: organization
  intersection of: Restriction
    on property: is-aggregate-of
    min qualified cardinality: 2
    on class: organization
subclass of: material entity
definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
definition editor: William R. Hogan Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

legal person role
type: Class
subclass of: role in human social processes
subclass of: Class
  intersection of: Restriction
    on property: inheres_in
    some values from: Class
      union of: Homo sapiens
      union of: collection of humans
  intersection of: Restriction
    on property: inheres_in
    all values from: Class
      union of: Homo sapiens
      union of: collection of humans
definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
definition editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
imported from: The Ontology of Medically Related Social Entities
comment: 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.

OMB ethnic identity datum
type: Class
subclass of: ethnic identity datum
definition: An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

racial identity datum
type: Class
equivalent class: Class
  intersection of: identity datum
  intersection of: Restriction
    on property: is part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: racial identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: identity datum
definition: A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 0

racial identification process
type: Class
subclass of: identification process
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is part of
      some values from: racial identity datum
imported from: The Ontology of Medically Related Social Entities

ethnic identity datum
type: Class
equivalent class: Class
  intersection of: identity datum
  intersection of: Restriction
    on property: is part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: ethnic identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: identity datum
definition: An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

ethnic identification process
type: Class
subclass of: identification process
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is part of
      some values from: ethnic identity datum
imported from: The Ontology of Medically Related Social Entities

hispanic or latino identity datum
type: Class
subclass of: OMB ethnic identity datum
definition: An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 38003563

not hispanic or latino identity datum
type: Class
subclass of: OMB ethnic identity datum
definition: An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

identity datum
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: information content entity
definition: An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: The Ontology of Medically Related Social Entities
creator: Amanda Hicks

gender identity datum
type: Class
equivalent class: Class
  intersection of: identity datum
  intersection of: Restriction
    on property: is part of
    some values from: documented identity
  intersection of: Restriction
    on property: has part
    some values from: Restriction
      on property: is_specified_output_of
      some values from: gender identification process
  intersection of: Restriction
    on property: is about
    some values from: Homo sapiens
subclass of: identity datum
definition: A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: The Ontology of Medically Related Social Entities
creator: Amanda Hicks

identification process
type: Class
subclass of: social act
subclass of: planned process
imported from: The Ontology of Medically Related Social Entities
creator: Amanda Hicks

gender identification process
type: Class
subclass of: identification process
subclass of: Class
  intersection of: identification process
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is part of
      some values from: gender identity datum
imported from: The Ontology of Medically Related Social Entities

female gender identity datum
type: Class
subclass of: gender identity datum
definition: a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 8532

male gender identity datum
type: Class
subclass of: gender identity datum
definition: a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 8507

American Indian or Alaska Native identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

Asian identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 8515

black or African American identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 8516

Native Hawaiian or other Pacific Islander identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

white identity datum
type: Class
subclass of: OMB racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities
has OMOP concept ID: 8527

OMB racial identity datum
type: Class
subclass of: racial identity datum
definition: A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
definition editor: Amanda Hicks
imported from: The Ontology of Medically Related Social Entities

concentration measurment datum
type: Class
subclass of: scalar measurement datum
imported from: osci.owl
creator: Bill Duncan <http://orcid.org/0000-0001-9625-1899>
date: 2018-06-05T19:24:37Z
comment: spelling!

age
type: Class
subclass of: time
editor preferred label: age
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl

biological sex
type: Class
subclass of: organismal quality
editor preferred label: biological sex
definition: 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.
imported from: obi.owl
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0000047
in_subset: attribute slim

morphology
type: Class
subclass of: physical object quality
editor preferred label: morphology
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0000051
in_subset: attribute slim

qualitative
type: Class
subclass of: quality
imported from: ontoneo.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0000068
comment: TODO: define this or obsolete it and move children somewhere else.

deviation(from_normal)
type: Class
subclass of: qualitative
definition: A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
imported from: ontoneo.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0000069
in_subset: attribute slim

size
type: Class
subclass of: morphology
editor preferred label: size
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0000117
in_subset: attribute slim
in_subset: scalar slim

height
type: Class
subclass of: size
subclass of: 1-D extent
definition: A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
definition: TO DO @pt
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: quality
id: PATO:0000119
in_subset: attribute slim
in_subset: scalar slim
label: altura @pt

length
type: Class
subclass of: quality
editor preferred label: length
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: pato.owl

mass
type: Class
subclass of: quality
editor preferred label: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: obi.owl
imported from: pato.owl

weight
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer that has mass near a gravitational body.
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0000128
in_subset: attribute slim
in_subset: scalar slim
label: peso @pt

time
type: Class
subclass of: physical quality
editor preferred label: time
definition: A quality in which events occur in sequence.
imported from: pato.owl

female
type: Class
subclass of: phenotypic sex
editor preferred label: female
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
imported from: obi.owl
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000383
in_subset: mpath slim
in_subset: value slim

male
type: Class
subclass of: phenotypic sex
editor preferred label: male
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
imported from: obi.owl
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000384
in_subset: mpath slim
in_subset: value slim

abnormal
type: Class
subclass of: deviation(from_normal)
definition: A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
imported from: ontoneo.owl
imported from: pdro.owl
has_obo_namespace: quality
has_related_synonym: aberrant
has_related_synonym: atypia
has_related_synonym: atypical
has_related_synonym: defective
id: PATO:0000460
in_subset: abnormal slim
in_subset: mpath slim
in_subset: value slim

volume
type: Class
subclass of: 3-D extent
editor preferred label: volume
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
imported from: pato.owl

physical quality
type: Class
subclass of: physical object quality
editor preferred label: physical quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_alternative_id: PATO:0002079
database_cross_reference: Wikipedia:Physical_property
alternative_term: relational physical quality
has_obo_namespace: quality
id: PATO:0001018
in_subset: attribute slim

pressure
type: Class
subclass of: physical quality
definition: A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
definition: TO DO @pt
imported from: ontoneo.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
has_obo_namespace: quality
id: PATO:0001025
in_subset: attribute slim
label: pressão @pt

physical object quality
type: Class
subclass of: quality
subclass of: Phenotypic abnormality
editor preferred label: physical object quality
definition: A quality which inheres in a continuant.
imported from: obi.owl
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
database_cross_reference: snap:Quality
alternative_term: monadic quality of a continuant
alternative_term: multiply inhering quality of a physical entity
alternative_term: quality of a continuant
alternative_term: quality of a single physical entity
alternative_term: quality of an object
alternative_term: quality of continuant
has_narrow_synonym: monadic quality of an object
has_narrow_synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: 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.

1-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
imported from: ontoneo.owl
imported from: pdro.owl
alternative_term: 1-D size
has_obo_namespace: quality
id: PATO:0001708
in_subset: attribute slim

3-D extent
type: Class
subclass of: size
editor preferred label: 3-D extent
definition: A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
imported from: pato.owl

phenotypic sex
type: Class
subclass of: biological sex
subclass of: organismal quality
editor preferred label: phenotypic sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
imported from: obi.owl
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001894
in_subset: attribute slim

organismal quality
type: Class
subclass of: quality
subclass of: physical object quality
editor preferred label: organismal quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: obi.owl
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
has_obo_namespace: quality
id: PATO:0001995

genotypic sex
type: Class
subclass of: biological sex
definition: A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
definition: TO DO @pt
imported from: ontoneo.owl
imported from: pato.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
created by: mah
has_obo_namespace: quality
id: PATO:0020000
comment: Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, we have XY, XX, though abnormal XXY, X0, XYY, and other combinations are possible.
label: genótipo do sexo @pt

health care prescription
type: Class
subclass of: document
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: author identification
  intersection of: Restriction
    on property: has part
    some values from: document creation time identification
  intersection of: Restriction
    on property: has part
    some values from: Class
      union of: medical record identifier
      union of: patient identification
subclass of: Restriction
  on property: mentions
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: bearer of
      some values from: patient role
example of usage: "For patient: Mr Smith, should exercise for at least 30 minutes, 3 times weekly. signed Dr. Ronnie Shuz. Date: 15/11/01"
has curation status: metadata complete
definition: A document authored by a health care provider that specifies how to realize some health care process for a particular patient.
definition: Un document créé par un fournisseur de soin indiquant comment réaliser une partie d'un processus de santé pour un patient particulier. @fr
imported from: pdro.owl
has synonym: prescription
label: prescription de santé @fr

prescriber identification
type: Class
subclass of: written name
has curation status: metadata incomplete
definition: An author identification where the author is a particular health care provider and the document authored is a prescription.
definition: Une identification d'auteur où l'auteur est un fournisseur de soins particulier et le document en question est une prescription. @fr
imported from: pdro.owl
label: identification de prescripteur @fr

patient identification
type: Class
subclass of: written name
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: complete personal name
    union of: health insurance identifier
subclass of: Restriction
  on property: denotes
  qualified cardinality: 1
  on class: patient
has curation status: metadata incomplete
definition: A written name denoting a particular patient.
definition: Un nom écrit faisant référence à un patient particulier. @fr
imported from: pdro.owl
label: identification d'un patient @fr

document creation time identification
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: denotes
  some values from: one-dimensional temporal region
has curation status: metadata incomplete
definition: A textual entity that denotes the time of document creation.
definition: Une entité textuelle indiquant l'instant de création d'un document. @fr
imported from: pdro.owl
elucidation: the granular time at which the author considers the document whole, ie ready for interpretation
label: identification de l'instant de création d'un document @fr

drug prescription
type: Class
subclass of: health care prescription
subclass of: Restriction
  on property: has part
  some values from: prescriber identification
subclass of: Restriction
  on property: has part
  some values from: drug prescription item
example of usage: "Prescription for John Smith : Ativan 2mg tablets, take 1 tablet twice daily by mouth as needed if anxious, dispense 60 tablets, renew 12 times. Signed by Dr Hazard. Date: 15/10/29"
has curation status: metadata complete
definition: A health care prescription specifying the initiation, modification or cessation of a drug administration.
definition: Une ordonnance indiquant une initiation, modification ou arrêt de l'administration de médicaments. @fr
imported from: pdro.owl
comment: There are prescription "order names" like "wheelchair" in PDS and upstream sources that clearly do not denote a drug. So it may be more appropriator for Drivetrain to instantiate PDRO_0000001, 'health care prescription'
label: prescription de médicaments @fr

drug prescription item
type: Class
subclass of: directive information content entity
example of usage: 'Aspirin 81 mg tablet PO DIE 12 x 30 tablets (stroke prevention)' 'Cease metoprolol and aspirin' 'Aspirin 81 mg PO DIE 12 x 30 tablets' on a first prescription for Mr. Fiennes on 2018/01/01. 'Aspirin 81 mg per mouth once a day, 6x2 months' on a second prescription for Mr. Fiennes on 2019/01/01. 'Aspirin 325 mg PO die, 12x1 months' on a third prescription for Mr. Fiennes on 2019/03/01. 'Cease Aspirin' on a fourth prescription for Mr. Fiennes on 2019/04/01.
definition: A directive information entity that is a part of a drug prescription and specifies some action(s) related to one or several drugs. It is intended to direct some actions to be performed by a patient and some pharmacist(s). It may also specify a healthcare objective.
imported from: pdro.owl

protein
type: Class
equivalent class: Class
  intersection of: amino acid chain
  intersection of: Restriction
    on property: output_of
    some values from: translation
subclass of: peptide
subclass of: amino acid chain
subclass of: Restriction
  on property: output_of
  some values from: translation
editor preferred label: protein
example of usage: antithrombin III is a protein
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
imported from: obi.owl
imported from: pr.owl
has_obo_namespace: protein
id: PR:000000001
comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].

receptor-type tyrosine-protein phosphatase C
type: Class
subclass of: protein
definition: A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule.
imported from: pr.owl
has_broad_synonym: T200
database_cross_reference: IUPHARobj:1852
database_cross_reference: PIRSF:PIRSF002004
alternative_term: CD45
alternative_term: L-CA
alternative_term: PTPRC
alternative_term: leukocyte common antigen
alternative_term: ly-5
alternative_term: lymphocyte antigen 5
has_obo_namespace: protein
id: PR:000001006
comment: Category=gene. Requested by=CL.

tumor necrosis factor receptor superfamily member 6
type: Class
subclass of: protein
definition: A protein that is a translation product of the human FAS gene or a 1:1 ortholog thereof.
imported from: pr.owl
has_alternative_id: PR:000002232
database_cross_reference: IUPHARobj:1875
database_cross_reference: PIRSF:PIRSF038809
alternative_term: CD95
alternative_term: FAS
alternative_term: FASLG receptor
alternative_term: apo-1 antigen
alternative_term: apoptosis-mediating surface antigen FAS
has_obo_namespace: protein
has_related_synonym: APT1
has_related_synonym: FAS1
has_related_synonym: TNFRSF6
id: PR:000001962
comment: Category=gene.

amino acid chain
type: Class
subclass of: organic amino compound
subclass of: Restriction
  on property: has part
  some values from: amino-acid residue
definition: An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
imported from: pr.owl
has_narrow_synonym: peptide
has_narrow_synonym: polypeptide
has_obo_namespace: protein
id: PR:000018263
comment: Category=external.

system
type: Class
subclass of: material entity
definition: A material entity consisting of multiple components that are causally integrated.
editor note: May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
definition editor: Chris Mungall
definition source: http://www.jbiomedsem.com/content/4/1/43
imported from: ro.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: 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.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: obi.owl
imported from: so.owl

sequence_feature
type: Class
subclass of: sequence feature or set
subclass of: Restriction
  on property: has_sequence
  some values from: biological sequence
subclass of: Restriction
  on property: has_location
  some values from: sequence feature location
definition: Any extent of continuous biological sequence.
editor note: GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
imported from: geno.owl
comment: A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.

genome
type: Class
subclass of: genomic feature set
subclass of: Restriction
  on property: in taxon
  some values from: organism
definition: A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)
editor note: Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence.
alternative term: 'genome sequence'
imported from: geno.owl
comment: A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.

loss_of_function_variant
type: Class
subclass of: genomic feature
definition: A sequence variant whereby the gene product has diminished or abolished function.
imported from: so.owl
created by: kareneilbeck
creation date: 2015-05-14T11:21:29Z
alternative_term: loss of function variant
has_obo_namespace: sequence
id: SO:0002054

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: uberon.owl
database_cross_reference: AnatomicalStructure
database_cross_reference: http://www.snomedbrowser.com/Codes/Details/362889002
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FBbt:00007001
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:D000825
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
alternative_term: biological structure
alternative_term: connected biological structure
has_obo_namespace: uberon
id: UBERON:0000061
in_subset: upper level

life cycle stage
type: Class
subclass of: biological_process
editor preferred label: life cycle stage
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
editor note: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
imported from: obi.owl
imported from: uberon.owl
external_ontology_notes: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
external_ontology_notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
database_cross_reference: BILS:0000105
database_cross_reference: EFO:0000399
database_cross_reference: FBdv:00007012
database_cross_reference: FMA:24120
database_cross_reference: HsapDv:0000000
database_cross_reference: MmusDv:0000000
database_cross_reference: OlatDv:0000010
database_cross_reference: PdumDv:0000090
database_cross_reference: WBls:0000002
database_cross_reference: XAO:1000000
database_cross_reference: ZFS:0000000
database_cross_reference: ZFS:0100000
database_cross_reference: ncithesaurus:Developmental_Stage
has_narrow_synonym: developmental stage
has_narrow_synonym: stage
has_obo_namespace: uberon
id: UBERON:0000105
in_subset: efo slim
in_subset: upper level

blood
type: Class
subclass of: organism substance
editor preferred label: blood
definition: A fluid that is composed of blood plasma and erythrocytes.
imported from: obi.owl
imported from: uberon.owl

breast
type: Class
subclass of: material anatomical entity
editor preferred label: breast
definition: The upper ventral region of the torso of an organism.
imported from: uberon.owl

organism substance
type: Class
subclass of: material anatomical entity
editor preferred label: organism substance
definition: 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.
imported from: obi.owl
imported from: uberon.owl

material anatomical entity
type: Class
subclass of: material entity
editor preferred label: material anatomical entity
definition: Anatomical entity that has mass.
imported from: obi.owl
imported from: uberon.owl
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FBbt:00007016
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in_subset: upper level

anatomical cluster
type: Class
subclass of: material entity
editor preferred label: anatomical cluster
definition: Anatomical group that has its parts adjacent to one another.
imported from: obi.owl
imported from: uberon.owl

tissue
type: Class
subclass of: material anatomical entity
editor preferred label: tissue
definition: 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.
imported from: obi.owl
imported from: uberon.owl

adipose tissue
type: Class
subclass of: tissue
editor preferred label: adipose tissue
definition: Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
imported from: uberon.owl

urine
type: Class
subclass of: material anatomical entity
definition: Excretion that is the output of a kidney
imported from: uberon.owl
taxon_notes: kidney excreta from some taxa (e.g. in aves) may not be liquid
database_cross_reference: Urine
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0042036
database_cross_reference: BTO:0001419
database_cross_reference: CALOHA:TS-1092
database_cross_reference: EFO:0001939
database_cross_reference: EMAPA:36554
database_cross_reference: ENVO:00002047
database_cross_reference: FMA:12274
database_cross_reference: GAID:1189
database_cross_reference: MA:0002545
database_cross_reference: MAT:0000058
database_cross_reference: MESH:D014556
database_cross_reference: MIAA:0000058
database_cross_reference: NCIT:C13283
database_cross_reference: OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA
database_cross_reference: UMLS:C0042036
database_cross_reference: galen:Urine
has_obo_namespace: uberon
id: UBERON:0001088
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim

skeletal muscle tissue
type: Class
subclass of: tissue
editor preferred label: skeletal muscle tissue
definition: Muscle tissue that consists primarily of skeletal muscle fibers.
imported from: obi.owl
imported from: uberon.owl

blood plasma
type: Class
subclass of: material anatomical entity
definition: The liquid component of blood, in which erythrocytes are suspended.
imported from: uberon.owl
has_broad_synonym: plasma
has_broad_synonym: portion of plasma
database_cross_reference: Blood plasma
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0032105
database_cross_reference: BTO:0000131
database_cross_reference: CALOHA:TS-0800
database_cross_reference: EFO:0001905
database_cross_reference: EMAPA:35690
database_cross_reference: FMA:62970
database_cross_reference: GAID:1178
database_cross_reference: MA:0002501
database_cross_reference: MAT:0000052
database_cross_reference: MESH:D010949
database_cross_reference: MIAA:0000052
database_cross_reference: NCIT:C13356
database_cross_reference: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
database_cross_reference: UMLS:C0032105
alternative_term: blood plasm
alternative_term: portion of blood plasma
has_obo_namespace: uberon
id: UBERON:0001969
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim

blood serum
type: Class
subclass of: material anatomical entity
definition: The portion of blood plasma that excludes clotting factors.
imported from: uberon.owl
database_cross_reference: Serum (blood)
database_cross_reference: http://linkedlifedata.com/resource/umls/id/C0229671
database_cross_reference: BTO:0000133
database_cross_reference: BTO:0001239
database_cross_reference: CALOHA:TS-0923
database_cross_reference: EHDAA2:0004728
database_cross_reference: EMAPA:35770
database_cross_reference: FMA:63083
database_cross_reference: MA:0002502
database_cross_reference: NCIT:C13325
database_cross_reference: UMLS:C0229671
alternative_term: serum
has_obo_namespace: uberon
id: UBERON:0001977
in_subset: pheno slim
in_subset: uberon slim

prostate gland
type: Class
subclass of: material anatomical entity
editor preferred label: prostate gland
definition: The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
imported from: uberon.owl

neonate stage
type: Class
equivalent class: Restriction
  on property: neonate stage OTR NTR
  some values from: neonate temporal region
subclass of: life cycle stage
definition: Of or pertaining to the period of time immediately following birth, or to the newborn.
editor note: consider splitting infant/newborn
imported from: uberon.owl
database_cross_reference: Infant
database_cross_reference: Category:Infant organism
database_cross_reference: Category:Newborn organism
database_cross_reference: BTO:0001762
database_cross_reference: EV:0300037
database_cross_reference: HsapDv:0000082
database_cross_reference: MmusDv:0000096
database_cross_reference: NIF_Organism:birnlex_695
database_cross_reference: OGES:000025
alternative_term: neonatal stage
has_narrow_synonym: fledgling stage
has_narrow_synonym: hatchling
has_narrow_synonym: hatchling stage
has_narrow_synonym: infant stage
has_narrow_synonym: nestling stage
has_narrow_synonym: pouch stage
has_narrow_synonym: puggle
has_narrow_synonym: puggle stage
has_obo_namespace: uberon
has_related_synonym: newborn stage
id: UBERON:0007221

life cycle temporal boundary
type: Class
subclass of: process boundary
definition: A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
imported from: uberon.owl
has_obo_namespace: uberon
id: UBERON:0035943
in_subset: upper level

start of neonate stage
type: Class
equivalent class: Restriction
  on property: starts
  some values from: neonate stage
equivalent class: Restriction
  on property: SNS OTR birth instant
  some values from: birth instant
equivalent class: Restriction
  on property: SNS starts neonate stage
  some values from: neonate stage
subclass of: life cycle temporal boundary
definition: A life cycle temporal boundary that marks the start of the neonate stage of the organism.
alternative term: SNS
alternative term: birth
imported from: uberon.owl
alternative_term: moment of birth
alternative_term: time of birth
has_obo_namespace: uberon
has_related_synonym: birth
id: UBERON:0035946

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: obi.owl
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: obi.owl
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: uo.owl

temperature unit
type: Class
subclass of: measurement unit label
definition: A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
imported from: uo.owl
created by: george gkoutos
has_alternative_id: UO:0000126
alternative_term: temperature derived unit
has_obo_namespace: unit.ontology
id: UO:0000005
in_subset: unit group slim

kilogram
type: Class
subclass of: mass unit
type: NamedIndividual
type: mass unit
has OMOP concept ID: 9529
in_subset: unit slim
alternative_term: kg
id: UO:0000009
definition: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
created by: george gkoutos
has_obo_namespace: unit.ontology

centimeter
type: Class
subclass of: length unit
type: NamedIndividual
type: length unit
has_obo_namespace: unit.ontology
alternative_term: cm
id: UO:0000015
alternative_term: centimetre
has OMOP concept ID: 8582
in_subset: unit slim
definition: A length unit which is equal to one hundredth of a meter or 10^[-2] m.
created by: george gkoutos

millimeter
type: Class
subclass of: length unit
type: NamedIndividual
type: length unit
alternative_term: micrometre
definition: A length unit which is equal to one thousandth of a meter or 10^[-3] m.
in_subset: unit slim
alternative_term: mm
id: UO:0000016
has OMOP concept ID: 8588
has_obo_namespace: unit.ontology
created by: george gkoutos

picogram
type: Class
subclass of: mass unit
type: NamedIndividual
type: mass unit
id: UO:0000025
in_subset: unit slim
has OMOP concept ID: 8564
definition: A mass unit which is equal to 10^[-12] g.
has_obo_namespace: unit.ontology
created by: george gkoutos
alternative_term: pg

degree Celsius
type: Class
subclass of: temperature unit
definition: A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
imported from: uo.owl
has OMOP concept ID: 586323
created by: george gkoutos
alternative_term: C
has_obo_namespace: unit.ontology
id: UO:0000027
in_subset: unit slim

concentration unit
type: Class
subclass of: measurement unit label
editor preferred label: concentration unit
definition: A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
imported from: obi.owl
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000051
in_subset: unit group slim

area density unit
type: Class
subclass of: density unit
definition: A density unit which is a standard measure of the mass exerting an influence on a given area.
imported from: uo.owl
created by: george gkoutos
alternative_term: mass per unit area unit
has_obo_namespace: unit.ontology
id: UO:0000054
in_subset: unit group slim

unit of molarity
type: Class
subclass of: concentration unit
definition: A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution.
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000061
in_subset: unit group slim

millimolar
type: Class
subclass of: unit of molarity
type: NamedIndividual
type: concentration unit
alternative term: millimole per liter
has_obo_namespace: unit.ontology
has OMOP concept ID: 8753
in_subset: unit slim
definition: A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
id: UO:0000063
alternative_term: mM
alternative term: mM
created by: george gkoutos
editor preferred label: millimolar
imported from: uo.owl

kilogram per square meter
type: Class
subclass of: area density unit
type: NamedIndividual
type: area density unit
IAO_0000115: An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared.
has OBO namespace: unit.ontology
created by: george gkoutos
has OMOP concept ID: 9531
has exact synonym: kilogram per square metre
has exact synonym: Body Mass Index (BMI)
id: UO:0000086
has exact synonym: kg/m^[2]
in subset: unit slim

volume unit
type: Class
subclass of: measurement unit label
editor preferred label: volume unit
definition: A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000095
in_subset: unit group slim

femtoliter
type: Class
subclass of: volume unit
definition: A volume unit which is equal to 10^[-15] L.
imported from: uo.owl
has OMOP concept ID: 8583
created by: george gkoutos
alternative_term: femtolitre
alternative_term: fl
has_obo_namespace: unit.ontology
id: UO:0000104
in_subset: unit slim

pressure unit
type: Class
subclass of: measurement unit label
definition: A unit which is a standard measure of the force applied to a given area.
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000109
in_subset: unit group slim

unit per volume unit
type: Class
subclass of: concentration unit
definition: A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution.
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000177

unit per liter
type: Class
subclass of: unit per volume unit
definition: A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter.
alternative term: U/L
alternative term: [U]/L
has OMOP concept ID: 8645
created by: george gkoutos
alternative_term: U/l
alternative_term: unit per litre
has_obo_namespace: unit.ontology
id: UO:0000179

density unit
type: Class
subclass of: measurement unit label
definition: A unit which is a standard measure of the influence exerted by some mass.
imported from: uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000182
in_subset: unit group slim

percent
type: Class
subclass of: concentration unit
type: NamedIndividual
type: concentration unit
IAO_0000115: A dimensionless ratio unit which denotes numbers as fractions of 100.
id: UO:0000187
comment: MAM manually copied class definition from UO, change from a class definition with a superclass to a named individual definition with a type, and pasted into TURBO ontology
in subset: unit group slim
has OBO namespace: unit.ontology
has OMOP concept ID: 8554
created by: george gkoutos
has exact synonym: %

pH
type: Class
subclass of: concentration unit
type: NamedIndividual
type: concentration unit
has OMOP concept ID: 8482
imported from: uo.owl
definition: A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
editor preferred label: pH

gram per deciliter
type: Class
subclass of: concentration unit
type: NamedIndividual
type: concentration unit
alternative_term: g/dl
id: UO:0000208
in_subset: unit slim
has_obo_namespace: unit.ontology
editor preferred label: gram per deciliter
has OMOP concept ID: 8713
created by: george gkoutos
alternative_term: gram per decilitre
imported from: uo.owl
definition: A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
alternative term: g/dl

millimetres of mercury
type: Class
subclass of: pressure unit
type: NamedIndividual
type: pressure unit
definition: A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
id: UO:0000272
alternative_term: mmHg
alternative term: mmHg
alternative_term: millimeters of mercury
imported from: uo.owl
has_obo_namespace: unit.ontology
created by: george gkoutos
in_subset: unit slim
has OMOP concept ID: 8876

nanogram per milliliter
type: Class
subclass of: concentration unit
type: NamedIndividual
type: concentration unit
has OMOP concept ID: 8842
created by: George Gkoutos
alternative_term: ng/ml
alternative_term: nanogram per millilitre
definition: A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters.
has_obo_namespace: unit.ontology
in_subset: unit slim
creation date: 2011-03-21T10:55:12Z
id: UO:0000275

blood pressure
type: Class
equivalent class: Class
  intersection of: pressure
  intersection of: Restriction
    on property: towards
    some values from: Wall of blood vessel
  intersection of: Restriction
    on property: inheres_in
    all values from: Class
      intersection of: Portion of blood
      intersection of: Restriction
        on property: participates in
        some values from: blood circulation
subclass of: vital sign
subclass of: pressure
editor preferred label: blood pressure
definition: The pressure exerted by circulating blood on the walls of blood vessels.
editor note: Unless otherwise specified, a clinical report of a blood pressure is systolic left ventricular pressure over diastolic left ventricular pressure.
definition editor: Albert Goldfain
alternative term: PA, pressão sanguínea @pt
definition source: http://en.wikipedia.org/wiki/Blood_pressure
imported from: ontoneo.owl
label: pressão arterial @pt

blood pressure measurement datum
type: Class
equivalent class: Restriction
  on property: is quality measurement of
  some values from: blood pressure
subclass of: scalar measurement datum
subclass of: measurement datum
alternative term: valor da pressão arterial @pt
imported from: ontoneo.owl
label: pressão arterial medida @pt

blood pressure measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: blood pressure measurement datum
subclass of: planned process
comment: this was pasted into the turbo ontology. remove, and reimplement as an ontofox import

cardiac cycle phase
type: Class
subclass of: process
editor note: These phases belong in some OBO foundry ontology of cardiac physiology. Should include the subprocesses of systole and diastole as illustrated here http://en.wikipedia.org/wiki/Cardiac_cycle .
imported from: ontoneo.owl
label: fase do ciclo cardíaco @pt

diastole
type: Class
subclass of: cardiac cycle phase
definition: The phase of the cardiac cycle in which the heart fills with blood.
imported from: ontoneo.owl
label: diástole @pt

diastolic blood pressure
type: Class
equivalent class: Class
  intersection of: blood pressure
  intersection of: Restriction
    on property: exists during
    some values from: diastole
subclass of: blood pressure
definition: The blood pressure during diastole.
alternative term: Pad, pressão sanguínea diastólica @pt
imported from: ontoneo.owl
label: pressão arterial diastólica @pt

systole
type: Class
subclass of: cardiac cycle phase
definition: The phase of the cardiac cycle in which the heart contracts.
imported from: ontoneo.owl
label: sístole @pt

systolic blood pressure
type: Class
equivalent class: Class
  intersection of: blood pressure
  intersection of: Restriction
    on property: exists during
    some values from: systole
subclass of: blood pressure
definition: The blood pressure during systole.
alternative term: Pas, pressão sanguínea sistólica @pt
imported from: ontoneo.owl
label: pressão arterial sistólica @pt

medical record part
type: Class
subclass of: Class
  intersection of: document part
  intersection of: Restriction
    on property: is part of
    some values from: medical record
definition editor: PERSON: Fernanda Farinelli
imported from: ontoneo.owl
imported from: pdro.owl
translated to Portuguese by: PERSON: Fernanda Farinelli
label: seção do prontuário médico @pt

registry denoter
type: Class
subclass of: data item
definition: a data item that denotes a centrally registered identifier registry
creator: Mark Miller
date: 2018-07-25T13:26:46Z

racial identity registry
type: Class
subclass of: centrally registered identifier registry
definition: a centrally registered identifier registry that serves as a controlled vocabulary for racial identity datums
creator: Mark Miller
date: 2018-07-25T13:30:25Z

racial identity CRID symbol
type: Class
subclass of: centrally registered identifier symbol
definition: the (string value) symbol part of a racial identity CRID
creator: Mark Miller
date: 2018-07-25T13:34:36Z

gene identifier registry
type: Class
subclass of: centrally registered identifier registry

biobank consenter
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: Class
      intersection of: consenter role
      intersection of: Restriction
        on property: realized in
        some values from: Class
subclass of: Homo sapiens
editor preferred label: biobank consenter
definition: a human that participates, along with a biobanking organization or one of its representatives, in a consenting process that has a (permission role? Fully signed consent document?) as its output
definition editor: Mark A. Miller
alternative term: biobank participant
definition source: Mark A. Miller/TURBO team
comment: As of July 2018, the one thing that holds true of all people modeled in the TURBO graph is that they have participated in a consent process in which a representative of the Penn Medicine Biobank also participated This concept of a consenter is currently under discussion by ICO representatives

biobank consenter CRID
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: biobank consenter CRID symbol
  intersection of: Restriction
    on property: has part
    some values from: patient registry denoter
  intersection of: Restriction
    on property: denotes
    some values from: biobank consenter
subclass of: CRID
subclass of: Restriction
  on property: denotes
  some values from: biobank consenter
editor preferred label: patient CRID
definition: a centrally registered identifier that denotes a biobank consenter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:06:07Z

biobank consenter CRID symbol
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: patient symbol
definition: the (string value) symbol part of a biobank consenter CRID
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:08:01Z

patient registry denoter
type: Class
equivalent class: Restriction
  on property: denotes
  some values from: patient identifier registry
subclass of: registry denoter
editor preferred label: patient registry denoter
definition: a (string) denoter that denotes a psatient identifier registry instance
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:16:34Z

patient identifier registry
type: Class
subclass of: centrally registered identifier registry
editor preferred label: patient identifier registry
definition: a dataset of identifiers (specifically the symbol parts) that denote people with patient roles. These may be patients whose data appears in a health care system's (electronic) medical records.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:15:30Z

genetic race determination process
type: Class
subclass of: planned process
definition: a planned process that uses genetic data to determine the population or populations to which a person belongs has participant: some person has input some genomic data has output: genetic population background datum parts of the process: sample collection DNA extraction sequencing data transformation
definition editor: Mark A. Miller

health care encounter CRID
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: health care encounter CRID symbol
  intersection of: Restriction
    on property: has part
    some values from: health care encounter registry denoter
  intersection of: Restriction
    on property: denotes
    some values from: health care encounter
subclass of: CRID
editor preferred label: health care encounter CRID
definition: a centrally registered identifier that denotes a health care encounter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:39:29Z

health care encounter CRID symbol
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: health care encounter symbol
definition: the (string value) symbol part of a health care encounter CRID
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:45:42Z

health care encounter registry denoter
type: Class
equivalent class: Restriction
  on property: denotes
  some values from: health care encounter identifier registry
subclass of: registry denoter
editor preferred label: health care encounter registry denoter
definition: a (string) denoter that denotes a health care encounter identifier registry instance
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:42:30Z

health care encounter start
type: Class
equivalent class: Restriction
  on property: starts
  some values from: health care encounter
subclass of: process boundary
editor preferred label: health care encounter start
definition: A process boundary that starts a health care encounter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T20:54:26Z

health care encounter start date
type: Class
equivalent class: Class
  intersection of: process start time measurement
  intersection of: Restriction
    on property: is about
    some values from: Restriction
      on property: starts
      some values from: health care encounter
subclass of: process start time measurement
editor preferred label: health care encounter start date
definition: a process start time measurement about the temporal boundary that starts a health care encounter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:00:18Z

health care encounter identifier registry
type: Class
subclass of: centrally registered identifier registry
editor preferred label: health care encounter identifier registry
definition: a dataset of identifiers (specifically the symbol parts) that denote health care encounters
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:44:09Z

R2R instantiation
type: Class
subclass of: data transformation
editor preferred label: R2R instantiation
definition: a data transformation in which data are consumed from tabular or relational sources and written back out in a semantic/RDF format
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: underdefined

biobank encounter
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_participant
  some values from: biobank organization
subclass of: Restriction
  on property: has_participant
  some values from: biobank consenter
editor preferred label: biobank encounter
definition: a planned process in which the following two kinds of people participate: a representative from a biobank and someone with a participant under investigation role or a donor role or a consenter role The output of this process could be demographic or vital statistics data items, like height or weight; case forms, consent documetns, etc.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-09T14:33:02Z

process start time measurement
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: process
editor preferred label: process start time measurement
example of usage: I began collecting stamps at noon, EST on January 1st, 1980. This is the start time measurement of my stamp collecting process.
definition: A time measurement datum that is the measure of the time when some process started
definition editor: Mark A. Miller
definition source: based on OBI_0001619 from Chris Stoeckert and Jie Zheng
date: 2017-04-12T14:00:00-05:00

biobank encounter start
type: Class
equivalent class: Restriction
  on property: starts
  some values from: biobank encounter
subclass of: process boundary
editor preferred label: biobank encounter start
definition: A process boundary that starts a biobank encounter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:11:04Z

biobank encounter start date
type: Class
subclass of: process start time measurement
editor preferred label: biobank encounter start date
definition: a process start time measurement about the temporal boundary that starts a biobank encounter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:01:45Z

biobank encounter CRID
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: biobank encounter CRID symbol
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: biobank encounter registry denoter
      intersection of: Restriction
        on property: denotes
        some values from: biobank encounter identifier registry
subclass of: CRID
subclass of: Restriction
  on property: denotes
  some values from: biobank encounter
editor preferred label: biobank encounter CRID
definition: a centrally registered identifier that denotes a biobank encounter
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:46:47Z

biobank encounter CRID symbol
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: biobank encounter symbol
definition: the (string value) symbol part of a biobank encounter CRID
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:47:32Z

biobank encounter registry denoter
type: Class
equivalent class: Restriction
  on property: denotes
  some values from: biobank encounter identifier registry
subclass of: registry denoter
editor preferred label: biobank encounter registry denoter
definition: a (string) denoter that denotes a biobank encounter identifier registry instance
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:48:11Z

biobank encounter identifier registry
type: Class
subclass of: centrally registered identifier registry
editor preferred label: biobank encounter identifier registry
definition: a dataset of identifiers (specifically the symbol parts) that denote biobank encounters
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:49:41Z

diagnosis CRID
type: Class
subclass of: CRID
editor preferred label: diagnosis CRID
definition: A centrally registered identifier that is about some diagnosis, billing code, etc. Consists of two parts: a registry denoter string that points to a particular disease coding registry, and a symbol string like "J123.5" that points to a particular disease within that registry.
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: If the turbo shortcut expansion method comes across either an isolated diagnosis code shortcut or an isolated diagnosis code registry URI shortcut, an exception should be thrown (because incomplete diagnosis CRIDs are worse than absent diagnosis CRIDs?)

diagnosis code CRID symbol
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: diagnosis code symbol
definition: the (string value) symbol part of a diagnosis CRID
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
comment: might be a billing or diagnosis code... something like an ICD9 or ICD10 code

diagnosis code registry denoter
type: Class
subclass of: registry denoter
editor preferred label: diagnosis code registry denoter
definition: A proper name string that denotes a diagnosis code/billing code registry such as ICD-9, having an URI like <http://purl.obolibrary.org/obo/NCIT_C71890>
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

diagnosis code registry
type: Class
subclass of: centrally registered identifier registry
editor preferred label: diagnosis code registry
definition: a dataset of identifiers (specifically the symbol parts) that denote diagnoses or billing codes, like those from the International Classification of Diseases
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-25T19:39:55Z

prescription CRID
type: Class
subclass of: CRID
editor preferred label: prescription CRID
definition: a centrally registered identifier that denotes a prescription
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-27T21:30:44Z
comment: at least for Penn Medicine Biobank data, it may be more appropriate to denote prescriptions (And possibly other classes) with a (yet-to-be modeled) prescription primary key

prescription CRID symbol
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: prescription CRID symbol
definition: the (string value) symbol part of a prescription CRID
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-27T21:31:30Z

prescription registry denoter
type: Class
subclass of: registry denoter
editor preferred label: prescription registry denoter
definition: a (string) denoter that denotes a prescription registry instance
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-27T21:32:06Z

prescription registry
type: Class
subclass of: centrally registered identifier registry
editor preferred label: prescription registry
definition: a dataset of identifiers (specifically the symbol parts) that denote prescriptions
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-02-27T21:37:11Z

genotype identifier registry
type: Class
subclass of: centrally registered identifier registry
editor preferred label: genotype identifier registry
definition: a dataset of identifiers (specifically the symbol parts) that denote samples intended as input into a genotyping process, and or the derived genotyping data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:27:10Z

genotype CRID
type: Class
subclass of: CRID
editor preferred label: genotype CRID
definition: a centrally registered identifier that denotes a sample intended as input into a genotyping process, and or the derived genotyping data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:54:15Z

genotype identifier registry denoter
type: Class
subclass of: registry denoter
editor preferred label: genotype identifier registry denoter
definition: a (string) denoter that denotes a genotype identifier registry instance
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:55:00Z

genotype CRID symbol
type: Class
subclass of: centrally registered identifier symbol
editor preferred label: genotype CRID symbol
definition: the (string value) symbol part of a genotype CRID
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:56:01Z

zygosity value specification
type: Class
subclass of: categorical value specification
editor preferred label: zygosity value specification
definition: a value specification that indicates whether a diploid individual is homozygous wild type (0) heterozygous (1) or homozygous (2) for some mutant
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-09T19:30:07Z

loss of function zygosity value specification
type: Class
subclass of: zygosity value specification
editor preferred label: loss of function zygosity value specification
definition: a zygosity value specification about the number of alleles of a gene that are believed to be non-functional (over specified… use zygosity value specification and bind the loss of function objective to the assay?)
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-09T19:31:31Z

retired placeholder for biobank consenter
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank consenter
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:21:52Z
retires: biobank consenter

retired placeholder for biobank consenter CRID
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank consenter CRID
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter CRID'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:27:36Z
retires: biobank consenter CRID

retired placeholder for biobank consenter symbol
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank consenter symbol
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter symbol'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:28:21Z
retires: biobank consenter CRID symbol

retired placeholder for biobank consenter registry denoter
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank consenter registry denoter
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter registry denoter'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:33:51Z
retires: patient registry denoter

retired placeholder for biobank consenter identifier registry
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank consenter identifier registry
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter identifier registry'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-25T16:47:49Z
retires: patient identifier registry

retired placeholder for health care encounter
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:37:32Z
retires: health care encounter

retired placeholder for health care encounter CRID
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter CRID
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter CRID'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:53:16Z
retires: health care encounter CRID

retired placeholder for health care encounter symbol
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter symbol
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter symbol'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T21:56:01Z
retires: health care encounter CRID symbol

retired placeholder for health care encounter registry denoter
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter registry denoter
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter registry denoter'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-16T22:09:18Z
retires: health care encounter registry denoter

retired placeholder for health care encounter start
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter start
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter start'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T20:57:47Z
retires: health care encounter start

retired placeholder for health care encounter start date
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter start date
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter start date'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:02:58Z
retires: health care encounter start date

retired placeholder for health care encounter identifier registry
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for health care encounter identifier registry
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter identifier registry'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-25T16:54:15Z
retires: health care encounter identifier registry

retired placeholder for biobank encounter
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-25T17:18:08Z
retires: biobank encounter

retired placeholder for biobank encounter start
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter start
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter start'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:12:32Z
retires: biobank encounter start

retired placeholder for biobank encounter start date
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter start date
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter start date'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:08:37Z
retires: biobank encounter start date

retired placeholder for biobank encounter CRID
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter CRID
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter CRID'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:53:55Z
retires: biobank encounter CRID

retired placeholder for biobank encounter symbol
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter symbol
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter symbol'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:54:46Z
retires: biobank encounter CRID symbol

retired placeholder for biobank encounter registry denoter
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter registry denoter
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter registry denoter'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-25T19:20:03Z
retires: biobank encounter registry denoter

retired placeholder for biobank encounter identifier registry
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biobank encounter identifier registry
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter identifier registry'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-18T21:55:23Z
retires: biobank encounter identifier registry

retired placeholder for neonate life stage
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for neonate life stage
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'neonate life stage'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
retires: neonate stage

patient MRN registry
type: Class
subclass of: patient identifier registry
editor preferred label: patient MRN registry
definition: a patient identifier registry in which the symbols correspond to medical record numbers
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T15:08:47Z

ENCOUNTER_PACK_ID biobank encounter registry
type: Class
subclass of: biobank encounter identifier registry
editor preferred label: ENCOUNTER_PACK_ID biobank encounter registry
definition: a patient identifier registry in which the symbols correspond to (biobank?) encounter packet identifiers
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-30T15:26:31Z

racial identity CRID
type: Class
subclass of: CRID
definition: a centrally registered identifier that denotes a racial identity
creator: Mark Miller
date: 2018-07-25T13:37:14Z

racial identity registry denoter
type: Class
subclass of: registry denoter
creator: Mark Miller
date: 2018-07-25T13:39:42Z

length measurement assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: length measurement datum
editor preferred label: length measurement assay
example of usage: In the doctors office, the nurse used a meter stick to perform a length measurement assay on the patient. The resulting length mesurement datum, 1.5 meters, is about the patient's height.
definition: a process to determine the length of an evaluant
definition editor: Mark A. Miller
definition source: based on mass measurement datum from OBI, specifically Helen Parkinson? Philippe Rocca-Serra?

TURBO assertion making process
type: Class
subclass of: planned process
editor preferred label: TURBO assertion making process
definition: A planned process that takes a datum as input and has a rdf:Statement as output
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-06-28T13:00:00-05:00

TURBO sex recoding process
type: Class
subclass of: TURBO assertion making process
editor preferred label: TURBO sex recoding process
example of usage: I saw the gender identity datum 'M' in a data set describing Joey. I used an instance of the TURBO sex recoding process (with some plan specification) to draw the conclusion that Joey has a quality of type PATO:male.
definition: A planned process that takes a gender identity datum as input and has a PATO:biological_sex as output
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-04-12T14:00:00-05:00

referent tracking
type: Class
subclass of: planned process
editor preferred label: referent tracking
definition: a data transformation with the objective of referring to entities in reality with a singular, unique Instance Unique Identifier (IUI) "Referent Tracking is a paradigm under which it is possible to refer explicitly to all of the concrete individual entities relevant to the accurate description of each patient's condition, therapies, and outcomes through the assignment of unique identifiers."
editor note: TURBO implements IUIs as IRIs with UUIDs on the righthand side
definition editor: Mark A. Miller
definition source: Clinical Data Wrangling using Ontological Realism and Referent Tracking http://www.referent-tracking.com/RTU/?page=papers.phtml http://www.referent-tracking.com/RTU/?page=reftrackparadigm.phtml
date: 2017-10-19T21:39:41Z

conclusionation frequency threshold value specification
type: Class
subclass of: scalar value specification
subclass of: Restriction
  on property:
    inverse of: has value specification
  some values from: conclusionating
subclass of: Restriction
  on property: has specified numeric value
  qualified cardinality: 1
  on data range: real
editor preferred label: conclusionation frequency threshold value specification
definition: a value specification that specifies the minumum frequency at which a value must appear in order for a comclusionation process to conclusde that it is the correct value
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-10-19T21:39:41Z

Encounter participation inferencing
type: Class
subclass of: denoter-based relationship insertion
editor preferred label: Encounter participation inferencing
definition: A planned process in which RDF triples are created (for example) stating that some person participated in some healthcare encounter, based on the co-occurrence of a value denoting the person and a value denoting the encoutner in the same row of a tabular/relational data source
definition editor: Mark A. Miller
alternative term: entity linking
definition source: Mark A. Miller/TURBO team
date: 2017-09-27T14:25:03Z

Mixed racial identity datum
type: Class
subclass of: racial identity datum
creator: Mark Miller
date: 2018-07-30T14:42:54Z

retired placeholder
type: Class
subclass of: Obsolete Class
editor preferred label: retired placeholder
definition: A class of individuals whose URI indicators were made obsolete in the course of referent tracking. The individuals of this class or its subclasses correspond to individuals that were previously instances of some subclass of 'entity'. The referent tracking processes that create instances of 'retired placeholder’ also create smaller numbers of new, unique and singular instances of those same entity subclasses. Also see the 'replaced with IUI' annotation property that documents the input and output
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-04-25T16:00:00-05:00

retired placeholder for adipose tissue
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for adipose tissue
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'adipose tissue'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-03T20:49:12Z
retires: adipose tissue

retired placeholder for biological sex
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for biological sex
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biological sex'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-04-25T16:00:00-05:00
retires: biological sex

retired placeholder for BMI datum
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for BMI datum
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'BMI datum'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-12-14T17:50:50Z
retires: body mass index

retired placeholder for value specification
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for value specification
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'value specification'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-01-10T20:59:27Z
retires: value specification

retired placeholder for height quality
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for height quality
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'height quality'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-17T15:27:16Z
retires: height

retired placeholder for process boundary
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for process boundary
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'process boundary'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-09-21T19:11:02Z
retires: process boundary

retired placeholder for process start time measurement
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for process start time measurement
has curation status: uncurated
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'process start time measurement'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
retires: process start time measurement

retired placeholder for weight quality
type: Class
subclass of: retired placeholder
editor preferred label: retired placeholder for weight quality
definition: A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'weight quality'
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-17T15:27:06Z
retires: weight

tumor grading datum
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: tumor grading
subclass of: data item
definition: a data item that is the ouput of a tumor grading process. may be part of a tumor grading report.
definition editor: Mark A. Miller

tumor grading start
type: Class
subclass of: process boundary

tumor grading end
type: Class
subclass of: process boundary

conclusionating
type: Class
subclass of: planned process
editor preferred label: conclusionating
definition: A planned process that takes one or more datums as input and has a single datum, statement, and or record of missing knowledge as output
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-06-28T13:00:00-05:00
comment: there may be potentially conflicting information about an entity that has gone through a referent tracking process. For example, Joey's gender could be asserted as male, male, male and female. Depending on the rules, conclusionating might decide that Joey is in fact male.

BMI conclusionating
type: Class
subclass of: conclusionating
editor preferred label: BMI conclusionating
definition: a conclusionating process in which one authoritative body mass index is derived from zero or more, potentially conflicting BMIs
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2017-11-17T15:15:20Z

prostate specific antigen assay
type: Class
subclass of: analyte assay
definition: an analyte assay which...
editor note: submit to OBI
definition editor: Mark A. Miller
definition source: https://www.cancer.gov/types/prostate/psa-fact-sheet
date: 2019-01-15T19:29:19Z

prostate specific antigen value specification
type: Class
subclass of: scalar value specification
creator: Mark Miller
date: 2019-01-16T17:35:53Z

prostate Gleason grading datum
type: Class
subclass of: tumor grading datum
creator: Mark Miller
date: 2019-01-17T21:14:20Z

prostate specific antigen concentration datum
type: Class
subclass of: concentration measurment datum
creator: Mark Miller
date: 2019-01-22T16:32:44Z

summarized stage of cancer progression
type: Class
subclass of: conclusion textual entity
creator: Mark Miller
date: 2019-01-22T17:21:47Z

summarizing the stage of cancer progression
type: Class
subclass of: drawing a conclusion based on data
creator: Mark Miller
date: 2019-01-22T17:23:27Z

dysregulation of cell proliferation
type: Class
subclass of: pathological bodily process
definition editor: Mark A. Miller
definition source: ws ONCONTO paper 5.pdf
definition source: Towards an Ontology for Representing Malignant Neoplasms William D. Duncan Carmelo Gaudioso and Alexander D. Diehl
date: 2019-02-07T19:55:15Z

neoplasm (material entity)
type: Class
subclass of: disorder
subclass of: Restriction
  on property: has part
  some values from: neoplastic cell
definition editor: Mark A. Miller
date: 2019-02-07T20:00:32Z

malignant neoplasm (material entity)
type: Class
subclass of: neoplasm (material entity)
subclass of: Restriction
  on property: has part
  some values from: malignant cell
definition editor: Mark A. Miller
date: 2019-02-07T20:04:15Z

primary neoplasm (material entity)
type: Class
subclass of: malignant neoplasm (material entity)
definition editor: Mark A. Miller
date: 2019-02-07T20:05:57Z

secondary neoplasm (matieral entity)
type: Class
subclass of: malignant neoplasm (material entity)
subclass of: Restriction
  on property: develops from
  some values from: primary neoplasm (material entity)
definition editor: Mark A. Miller
date: 2019-02-07T20:06:12Z

patient CRID
type: Class
subclass of: CRID
definition editor: Mark A. Miller
date: 2019-03-01T16:58:34Z

patient CRID symbol
type: Class
subclass of: centrally registered identifier symbol
definition editor: Mark A. Miller
date: 2019-03-01T16:59:03Z

named graph
type: Class
subclass of: data set
definition editor: Mark A. Miller
date: 2019-03-01T17:10:17Z

given name
type: Class
subclass of: personal name
definition editor: Mark A. Miller
date: 2019-03-01T20:00:13Z

family name
type: Class
subclass of: personal name
definition editor: Mark A. Miller
date: 2019-03-01T20:00:23Z

OntoRefine project
type: Class
subclass of: data set
definition editor: Mark A. Miller
date: 2019-03-01T22:46:07Z

CSV file
type: Class
subclass of: delimited data file
definition editor: Mark A. Miller
date: 2019-03-01T22:46:55Z

OntoRefine configuration, url-encoded
type: Class
subclass of: action specification
definition editor: Mark A. Miller
date: 2019-03-01T23:05:20Z

SPARQL insert statement, url-encoded
type: Class
subclass of: action specification
definition editor: Mark A. Miller
date: 2019-03-01T23:05:43Z

relational primary key
type: Class
subclass of: relational key
subclass of: Restriction
  on property: has part
  some values from: symbol
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: denotes
      some values from: identifier source
subclass of: Restriction
  on property: denotes
  some values from: entity
comment: A primary key may or may not be a CRID. It is useful for linking rows between tables in the same database. It may only be reliable for one version, snapshot, etc.

length value specification
type: Class
subclass of: scalar value specification

TURBO data model
type: Class
subclass of: data representational model
alternative term: TURBO shortcut entity

allele information data model
type: Class
subclass of: TURBO data model
alternative term: shortcut allele information

blood pressure value specification
type: Class
subclass of: scalar value specification

systolic blood pressure value specification
type: Class
subclass of: blood pressure value specification

diastolic blood pressure value specification
type: Class
subclass of: blood pressure value specification

BMI value specification
type: Class
subclass of: scalar value specification
alternative term: body mass index value specification
comment: is there any controversy about whether BMIs have units (and are therefore scalar in nature)?

BMI determination process
type: Class
subclass of: planned process
comment: it is expected that this would typically be a data transforation, taking a mass (datum? value specification) and a length as inputs. could possibly be an assay?

blood glucose measurement datum
type: Class
subclass of: concentration measurment datum
has OMOP concept ID: 8840

Hemoglobin with A1c glycosylation percentage datum
type: Class
subclass of: concentration measurment datum
has OMOP concept ID: 3004410

Hemoglobin A1c glycosylation assay
type: Class
subclass of: analyte assay

Hemoglobin with A1c glycosylation percentage value specification
type: Class
subclass of: scalar value specification

blood glucose concentration specification
type: Class
subclass of: scalar value specification

health care encounter data model
type: Class
subclass of: TURBO data model
alternative term: shortcut helath care encounter

healthcare prescription data model
type: Class
subclass of: TURBO data model
alternative term: shortcut prescription

diagnosis data model
type: Class
subclass of: TURBO data model
alternative term: shortcut diagnosis

person data model
type: Class
subclass of: TURBO data model
alternative term: shortcut person

data item data model
type: Class
subclass of: TURBO data model
alternative term: data item or measurement shortcut

person primary key
type: Class
subclass of: relational primary key
subclass of: Restriction
  on property: denotes
  some values from: Homo sapiens

patient primary key
type: Class
subclass of: person primary key
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has role
      some values from: patient role

encounter primary key
type: Class
subclass of: relational primary key

health care encounter primary key
type: Class
subclass of: encounter primary key
subclass of: Restriction
  on property: denotes
  some values from: health care encounter

biobank encounter primary key
type: Class
subclass of: encounter primary key
subclass of: Restriction
  on property: denotes
  some values from: biobank encounter

person CRID data model
type: Class
subclass of: TURBO data model

biobank encounter data model
type: Class
subclass of: TURBO data model

semantic expansion of person model
type: Class
subclass of: semantic expansion of data model
definition: a data transformation that reads triples about a Homo sapiens data model and writes triples about a Homo sapiens, including related classes like identity datums, date of birth, etc.
alternative term: homoSapiensExpansionProcess

semantic expansion of biobank encounter model
type: Class
subclass of: semantic expansion of data model
definition: a data transformation that reads triples about a biobank encounter data model and writes triples about a biobank encounter, including related classes like process boundary and time mesuremnt datum
alternative term: biobankEncounterExpansionProcess

semantic expansion of data model
type: Class
subclass of: data transformation
definition: a data transformation that reads triplesa bout a data model and writes triples about something in reality, like a material entity or planned process
editor note: still trying to idenitfy the domain and range

semantic expansion of health care encounter model
type: Class
subclass of: semantic expansion of data model
definition: a data transformation that reads triples about a health care encounter data model and writes triples about a biobank encounter, including related classes like process boundary and time mesuremnt datum
alternative term: http://transformunify.org/ontologies/healthcareEncounterExpansionProcess

semantic expansion of allele information model
type: Class
subclass of: semantic expansion of data model
alternative term: lossOfFunctionExpansionProcess
alternative term: a planned process that reads triples about an allele information data model and writes triples about an allele information instance, as well as related instances like the data transformation that outputs and the genetic matierial that 'is about'

denoter-based relationship insertion
type: Class
subclass of: drawing a conclusion based on data

biobank encounter participation inferencing
type: Class
subclass of: Encounter participation inferencing
alternative term: biobankEncounterLinkingProcess
alternative term: an encounter participation inferencing process in which the some value is found to denote a biobank encounter

health care encounter participation inferencing
type: Class
subclass of: Encounter participation inferencing
definition: an encounter participation inferencing process in which the some value is found to denote a health care encounter
alternative term: healthcareEncounterLinkingProcess

Metriq/ORQID tumor CRID
type: Class
subclass of: CRID

tumor registry
type: Class
subclass of: centrally registered identifier registry

tumor data model
type: Class
subclass of: TURBO data model

day of birth
type: Class
subclass of: one-dimensional temporal region

neonate temporal region
type: Class
subclass of: one-dimensional temporal region
alternative term: NTR

birth instant
type: Class
equivalent class: Restriction
  on property: birth instant starts NTR
  some values from: neonate temporal region
subclass of: zero-dimensional temporal region

biological sex datum
type: Class
subclass of: data item

male biological sex datum
type: Class
subclass of: biological sex datum

female biologcal sex datum
type: Class
subclass of: biological sex datum

biological sex or gender identity data item
type: Class
subclass of: data item
disjoint union of: gender identity datum
disjoint union of: biological sex datum

male data item
type: Class
subclass of: biological sex or gender identity data item
disjoint union of: male gender identity datum
disjoint union of: male biological sex datum

female data item
type: Class
subclass of: biological sex or gender identity data item
disjoint union of: female gender identity datum
disjoint union of: female biologcal sex datum

identifier source
type: Class
subclass of: data item
comment: in the case of less-than-stable identifiers like primary keys, an identifier source is analogous to a CRID registry

health care encounter identifier source
type: Class
equivalent class: Restriction
  on property: denotes
  some values from: health care encounter identifier source
subclass of: identifier source

identifier source denoter
type: Class
subclass of: data item

health care encounter identifier source denoter
type: Class
subclass of: identifier source denoter

primary key symbol
type: Class
subclass of: symbol

health care encounter primary key symbol
type: Class
subclass of: primary key symbol

tumor registry denoter
type: Class
subclass of: registry denoter

specimen data model
type: Class
subclass of: TURBO data model

genome data model
type: Class
subclass of: TURBO data model

allele information determination process
type: Class
equivalent class: Restriction
  on property: has specified allele information output
  some values from: allele information
subclass of: planned process

genome sequencing specimen
type: Class
subclass of: sample from organism
definition: a specimen that is suitable for genomic (DNA) sequencing. collected in the course of some process like a biobank encounter. could become the input into DNA extraction and (exome?) sequencing, followed by data transformation.
elucidation: isolation-of-genomic-cdna-from-large-volume-of-buffy-coat-using-maxwell-16

genome sequencing specimen CRID
type: Class
equivalent class: Restriction
  on property: denotes
  some values from: genome sequencing specimen
subclass of: CRID

genome sequencing specimen identifier source denoter
type: Class
equivalent class: Restriction
  on property: denotes
  some values from: genome sequencing specimen identifier source
subclass of: identifier source denoter

genome sequencing specimen identifier source
type: Class
subclass of: identifier source

patient identifier source
type: Class
subclass of: identifier source

graph manipulation
type: Class
subclass of: data transformation
comment: define graph

RDF graph manipulation
type: Class
subclass of: graph manipulation
comment: define RDF

edge-vertex graph
type: Class
subclass of: data set
definition source: Graph (discrete mathematics)
comment: define edges and vertices

RDF graph
type: Class
subclass of: edge-vertex graph
comment: the FORMAT is defined at https://en.wikipedia.org/wiki/Resource_Description_Framework

SPARQL update process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: SPARQL update plan
equivalent class: Restriction
  on property: realizes
  some values from: Class
    intersection of: plan
    intersection of: Restriction
      on property: concretizes
      some values from: SPARQL update statement
subclass of: RDF graph manipulation
subclass of: Restriction
  on property: has_specified_input
  some values from: RDF graph
subclass of: Restriction
  on property: has_specified_output
  some values from: RDF graph

SPARQL language
type: Class
subclass of: directive information content entity

update specification portionof SPARQL language
type: Class
subclass of: SPARQL language
comment: disregarding versions... is this a named individual?

database statement
type: Class
subclass of: plan specification

SPARQL update statement generation
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: SPARQL update statement generation plan
equivalent class: Restriction
  on property: has_specified_output
  some values from: SPARQL update statement
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: plan
    intersection of: Restriction
      on property: concretizes
      some values from: SPARQL update statement generation specification

database update statement
type: Class
subclass of: database statement

SPARQL update statement
type: Class
subclass of: database update statement

SPARQL update statement generation specification
type: Class
equivalent class: Restriction
  on property: has part
  some values from: update specification portionof SPARQL language
subclass of: plan specification

Acorn SPARQL update fragment recipe
type: Class
subclass of: plan specification
comment: either where, insert or delete blocks?

Acorn specification
type: Class
subclass of: SPARQL update statement generation specification
subclass of: Restriction
  on property: has part
  some values from: Acorn SPARQL update fragment recipe
alternative term: Acorn recipe-based SPARQL update statement generation specification

SPARQL update plan
type: Class
equivalent class: Restriction
  on property: concretizes
  some values from: SPARQL update statement
subclass of: plan
comment: I wanted to say that this inheres in some SPARQL engine, but those are currently GDCs, not IDCs

SPARQL update statement generation plan
type: Class
equivalent class: Restriction
  on property: concretizes
  some values from: SPARQL update statement generation specification
subclass of: plan

SPARQL engine / triplestore
type: Class
subclass of: software application

Acorn interpreter
type: Class
subclass of: software application

Acorn SPARQL update statement generation plan
type: Class
equivalent class: Restriction
  on property: concretizes
  some values from: Acorn specification
subclass of: SPARQL update statement generation plan
comment: I wanted to say that this inheres in some Acorn interpreter, bu that's currently a GDC not an IDC

SPARQL update statement generation by Acorn
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Acorn SPARQL update statement generation plan
subclass of: SPARQL update statement generation

Acorn domain specific language
type: Class
subclass of: directive information content entity
alternative term: Acorn DSL

office vist
type: Class
subclass of: outpatient encounter

patient identifier source denoter
type: Class
subclass of: identifier source denoter

provenance data item
type: Class
subclass of: data item

data column
type: Class
subclass of: data set
comment: could come from a relational database table, a view or ephemeral query result, or a delimited file.

value_as_number column
type: Class
subclass of: data column

relational database
type: Class
subclass of: data item

relational schema
type: Class
subclass of: data item

data table
type: Class
subclass of: data item

relational data table
type: Class
subclass of: data table

delimited data file
type: Class
subclass of: data table

omop measurement table
type: Class
subclass of: relational data table

query result
type: Class
subclass of: data item

omop person table
type: Class
subclass of: relational data table

gender_concept_id column
type: Class
subclass of: data column

relational key
type: Class
subclass of: information content entity

database query process
type: Class
subclass of: planned process

birth_datetime column
type: Class
subclass of: data column

person_id column
type: Class
subclass of: data column

person_source_value column
type: Class
subclass of: data column

Neo4J property graph
type: Class
subclass of: edge-vertex graph

Carnval graph
type: Class
subclass of: Neo4J property graph

race_concept_id column
type: Class
subclass of: data column

omop visit_occurrence table
type: Class
subclass of: relational data table

visit_concept_id column
type: Class
subclass of: data column

visit_end_date column
type: Class
subclass of: data column

visit_occurrence_id column
type: Class
subclass of: data column

visit_source_value column
type: Class
subclass of: data column

visit_start_date column
type: Class
subclass of: data column

preceding_visit_occurrence_id column
type: Class
subclass of: data column

omop procedure_occurrence table
type: Class
subclass of: relational data table

procedure_occurrence_id column
type: Class
subclass of: data column

procedure_source_value column
type: Class
subclass of: data column

procedure_source_concept_id
type: Class
subclass of: data column

procedure_date column
type: Class
subclass of: data column

measurement_id column
type: Class
subclass of: data column

measurement_concept_id column
type: Class
subclass of: data column

measurement_datetime column
type: Class
subclass of: data column

value_as_concept_id column
type: Class
subclass of: data column

unit_concept_id column
type: Class
subclass of: data column

measurement_source_value column
type: Class
subclass of: data column

measurement_source_concept_id column
type: Class
subclass of: data column

vocabulary_id column
type: Class
subclass of: data column

omop condition_occurrence table
type: Class
subclass of: relational data table

omop drug_exposure table
type: Class
subclass of: relational data table

condition_occurrence_id column
type: Class
subclass of: data column

condition_start_datetime column
type: Class
subclass of: data column

condition_end_datetime column
type: Class
subclass of: data column

condition_source_value column
type: Class
subclass of: data column

condition_source_concept_id column
type: Class
subclass of: data column

drug_exposure_id column
type: Class
subclass of: data column

drug_exposure_start_datetime column
type: Class
subclass of: data column

drug_exposure_end_date column
type: Class
subclass of: data column

verbatim_end_date column
type: Class
subclass of: data column

drug_type_concept_id column
type: Class
subclass of: data column
comment: Synthea omop: |drug_type_concept_id|count| |--------------------|-----| |38000177|8468| |581452|22798| |concept_id|concept_name| |----------|------------| |581452|Dispensed in Outpatient office| |38000177|Prescription written|

days_supply column
type: Class
subclass of: data column

drug_source_value column
type: Class
subclass of: data column

drug_source_concept_id column
type: Class
subclass of: data column

prescription writing process
type: Class
subclass of: planned process
has OMOP concept ID: 38000177

thousand unit per liter unit
type: Class
subclass of: unit per volume unit
alternative term: kU/L
comment: used by Synthea, but doesn't appear to have a UCUM term

prescription identifier source
type: Class
subclass of: identifier source

prescription identifier source denoter
type: Class
subclass of: identifier source denoter

blood serum or plasma union class
type: Class
equivalent class: Class
  union of: blood plasma
  union of: blood serum
subclass of: material anatomical entity

point-in time, quantitative, mass/volume blood plasma or serum glucose concentration assay
type: Class
subclass of: assay

blood serum or plasma specimen
type: Class
subclass of: processed specimen

Point-in-time sample collection specification
type: Class
subclass of: action specification
definition: An action specification indicating that an assay, especially the sample collection, should occur at a single point in time. "...to identify measures at a point in time. This is a synonym for 'spot' or 'random' as applied to urine measurements."
editor note: LThe orders for, or the results from, laboratory assays, when communicated according to LOINC, must indicate the nominal time span over which the sample was collected or over which the assay was performed. Urine samples, for example, are frequently collected in a cumulative fashion, over a period such as 24 hours. THAT EXAMPLE WOULD NOT BE A Pt ASSAY. The time scope for a Pt assay is nominally one point in time. Obviously it takes several seconds or more to fill a vacutainer with blood,
alternative term: Pt
definition source: loinc-users-guide
LOBO_0100003: LP208893-0

24 hour sample collection specification
type: Class
subclass of: action specification

point-in time, quantitative, mass/volume blood glucose concentration assay
type: Class
subclass of: assay

point-in time, quantitative, mass/volume blood hemoglobin concentration assay
type: Class
subclass of: assay

point-in time, quantitative, mass/volume urine urobilinogen concentration assay
type: Class
subclass of: assay

24 hour, quantitative, mass/volume urine urobilinogen concentration assay
type: Class
subclass of: assay

point-in time, quantitative, confirmatory, mass/volume urine ALPRAZolam concentration assay
type: Class
subclass of: assay

point-in time, quantitative, mass/volume blood plasma or serum benzodiazepines concentration assay
type: Class
subclass of: assay

point-in time, quantitative, count/volume blood neutrophil assay
type: Class
subclass of: assay

point-in time, quantitative, automated, volume/volume blood hematocrit assay
type: Class
subclass of: assay

count per volume
type: Class
subclass of: concentration unit

count per volume datum
type: Class
subclass of: scalar measurement datum

volume per volume datum
type: Class
subclass of: scalar measurement datum
comment: http://purl.obolibrary.org/obo/UO_0000205

automated assay
type: Class
subclass of: planned process

confirmatory assay
type: Class
subclass of: planned process

mass/volume concentration datum
type: Class
subclass of: concentration measurment datum

volume/volume percentage concentration datum
type: Class
subclass of: concentration measurment datum

arbitrary units per 24 hours datum
type: Class
subclass of: scalar measurement datum

ethnic group
type: Class
subclass of: population
definition: A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
definition: An ethnic group is a population whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait.
alternative term: Ethnicity
alternative term: race
imported from: efo.owl

African American
type: Class
subclass of: American
definition: A term used in the United States to categorize a population group comprised of persons having origins in any of the black racial groups of Africa. Includes population subgroups (e.g., Kenyan, Nigerian, Haitian). The concept refers also to individuals who classify themselves as described.
alternative term: Afro American
alternative term: BLACK OR AFRICAN AMERICAN
alternative term: Black
alternative term: Black Populations
imported from: efo.owl

American
type: Class
subclass of: ethnic group
imported from: efo.owl

Asian
type: Class
subclass of: ethnic group
definition: Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including Cambodia, China, India, Japan, Korea, Malaysia, Mongolia, Pakistan, the Philippine Islands, Thailand, and Vietnam.
alternative term: Asians
imported from: efo.owl

Asian Indian
type: Class
subclass of: Asian
definition: In North America the term is used to distinguish a person having origins in the original peoples of the Indian sub-continent from Native Americans.
alternative term: Asian Indians
alternative term: Hindu
alternative term: Indian
imported from: efo.owl

Chinese
type: Class
subclass of: Asian
definition: Denotes the inhabitants of China, a person from there, or their descendants elsewhere.
imported from: efo.owl

European-American
type: Class
subclass of: American
imported from: efo.owl

Japanese
type: Class
subclass of: Asian
definition: Denotes the inhabitants of Japan, a person from there, or their descendants elsewhere.
alternative term: JPT
imported from: efo.owl

Latino
type: Class
subclass of: American
definition: A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification.
alternative term: Hispanic
alternative term: Hispanic Populations
alternative term: Hispanic or Latino
alternative term: Hispanics or Latinos
alternative term: Latino Population
alternative term: Spanish Origin
imported from: efo.owl

body mass index
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: adipose tissue
definition: An indicator of body density as determined by the relationship of BODY WEIGHT to BODY HEIGHT. BMI=weight (kg)/height squared (m2). BMI correlates with body fat (ADIPOSE TISSUE). Their relationship varies with age and gender. For adults, BMI falls into these categories: below 18.5 (underweight); 18.5-24.9 (normal); 25.0-29.9 (overweight); 30.0 and above (obese). (National Center for Health Statistics, Centers for Disease Control and Prevention)
definition editor: Dani Welter
imported from: efo.owl
has OMOP concept ID: 3038553
definition_citation: https://en.wikipedia.org/wiki/Body_mass_index
gwas trait: true
database_cross_reference: ICD9:V85-V85.99
database_cross_reference: MSH:D015992
database_cross_reference: NCIt:C16358
database_cross_reference: SNOMEDCT:60621009
alternative_term: BMI
alternative_term: Quetelet's Index

milligram per deciliter
type: Class
subclass of: concentration unit
type: NamedIndividual
type: concentration unit
database_cross_reference: NCIt:C67015
comment: NCIt:C67015
has OMOP concept ID: 8840
imported from: efo.owl

date of birth
type: Class
equivalent class: Restriction
  on property: DOB about day of birth
  some values from: day of birth
subclass of: time measurement datum
definition: The point in time at which an individual was born.
imported from: efo.owl
comment: Propsed equivalency 'is duration of' some (process and ('ends with' some (one-dimensional temporal region' and ('has temporal part') some ('zero-dimensional temporal region' and ('has temporal occupant' some 'start of neonate stage')))))) MAM: occurent instead of process? ends instead of has_temporal_part?

database_cross_reference
type: Class
subclass of: data about an ontology part
imported from: geno.owl

Obsolete Class
type: Class
subclass of: Thing
imported from: iao.owl

International Classification of Diseases, Ninth Revision
type: NamedIndividual
type: International Classification of Diseases
code: C71890
alternative term: ICD 9
alternative term: ICD-9
alternative term: ICD9
comment: hard-imported from NCIT into the base turbo.owl file

International Classification of Diseases, Tenth Revision
type: NamedIndividual
type: International Classification of Diseases
code: C71892
alternative term: ICD 10
alternative term: ICD-10
alternative term: ICD10
comment: hard-imported from NCIT into the base turbo.owl file

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred label: example to be eventually removed

failed exploratory term
type: Thing
type: NamedIndividual
type: obsolescence reason specification
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
definition editor: Person:Alan Ruttenberg

metadata complete
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: metadata complete
definition: 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
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: organizational term
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release
definition editor: PERSON:Alan Ruttenberg

ready for release
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: ready for release
has curation status: pending final vetting
definition: 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
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: pending final vetting
definition: 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.

placeholder removed
type: Thing
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

other
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.
deprecated: true

universal
type: NamedIndividual
type: denotator type
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
definition editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
definition editor: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
editor preferred label: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
definition editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred label: requires discussion
has curation status: pending final vetting
definition: 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.
definition editor: Alan Ruttenberg
definition source: group:OBI

International Classification of Diseases, Tenth Revision, Clinical Modification
type: NamedIndividual
type: International Classification of Diseases
definition: An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. [def-source: NCI]
alternative term: ICD-10-CM
alternative term: ICD-10CM
alternative term: ICD10CM
comment: hard-imported from NCIT into the base turbo.owl file

Gleason Grade Group 1
type: NamedIndividual
type: Gleason Grading System
definition: Only individual discrete well-formed glands.
alternative_term: Gleason Grade Group 1
alternative_term: Gleason Score Less Than or Equal to 6
alternative_term: Grade Group 1

Gleason Grade Group 2
type: NamedIndividual
type: Gleason Grading System
definition: Predominantly well-formed glands with lesser component of poorly-formed/fused/cribriform glands.
alternative_term: Gleason Grade Group 2
alternative_term: Gleason Score 7: (3 plus 4)
alternative_term: Grade Group 2

Gleason Grade Group 3
type: NamedIndividual
type: Gleason Grading System
alternative_term: Gleason Grade Group 3
alternative_term: Gleason Score 7: (4 plus 3)
alternative_term: Grade Group 3

Gleason Grade Group 4
type: NamedIndividual
type: Gleason Grading System
definition: Only poorly-formed/fused/cribriform glands or Predominantly well-formed glands and lesser component lacking glands or Predominantly lacking glands and lesser component of well-formed gland. Poorly-formed/fused/cribriform glands can be a more minor component.
alternative_term: Gleason Grade Group 4
alternative_term: Gleason Score 8: (4 plus 4) or (3 plus 5) or (5 plus 3)
alternative_term: Grade Group 4

Gleason Grade Group 5
type: NamedIndividual
type: Gleason Grading System
definition: Lacks gland formation (or with necrosis) with or without poorly formed/fused/cribriform glands. For cases with greater than 95% poorly formed/fused/cribriform glands or lack of glands on a core or at RP, the component of less than 5% well-formed glands is not factored into the grade.
alternative_term: Gleason Grade Group 5
alternative_term: Gleason Score 9 or 10
alternative_term: Grade Group 5

Gleason Pattern 1
type: NamedIndividual
type: Gleason Grading System
definition: A pattern of prostate carcinoma characterized by the presence of a well circumscribed nodule of separate glands which are closely packed. There is no infiltration of the surrounding parenchyma. The epithelial polarity of the malignant cells is preserved and luminal differentiation is present in all glands.
alternative_term: Gleason Grade 1
alternative_term: Gleason Pattern 1

Gleason Pattern 2
type: NamedIndividual
type: Gleason Grading System
definition: A pattern of prostate carcinoma characterized by the presence of glands that are more loosely arranged and less uniform compared to Gleason pattern 1. Minimal invasion of the surrounding parenchyma may be present. The epithelial polarity of the malignant cells is preserved and luminal differentiation is present in all glands.
alternative_term: Gleason Grade 2
alternative_term: Gleason Pattern 2

Gleason Pattern 3
type: NamedIndividual
type: Gleason Grading System
definition: A pattern of prostate carcinoma characterized by the presence of glands that are infiltrative and vary in size and shape. The epithelial polarity of the malignant cells is preserved and luminal differentiation is present in all glands.
alternative_term: Gleason Grade 3
alternative_term: Gleason Pattern 3

Gleason Pattern 4
type: NamedIndividual
type: Gleason Grading System
definition: A pattern of prostate carcinoma characterized by the presence of fused, cribriform, or poorly defined glands. There is partial loss of normal epithelial polarity.
alternative_term: Gleason Grade 4
alternative_term: Gleason Pattern 4

Gleason Pattern 5
type: NamedIndividual
type: Gleason Grading System
definition: A pattern of prostate carcinoma characterized by almost complete loss of epithelial polarity and luminal differentiation.
alternative_term: Gleason Grade 5
alternative_term: Gleason Pattern 5

Gleason Score 6
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that indicates a low-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 6

Gleason Score 7
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that indicates an intermediate-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 7

Gleason Score 8
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that indicates a histologically aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 8

Gleason Score 9
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that indicates a high-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 9

Gleason Score 10
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that indicates a highly aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 10

Gleason Score 2
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A low Gleason score that is exceptionally uncommon and indicates a low-grade, non-aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 2

Gleason Score 3
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that is exceptionally assigned and indicates a low-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 3

Gleason Score 4
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: A Gleason score that is relatively uncommon and indicates a low-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 4

Gleason Score 5
type: NamedIndividual
type: Gleason Score for Prostate Cancer
definition: An exceptionally uncommon Gleason score that indicates a less aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
alternative_term: Gleason Score 5

Ensembl
type: NamedIndividual
type: gene identifier registry
definition: Ensembl is a joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. The Ensembl Genome Browser can be accessed through www.ensembl.org.
comment: hard-imported from NCIT into the base turbo.owl file

International Classification of Diseases, Ninth Revision, Clinical Modification
type: NamedIndividual
type: International Classification of Diseases
definition: An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. [def-source: NCI]
alternative term: ICD-9-CM
alternative term: ICD-9CM
alternative term: ICD9CM
comment: hard-imported from NCIT into the base turbo.owl file

Affymetrix
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: material supplier role
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Affymetrix
example of usage: Affymetrix supplied microarray
has curation status: metadata incomplete
definition: An organization which supplies technology, tools and protocols for use in high throughput applications

Thermo
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Thermo
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Waters
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Waters
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

BIO-RAD
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: BIO-RAD
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Ambion
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Ambion
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Helicos
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Helicos
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Roche
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Roche
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Illumina
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Illumina
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Agilent
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Agilent
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Li-Cor
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Li-Cor
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Bruker Corporation
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Bruker Corporation
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Applied Biosystems
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Applied Biosystems
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Bruker Daltonics
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Bruker Daltonics
has curation status: metadata incomplete
definition editor: Philippe Rocca-Serra

Sysmex Corporation, Kobe, Japan
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Sysmex Corporation, Kobe, Japan
has curation status: metadata complete
definition source: WEB:http://www.sysmex.com/@2009/08/06
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case

U.S. Food and Drug Administration
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: regulator role
editor preferred label: U.S. Food and Drug Administration
has curation status: metadata incomplete
alternative term: FDA

Edingburgh handedness inventory
type: NamedIndividual
type: questionnaire
editor preferred label: Edingburgh handedness inventory
has curation status: metadata complete
definition: The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Jessica Turner
definition source: PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
definition source: WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html

eBioscience
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: eBioscience
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.ebioscience.com/@2011/04/11

Cytopeia
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Cytopeia
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.cytopeia.com/@2011/04/11

Exalpha Biological
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Exalpha Biological
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.exalpha.com/@2011/04/11

Apogee Flow Systems
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Apogee Flow Systems
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.apogeeflow.com/@2011/04/11

Exbio Antibodies
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Exbio Antibodies
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.exbio.cz/@2011/04/11

Becton Dickinson (BD Biosciences)
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Becton Dickinson (BD Biosciences)
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.bdbiosciences.com/@2011/04/11

Dako Cytomation
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Dako Cytomation
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.dakousa.com/@2011/04/11

Millipore
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Millipore
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.guavatechnologies.com/@2011/04/11

Antigenix
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Antigenix
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.antigenix.com/@2011/04/11

Partec
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Partec
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.partec.de/@2011/04/11

Beckman Coulter
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Beckman Coulter
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.beckmancoulter.com/@2011/04/11

Advanced Instruments Inc. (AI Companies)
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Advanced Instruments Inc. (AI Companies)
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.aicompanies.com/@2011/04/11

Miltenyi Biotec
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Miltenyi Biotec
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.miltenyibiotec.com/@2011/04/11

AES Chemunex
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: AES Chemunex
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.aeschemunex.com/@2011/04/11

Bentley Instruments
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Bentley Instruments
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://bentleyinstruments.com/@2011/04/11

Invitrogen
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Invitrogen
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.invitrogen.com/@2011/04/11

Luminex
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Luminex
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.luminexcorp.com/@2011/04/11

CytoBuoy
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: CytoBuoy
has curation status: metadata complete
definition: A supplier of flow cytometry analyzers
definition editor: Karin Breuer
definition source: WEB:http://www.cytobuoy.com/@2011/04/11

Nimblegen
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Nimblegen
has curation status: metadata incomplete
definition: An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
definition editor: Person: Jie Zheng

Pacific Biosciences
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: Pacific Biosciences
has curation status: metadata incomplete
definition: An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
definition editor: Person: Jie Zheng

NanoString Technologies
type: NamedIndividual
type: organization
type: Restriction
  on property: has role
  some values from: manufacturer role
editor preferred label: NanoString Technologies
has curation status: metadata incomplete
definition: An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.

Thermo Fisher Scientific
type: NamedIndividual
type: organization
editor preferred label: Thermo Fisher Scientific
has curation status: metadata complete
definition: An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific
ontology term requester: NCI BBRB

G1: Well differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G1: Well differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G1
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G2: Moderately differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G2: Moderately differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G2
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G3: Poorly differentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G3: Poorly differentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G3
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G4: Undifferentiated
type: NamedIndividual
type: histologic grade according to AJCC 7th edition
editor preferred label: G4: Undifferentiated
has curation status: metadata complete
definition: A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G4
definition source: https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet
ontology term requester: NCI BBRB

G1 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G1 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G2 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G3 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (Fuhrman)
type: NamedIndividual
type: histologic grade according to the Fuhrman Nuclear Grading System
editor preferred label: G4 (Fuhrman)
has curation status: metadata complete
definition: A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Grade 4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

Low grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred label: Low grade ovarian tumor
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Low grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

High grade ovarian tumor
type: NamedIndividual
type: histologic grade for ovarian tumor according to a two-tier grading system
editor preferred label: High grade ovarian tumor
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: High grade
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G1 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G1 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G1
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G2 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G2 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G2
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G3 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G3 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G3
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

G4 (WHO)
type: NamedIndividual
type: histologic grade for ovarian tumor according to the World Health Organization
editor preferred label: G4 (WHO)
has curation status: metadata complete
definition: A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: G4
definition source: NCI BBRB, OBI
ontology term requester: NCI BBRB

pT0 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT0 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pTis (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pTis (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT1 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT1 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT2 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT2 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT3 (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT3 (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4a (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT4a (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT4b (colon)
type: NamedIndividual
type: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
editor preferred label: pT4b (colon)
has curation status: metadata complete
definition: A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/
ontology term requester: NCI BBRB

pT0 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT0 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pTis (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pTis (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1a (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT1b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT1b (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2a (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2a (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT2b (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT2b (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT3 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT3 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT4 (lung)
type: NamedIndividual
type: pathologic primary tumor stage for lung according to AJCC 7th edition
editor preferred label: pT4 (lung)
has curation status: metadata complete
definition: A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/
ontology term requester: NCI BBRB

pT0 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT0 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT1b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT1b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT2b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT2b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3a (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3a (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3b (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3b (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT3c (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT3c (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT4 (kidney)
type: NamedIndividual
type: pathologic primary tumor stage for kidney according to AJCC 7th edition
editor preferred label: pT4 (kidney)
has curation status: metadata complete
definition: A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/
ontology term requester: NCI BBRB

pT0 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT0 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT1c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT1c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT2c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT2c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3 (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3 (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3a (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3a (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3b (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3b (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pT3c (ovary)
type: NamedIndividual
type: pathologic primary tumor stage for ovary according to AJCC 7th edition
editor preferred label: pT3c (ovary)
has curation status: metadata complete
definition: A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/
ontology term requester: NCI BBRB

pN0 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN0 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1a (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1b (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN1c (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN1c (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2 (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2 (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2a (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2a (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN2b (colon)
type: NamedIndividual
type: pathologic lymph node stage for colon and rectum according to AJCC 7th edition
editor preferred label: pN2b (colon)
has curation status: metadata complete
definition: A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/
ontology term requester: NCI BBRB

pN0 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN0 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN1 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN1 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN2 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN2 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN3 (lung)
type: NamedIndividual
type: pathologic lymph node stage for lung according to AJCC 7th edition
editor preferred label: pN3 (lung)
has curation status: metadata complete
definition: A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/
ontology term requester: NCI BBRB

pN0 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred label: pN0 (kidney)
has curation status: metadata complete
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN1 (kidney)
type: NamedIndividual
type: pathologic lymph node stage for kidney according to AJCC 7th edition
editor preferred label: pN1 (kidney)
has curation status: metadata complete
definition: A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/
ontology term requester: NCI BBRB

pN0 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred label: pN0 (ovary)
has curation status: metadata complete
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

pN1 (ovary)
type: NamedIndividual
type: pathologic lymph node stage for ovary according to AJCC 7th edition
editor preferred label: pN1 (ovary)
has curation status: metadata complete
definition: A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/
ontology term requester: NCI BBRB

cM0 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM0 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29
ontology term requester: NCI BBRB

cM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1a (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: cM1b (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1 (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1 (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1a (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1a (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

pM1b (colon)
type: NamedIndividual
type: pathologic distant metastases stage for colon according to AJCC 7th edition
editor preferred label: pM1b (colon)
has curation status: metadata complete
definition: A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/
ontology term requester: NCI BBRB

cM0 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM0 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1a (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: cM1b (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1 (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1 (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1a (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1a (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

pM1b (lung)
type: NamedIndividual
type: pathologic distant metastases stage for lung according to AJCC 7th edition
editor preferred label: pM1b (lung)
has curation status: metadata complete
definition: A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/
ontology term requester: NCI BBRB

cM0 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: cM0 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: cM1 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

pM1 (kidney)
type: NamedIndividual
type: pathologic distant metastases stage for kidney according to AJCC 7th edition
editor preferred label: pM1 (kidney)
has curation status: metadata complete
definition: A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/
ontology term requester: NCI BBRB

cM0 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: cM0 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

cM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: cM1 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

pM1 (ovary)
type: NamedIndividual
type: pathologic distant metastases stage for ovary according to AJCC 7th edition
editor preferred label: pM1 (ovary)
has curation status: metadata complete
definition: A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
definition editor: Chris Stoeckert, Helena Ellis
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/
ontology term requester: NCI BBRB

Occult Carcinoma (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Occult Carcinoma (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Occult Carcinoma
definition source: http://www.medilexicon.com/dictionary/14371
ontology term requester: NCI BBRB

Stage 0 (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage 0 (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 0
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage I (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage I (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage I
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIC (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IIIC (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IIIC (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIC
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVA (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IVA (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IVB (AJCC 7th)
type: NamedIndividual
type: clinical tumor stage group according to AJCC 7th edition
editor preferred label: Stage IVB (AJCC 7th)
has curation status: metadata complete
definition: A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cancer_staging
ontology term requester: NCI BBRB

Stage IA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IA2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IB1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IB2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IB2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IB2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA1 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA1
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIA2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIA2 (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIA2
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIIA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IIIB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IIIB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IIIB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVA (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IVA (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVA
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage IVB (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics cervical cancer stage value specification
editor preferred label: Stage IVB (FIGO)
has curation status: metadata complete
definition: An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage IVB
definition source: https://en.wikipedia.org/wiki/Cervical_cancer_staging
ontology term requester: NCI BBRB

Stage 1 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 1C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 1C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 1C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 2C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 2C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 2C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3A (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3A (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3A
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3B (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3B (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3B
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 3C (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 3C (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 3C
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage 4 (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage 4 (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage 4
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

Stage Unknown (FIGO)
type: NamedIndividual
type: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
editor preferred label: Stage Unknown (FIGO)
has curation status: metadata complete
definition: A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
definition editor: Chris Stoeckert, Helena Ellis
alternative term: Stage Unknown
definition source: https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/
ontology term requester: NCI BBRB

axiom holds for all times
type: NamedIndividual
editor preferred label: axiom holds for all times
definition: ## 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

meter
type: NamedIndividual
type: length unit
definition: A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
has OMOP concept ID: 9546
created by: george gkoutos
alternative_term: m
alternative_term: metre
has_obo_namespace: unit.ontology
id: UO:0000008
in_subset: unit slim
comment: is this the unit preferred by OMOP for height 3036277 / LOINC 8302-2

second
type: NamedIndividual
type: time unit
editor preferred label: second
definition: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
alternative term: s
alternative term: sec
imported from: uo.owl

micrometer
type: NamedIndividual
type: length unit
definition: A length unit which is equal to one millionth of a meter or 10^[-6] m.
created by: george gkoutos
alternative_term: micrometre
alternative_term: micron
alternative_term: um
has_obo_namespace: unit.ontology
id: UO:0000017
in_subset: unit slim

nanometer
type: NamedIndividual
type: length unit
definition: A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
created by: george gkoutos
alternative_term: nanometre
alternative_term: nm
has_obo_namespace: unit.ontology
id: UO:0000018
in_subset: unit slim

angstrom
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 10 [-10] m.
created by: george gkoutos
alternative_term: Å
has_obo_namespace: unit.ontology
id: UO:0000019
in_subset: unit slim

picometer
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 10^[-12] m.
created by: george gkoutos
alternative_term: picometre
alternative_term: pm
has_obo_namespace: unit.ontology
id: UO:0000020
in_subset: unit slim

gram
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
created by: george gkoutos
alternative_term: g
has_obo_namespace: unit.ontology
id: UO:0000021
in_subset: unit slim

milligram
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
created by: george gkoutos
alternative_term: mg
has_obo_namespace: unit.ontology
id: UO:0000022
in_subset: unit slim

microgram
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to one millionth of a gram or 10^[-6] g.
created by: george gkoutos
alternative_term: ug
has_obo_namespace: unit.ontology
id: UO:0000023
in_subset: unit slim

nanogram
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
created by: george gkoutos
alternative_term: ng
has_obo_namespace: unit.ontology
id: UO:0000024
in_subset: unit slim

femtogram
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to 10^[-15] g.
created by: george gkoutos
alternative_term: fg
has_obo_namespace: unit.ontology
id: UO:0000026
in_subset: unit slim

minute
type: NamedIndividual
type: time unit
editor preferred label: minute
definition: A time unit which is equal to 60 seconds.
alternative term: min
imported from: uo.owl

hour
type: NamedIndividual
type: time unit
editor preferred label: hour
definition: A time unit which is equal to 3600 seconds or 60 minutes.
alternative term: h
alternative term: hr
imported from: uo.owl

day
type: NamedIndividual
type: time unit
editor preferred label: day
definition: A time unit which is equal to 24 hours.
imported from: uo.owl

week
type: NamedIndividual
type: time unit
editor preferred label: week
definition: A time unit which is equal to 7 days.
imported from: uo.owl

month
type: NamedIndividual
type: time unit
editor preferred label: month
definition: A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
imported from: uo.owl

year
type: NamedIndividual
type: time unit
editor preferred label: year
definition: A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
imported from: uo.owl

molar mass unit
type: NamedIndividual
type: mass unit
definition: A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules.
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000055
in_subset: unit group slim

molar
type: NamedIndividual
type: concentration unit
editor preferred label: molar
definition: A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
alternative term: M
imported from: uo.owl

micromolar
type: NamedIndividual
type: concentration unit
editor preferred label: micromolar
definition: A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
alternative term: uM
imported from: uo.owl

nanomolar
type: NamedIndividual
type: concentration unit
editor preferred label: nanomolar
definition: A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
alternative term: nM
imported from: uo.owl

picomolar
type: NamedIndividual
type: concentration unit
editor preferred label: picomolar
definition: A unit of molarity which is equal to 10^[-12] M.
alternative term: pM
imported from: uo.owl

kilogram per cubic meter
type: NamedIndividual
type: concentration unit
definition: A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters.
created by: george gkoutos
alternative_term: kg/m^[3]
alternative_term: kilogram per cubic metre
has_obo_namespace: unit.ontology
id: UO:0000083
in_subset: unit slim

gram per cubic centimeter
type: NamedIndividual
type: concentration unit
definition: A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters.
created by: george gkoutos
alternative_term: g/cm^[3]
alternative_term: gram per cubic centimetre
has_obo_namespace: unit.ontology
id: UO:0000084
in_subset: unit slim

mass percentage
type: NamedIndividual
type: concentration unit
editor preferred label: mass percentage
definition: A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
alternative term: % w/w
alternative term: percent weight pr weight
imported from: uo.owl

mass volume percentage
type: NamedIndividual
type: concentration unit
editor preferred label: mass volume percentage
definition: A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
alternative term: % w/v
alternative term: percent vol per vol
imported from: uo.owl

volume percentage
type: NamedIndividual
type: concentration unit
editor preferred label: volume percentage
definition: A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
alternative term: % v/v
alternative term: percent vol per vol
imported from: uo.owl

gram per milliliter
type: NamedIndividual
type: concentration unit
definition: A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter.
created by: george gkoutos
alternative_term: g/ml
alternative_term: gram per millilitre
has_obo_namespace: unit.ontology
id: UO:0000173
in_subset: unit slim

kilogram per liter
type: NamedIndividual
type: concentration unit
definition: A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters.
created by: george gkoutos
alternative_term: kg/L
alternative_term: kilogram per litre
has_obo_namespace: unit.ontology
id: UO:0000174
in_subset: unit slim

gram per liter
type: NamedIndividual
type: concentration unit
editor preferred label: gram per liter
definition: A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
alternative term: g per L
alternative term: g/L
imported from: uo.owl
has OMOP concept ID: 8636
created by: george gkoutos
alternative_term: g/L
alternative_term: gram per litre
has_obo_namespace: unit.ontology
id: UO:0000175
in_subset: unit slim

milligram per milliliter
type: NamedIndividual
type: concentration unit
editor preferred label: milligram per milliliter
definition: A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
alternative term: mg per ml
alternative term: mg/ml
imported from: uo.owl
created by: george gkoutos
alternative_term: mg/ml
alternative_term: milligram per millilitre
has_obo_namespace: unit.ontology
id: UO:0000176
in_subset: unit slim

milliliter per liter
type: NamedIndividual
type: concentration unit
editor preferred label: milliliter per liter
definition: A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
alternative term: ml per L
alternative term: ml/l
imported from: uo.owl

colony forming unit per volume
type: NamedIndividual
type: concentration unit
editor preferred label: colony forming unit per volume
definition: A concentration unit which a measure of viable bacterial numbers in a given volume.
imported from: uo.owl

dalton
type: NamedIndividual
type: mass unit
definition: An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state.
created by: george gkoutos
alternative_term: Da
alternative_term: amu
alternative_term: u
alternative_term: unified atomic mass unit
has_obo_namespace: unit.ontology
id: UO:0000221
in_subset: unit slim

kilodalton
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to one thousand daltons.
created by: george gkoutos
alternative_term: kDa
has_obo_namespace: unit.ontology
id: UO:0000222
in_subset: unit slim

milligram per liter
type: NamedIndividual
type: concentration unit
definition: A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters.
created by: george
creation date: 2011-03-21T10:35:01Z
alternative_term: mg/L
alternative_term: milligram per litre
has_obo_namespace: unit.ontology
id: UO:0000273
in_subset: unit slim

microgram per milliliter
type: NamedIndividual
type: concentration unit
definition: A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters.
created by: George Gkoutos
creation date: 2011-03-21T10:40:21Z
alternative_term: ug/ml
has_obo_namespace: unit.ontology
has_related_synonym: microgram per millilitre
id: UO:0000274
in_subset: unit slim

microgram per liter
type: NamedIndividual
type: concentration unit
editor preferred label: microgram per liter
definition: A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
alternative term: ng/ml
alternative term: ug/L
imported from: uo.owl
created by: george gkoutos
alternative_term: microgram per litre
alternative_term: ug/L
has_obo_namespace: unit.ontology
id: UO:0000301
in_subset: unit slim

centiMorgan
type: NamedIndividual
type: length unit
definition: A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination.
created by: gkoutos
creation date: 2013-12-06T12:25:17Z
alternative_term: cM
has_obo_namespace: unit.ontology
id: UO:0000326
in_subset: unit slim

centiRay
type: NamedIndividual
type: length unit
definition: A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability.
created by: gkoutos
creation date: 2013-12-06T12:26:29Z
alternative_term: cR
has_obo_namespace: unit.ontology
id: UO:0000327
in_subset: unit slim

milli
type: NamedIndividual
type: mass unit
definition: A mass unit which is equal to 1/12 the mass of 12C
created by: Luke Slater
alternative_term: mDa
alternative_term: milli unified atomic mass unit
alternative_term: millidalton
alternative_term: mmu
has_obo_namespace: unit.ontology
id: UO:0010009
in_subset: unit slim

inch
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 0.0254 metres.
created by: Luke Slater
alternative_term: in
has_obo_namespace: unit.ontology
id: UO:0010011
in_subset: unit slim

thou
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 0.0254 millimetres.
created by: Luke Slater
alternative_term: mil
alternative_term: th
has_obo_namespace: unit.ontology
id: UO:0010012
in_subset: unit slim

foot
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 0.3048 metres, or 12 inches.
created by: Luke Slater
alternative_term: ft
has_obo_namespace: unit.ontology
id: UO:0010013
in_subset: unit slim

yard
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 0.9144 metres, or 3 feet.
created by: Luke Slater
alternative_term: yd
has_obo_namespace: unit.ontology
id: UO:0010014
in_subset: unit slim

chain
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards.
created by: Luke Slater
alternative_term: ch
has_obo_namespace: unit.ontology
id: UO:0010015
in_subset: unit slim

furlong
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains.
created by: Luke Slater
alternative_term: fur
has_obo_namespace: unit.ontology
id: UO:0010016
in_subset: unit slim

mile
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 1,609.344 metres, or 8 furlongs.
created by: Luke Slater
alternative_term: mi
has_obo_namespace: unit.ontology
id: UO:0010017
in_subset: unit slim

league
type: NamedIndividual
type: length unit
definition: A length unit which is equal to 3 miles, or 4,828.032 metres
created by: Luke Slater
alternative_term: lea
has_obo_namespace: unit.ontology
id: UO:0010018
in_subset: unit slim

maritime length unit
type: NamedIndividual
type: length unit
definition: A maritime length unit is one used primarily at sea.
created by: Luke Slater
has_obo_namespace: unit.ontology
id: UO:0010019
in_subset: unit slim

grain
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 64.798,91 milligrams.
created by: Luke Slater
alternative_term: gr
has_obo_namespace: unit.ontology
id: UO:0010031
in_subset: unit slim

drachm
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound.
created by: Luke Slater
alternative_term: dr
has_obo_namespace: unit.ontology
id: UO:0010032
in_subset: unit slim

ounce
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound.
created by: Luke Slater
alternative_term: oz
has_obo_namespace: unit.ontology
id: UO:0010033
in_subset: unit slim

pound
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 453.592,37 grams.
created by: Luke Slater
alternative_term: lb
has_obo_namespace: unit.ontology
id: UO:0010034
in_subset: unit slim

stone
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds.
created by: Luke Slater
alternative_term: st
has_obo_namespace: unit.ontology
id: UO:0010035
in_subset: unit slim

quarter
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds.
created by: Luke Slater
alternative_term: qr
alternative_term: qtr
has_obo_namespace: unit.ontology
id: UO:0010036
in_subset: unit slim

hundredweight
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone.
created by: Luke Slater
alternative_term: cwt
has_obo_namespace: unit.ontology
id: UO:0010037
in_subset: unit slim

ton
type: NamedIndividual
type: mass unit
definition: An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds.
created by: Luke Slater
alternative_term: t
has_obo_namespace: unit.ontology
id: UO:0010038
in_subset: unit slim

obi.owl
type: NamedIndividual
default language: en
OBO foundry unique label: Ontology for Biomedical Investigations
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
creator: Chris Stoeckert
creator: Chris Taylor
creator: Christian Bolling
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James A. Overton
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
creator: Philip Lord
creator: Philippe Rocca-Serra
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
date: 2009-07-31
description: 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.
Format: OWL-DL
subject: An ontology for the annotation of biomedical and functional genomics experiments.
license: http://creativecommons.org/licenses/by/4.0/
comment: 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.
version info: 2019-06-05
version info: 2019-11-12

Penn Medicine Biobak organizastion
type: NamedIndividual
type: biobank organization
editor preferred label: Penn Medicine Biobak organizastion
definition: A 'biobank organization' affiliated with the Institute for Translational Medicine and Therapeutics at the Perelman School of Medicine at the University of Pennsylvania and 'Penn Medicine': the University of Pennsylvania Health System
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

UPHS EMPI patient identifier registry
type: NamedIndividual
type: patient identifier registry
editor preferred label: PDS EMPI patient identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T14:41:32Z
comment: EMPI - Enterprise Master Patient Identifier - PDS generated internal patient identifier. Should be unique to a person (every person should have at most one EMPI, every EMPI belongs to only one person). This identifier is stable in that it should not change over time, however it is not complete in that not all patients are assigned an EMPI.

PDS PK_PATIENT_ID patient identifier source
type: NamedIndividual
type: patient identifier source
editor preferred label: PDS PK_PATIENT_ID patient identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T15:13:50Z
comment: PDS generated internal patient identifier. Should be unique to a person (every PK_PATIENT_ID belongs to only one person).PK_PATIENT_ID is complete in that all patients do have PK_PATIENT_IDs, however it is not stable in that the value assigned to a person will change over time. Specifically, PK_PATIENT_IDs are regenerated over the weekend, so PK_PATIENT_IDs can be used to query PDS within the same work week to get consistent results, but particular PK_PATIENT_IDs from the previous week should not be used to requery PDS.

HUP MRN patient identifier registry
type: NamedIndividual
type: patient MRN registry
editor preferred label: HUP MRN patient identifier registry
definition: the registry of MRNs from the Hospital University of Pennsylvania
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T14:46:20Z

PMC MRN patient identifier registry
type: NamedIndividual
type: patient MRN registry
editor preferred label: PMC MRN patient identifier registry
definition: the registry of MRNs from the Penn Presbyterian Medical Center
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T14:46:20Z

PAH MRN patient identifier registry
type: NamedIndividual
type: patient MRN registry
editor preferred label: PAH MRN patient identifier registry
definition: the registry of MRNs from the Pennsylvania Hospital
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T14:46:20Z

CCH MRN patient identifier registry
type: NamedIndividual
type: patient MRN registry
editor preferred label: CCH MRN patient identifier registry
definition: the registry of MRNs from the Chester County Hosptial
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T14:46:20Z

CGI ENCOUNTER_PACK_ID biobank encounter identifier registry
type: NamedIndividual
type: ENCOUNTER_PACK_ID biobank encounter registry
editor preferred label: CGI ENCOUNTER_PACK_ID biobank encounter identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T15:25:43Z
comment: Integer. Generated when the CRFs are created. All CGI encounters must have this identifier. Used to link to both CRF data and inventory data.

PMBB ENCOUNTER_PACK_ID biobank encounter identifier registry
type: NamedIndividual
type: ENCOUNTER_PACK_ID biobank encounter registry
editor preferred label: PMBB ENCOUNTER_PACK_ID biobank encounter identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T15:30:20Z
comment: UUID. Generated when the CRFs are created. Used to link to CRF data. All PMBB encounters must have this identifier.

PMBB Blood ENCOUNTER_PACK_ID biobank encounter identifier registry
type: NamedIndividual
type: ENCOUNTER_PACK_ID biobank encounter registry
editor preferred label: PMBB Blood ENCOUNTER_PACK_ID biobank encounter identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

PMBB Tissue ENCOUNTER_PACK_ID biobank encounter identifier registry
type: NamedIndividual
type: ENCOUNTER_PACK_ID biobank encounter registry
editor preferred label: PMBB Tissue ENCOUNTER_PACK_ID biobank encounter identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team

PMBB ENCOUNTER_LAB_ID biobank encounter identifier registry
type: NamedIndividual
type: biobank encounter identifier registry
editor preferred label: PMBB ENCOUNTER_LAB_ID biobank encounter identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T15:30:20Z
comment: Integer. Generated when blood specimens are processed. Used to link to inventory data. Not all encounters have this identifier; if no specimens are received, this identifier is not generated.

PDS PK_Encounter_ID health care encounter identifier source
type: NamedIndividual
type: health care encounter identifier source
editor preferred label: PDS PK_Encounter_ID health care encounter identifier registry
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
Contributor: Heather J Williams
date: 2018-01-30T15:47:02Z
comment: PDS generated internal healthcare encounter identifier. Probably not stable over time.

Regeneron genotype identifier registry
type: NamedIndividual
type: genotype identifier registry
editor preferred label: Regeneron genotype identifier registry
definition: A 'genotype identifier registry' containing identifies issued by Regeneron to identify samples submitted by the 'Penn Medicine Biobank organization' and the resulting genotype data
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-05-16T20:29:12Z

-/- loss of function zygosity value specification
type: NamedIndividual
type: loss of function zygosity value specification
has literal value: 2
editor preferred label: -/- loss of function zygosity value specification
definition: a 'loss of function zygosity value specification' instance indicating the conclusion that some diploid individual is homozygous for a mutant or minor allele at some locus
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-20T19:21:43Z

-/+ loss of function zygosity value specification
type: NamedIndividual
type: loss of function zygosity value specification
has literal value: 1
editor preferred label: -/+ loss of function zygosity value specification
definition: a 'loss of function zygosity value specification' instance indicating the conclusion that some diploid individual is heterozygous for loss of function alleles at some locus
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-20T19:22:03Z

+/+ loss of function zygosity value specification
type: NamedIndividual
type: loss of function zygosity value specification
has literal value: 0
editor preferred label: +/+ loss of function zygosity value specification
definition: a 'loss of function zygosity value specification' instance indicating the conclusion that some diploid individual is wild-type homozygous at some locus
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-20T19:22:21Z

-/- zygosity value specification
type: NamedIndividual
type: zygosity value specification
has literal value: 2
editor preferred label: -/- zygosity value specification
definition: a 'zygosity value specification' instance indicating the conclusion that some diploid individual is homozygous for a mutant or minor allele at some locus
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-20T19:21:43Z

-/+ zygosity value specification
type: NamedIndividual
type: zygosity value specification
has literal value: 1
editor preferred label: -/+ zygosity value specification
definition: a 'zygosity value specification' instance indicating the conclusion that some diploid individual is heterozygous for a mutant or minor allele at some locus
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-20T19:22:03Z

+/+ zygosity value specification
type: NamedIndividual
type: zygosity value specification
has literal value: 0
editor preferred label: +/+ zygosity value specification
definition: a 'zygosity value specification' instance indicating the conclusion that some diploid individual is wild-type homozygous at some locus
definition editor: Mark A. Miller
definition source: Mark A. Miller/TURBO team
date: 2018-04-20T19:22:21Z

PDS placeholder racial identity registry
type: NamedIndividual
type: racial identity registry
creator: Mark Miller
date: 2018-07-25T13:55:09Z
comment: Requires more discussion... what are the racial identity authorities that offer values that are used in our inpout data?

Synthea patient registry
type: NamedIndividual
type: patient identifier registry
definition editor: Mark A. Miller
date: 2019-03-01T15:21:15Z

Synthea health care encounter registry
type: NamedIndividual
type: health care encounter identifier registry
definition editor: Mark A. Miller
date: 2019-03-02T19:04:43Z

Metriq/ORQID tumor registry
type: NamedIndividual
type: tumor registry

Patient 946
type: NamedIndividual
type: Homo sapiens
participates in: Neonate stage (process) 946

Neonate stage (process) 946
type: NamedIndividual
type: neonate stage
neonate stage OTR NTR: Neonate stage temporal region 946

Start of neonate stage/birth 946
type: NamedIndividual
type: start of neonate stage
temporal part of: Neonate stage (process) 946
SNS OTR birth instant: Birth instant 946

DOB TMD 946
type: NamedIndividual
type: date of birth
DOB about day of birth: Day of birth 946

Day of birth 946
type: NamedIndividual
type: day of birth

Birth instant 946
type: NamedIndividual
type: birth instant
birth instant TPO birth day: Day of birth 946
birth instant starts NTR: Neonate stage temporal region 946

Neonate stage temporal region 946
type: NamedIndividual
type: neonate temporal region

Male GID 946
type: NamedIndividual
type: male gender identity datum
is about: Patient 946

(denoter of the) Synthea patient registry
type: NamedIndividual
type: patient registry denoter
denotes: Synthea patient registry

(denoter of the) Synthea health care encounter registry
type: NamedIndividual
type: health care encounter registry denoter
denotes: Synthea health care encounter registry

OMOP health care identifier source
type: NamedIndividual
type: health care encounter identifier source

(denoter of the) OMOP health care encounter identifier source
type: NamedIndividual
type: health care encounter identifier source denoter
denotes: OMOP health care identifier source

Metriq/ORQID tumor registry denoter
type: NamedIndividual
type: tumor registry denoter
denotes: Metriq/ORQID tumor registry

HUP MRN registry denoter
type: NamedIndividual
type: patient registry denoter
denotes: HUP MRN patient identifier registry

PDS PK_Encounter_ID health care encounter identifier source denoter
type: NamedIndividual
type: health care encounter identifier source denoter

UPHS EMPI patient registry denoter
type: NamedIndividual
type: patient registry denoter

CGI Biobank Encounter registry denoter
type: NamedIndividual
type: biobank encounter registry denoter

PMBB Blood biobank encounter registry denoter
type: NamedIndividual
type: biobank encounter registry denoter

PMBB Tissue biobank encounter registry denoter
type: NamedIndividual
type: biobank encounter registry denoter

CCH MRN registry denoter
type: NamedIndividual
type: patient registry denoter

PAH MRN registry denoter
type: NamedIndividual
type: patient registry denoter

PMC MRN registry denoter
type: NamedIndividual
type: patient registry denoter

OMOP patient identifier source
type: NamedIndividual
type: patient identifier source
denotes: PDS med order identfier source

(denoter of the) OMOP patient identifier source
type: NamedIndividual
type: patient identifier source denoter
denotes: OMOP patient identifier source

OMOP measurement identifier source
type: NamedIndividual
type: identifier source

(denoter of the) OMOP measurement identifier source
type: NamedIndividual
type: identifier source denoter
denotes: OMOP measurement identifier source

Synthea measurement registry
type: NamedIndividual
type: centrally registered identifier registry

(denoter of the) Synthea measurement registry
type: NamedIndividual
type: registry denoter
denotes: Synthea measurement registry

Synthea procudure registry
type: NamedIndividual
type: centrally registered identifier registry

(denoter of the) Synthea procedure registry
type: NamedIndividual
type: registry denoter
denotes: Synthea procudure registry

(denoter of the) OMOP procedure identifier source
type: NamedIndividual
type: identifier source denoter
denotes: OMOP procedure identifier source

OMOP procedure identifier source
type: NamedIndividual
type: identifier source

value_as_number column from measurement query result
type: NamedIndividual
type: value_as_number column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: relational database

cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: relational schema
is part of: syntheaomop_post_icbo at pennturbo.org port 5432

measurement in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: omop measurement table
is part of: cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

omop measurements query result, including vocab and manually asserted mmHg units for BP
type: NamedIndividual
type: query result
derives from: measurement in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
comment: PREFIX : <http://api.stardog.com/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX stardog: <tag:stardog:api:> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> MAPPING FROM SQL { -- SELECT * -- FROM "cdm_synthea10"."measurement" select m.*, c.vocabulary_id, (case when m.unit_source_value = 'mmHg' then 8876 when m.unit_source_value = 'U/L' then 8645 else m.unit_concept_id end ) as more_units from cdm_synthea10.measurement m join cdm_synthea10.concept c on m.measurement_source_concept_id = c.concept_id -- WHERE "measurement_date" IS NOT NULL AND "measurement_time" IS NOT NULL AND "operator_concept_id" IS NOT NULL AND "value_as_number" IS NOT NULL AND "value_as_concept_id" IS NOT NULL AND "unit_concept_id" IS NOT NULL AND "range_low" IS NOT NULL AND "range_high" IS NOT NULL AND "provider_id" IS NOT NULL AND "visit_occurrence_id" IS NOT NULL AND "visit_detail_id" IS NOT NULL AND "measurement_source_value" IS NOT NULL AND "unit_source_value" IS NOT NULL AND "value_source_value" IS NOT NULL -- WHERE "visit_occurrence_id" < 100 -- WHERE "person_id" <= 500 } TO { ?subject <http://api.stardog.com/measurement#measurement_concept_id> ?measurement_concept_id . ?subject <http://api.stardog.com/measurement#measurement_date> ?measurement_date . ?subject <http://api.stardog.com/measurement#measurement_datetime> ?measurement_datetime . ?subject <http://api.stardog.com/measurement#measurement_id> ?measurement_id . ?subject <http://api.stardog.com/measurement#measurement_source_concept_id> ?measurement_source_concept_id . ?subject <http://api.stardog.com/measurement#measurement_source_value> ?measurement_source_value . ?subject <http://api.stardog.com/measurement#measurement_time> ?measurement_time . ?subject <http://api.stardog.com/measurement#measurement_type_concept_id> ?measurement_type_concept_id . ?subject <http://api.stardog.com/measurement#operator_concept_id> ?ope…

more_units column from omop measurements query result...
type: NamedIndividual
type: data column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

enc_type_code
type: NamedIndividual
type: data column
is part of: patient_encounter

patient_encounter
type: NamedIndividual
type: data table
is part of: Penn Data Store Master Data Managment schema

Penn Data Store Master Data Managment schema
type: NamedIndividual
type: relational schema
is part of: Penn Data Store database
alternative term: MDM

Penn Data Store database
type: NamedIndividual
type: relational database
alternative term: PDS
alternative term: host = pdsprd.uphs.upenn.edu (oracle)

person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: omop person table
is part of: cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

gender_concept_id column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: gender_concept_id column
is part of: person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

race_concept_id column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: race_concept_id column
is part of: person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

person_id column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: person_id column
is part of: person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

birth_datetime column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: birth_datetime column
is part of: person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

person_source_value column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: person_source_value column
is part of: person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: omop visit_occurrence table

person_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: person_id column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_concept_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_concept_id column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_end_date column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_end_date column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_occurrence_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_occurrence_id column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_source_value column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_source_value column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_start_date column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_start_date column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

preceding_visit_occurrence_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: preceding_visit_occurrence_id column
is part of: visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: omop procedure_occurrence table

person_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: person_id column
is part of: procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

procedure_occurrence_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: procedure_occurrence_id column
is part of: procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_occurrence_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_occurrence_id column
is part of: procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

procedure_source_concept_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: procedure_source_concept_id
is part of: procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

procedure_source_value column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: procedure_source_value column
is part of: procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

procedure_date column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: procedure_date column
is part of: procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

measurement_id column from measurement query result
type: NamedIndividual
type: measurement_id column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

person_id column from measurement query result
type: NamedIndividual
type: person_id column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

measurement_datetime column from measurement query result
type: NamedIndividual
type: measurement_datetime column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

unit_concept_id column from measurement query result
type: NamedIndividual
type: unit_concept_id column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

visit_occurrence_id column from measurement query result
type: NamedIndividual
type: visit_occurrence_id column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

measurement_source_value column from measurement query result
type: NamedIndividual
type: measurement_source_value column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

measurement_source_concept_id column from measurement query result
type: NamedIndividual
type: measurement_source_concept_id column
is part of: omop measurements query result, including vocab and manually asserted mmHg units for BP

condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: omop condition_occurrence table
is part of: cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

omop drug_exposure plus vocabulary
type: NamedIndividual
type: query result
derives from: drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
comment: PREFIX : <http://api.stardog.com/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX stardog: <tag:stardog:api:> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> MAPPING FROM SQL { SELECT de.*, c.vocabulary_id FROM "cdm_synthea10"."drug_exposure" de join cdm_synthea10.concept c on de.drug_source_concept_id = c.concept_id -- WHERE "measurement_date" IS NOT NULL AND "measurement_time" IS NOT NULL AND "operator_concept_id" IS NOT NULL AND "value_as_number" IS NOT NULL AND "value_as_concept_id" IS NOT NULL AND "unit_concept_id" IS NOT NULL AND "range_low" IS NOT NULL AND "range_high" IS NOT NULL AND "provider_id" IS NOT NULL AND "visit_occurrence_id" IS NOT NULL AND "visit_detail_id" IS NOT NULL AND "measurement_source_value" IS NOT NULL AND "unit_source_value" IS NOT NULL AND "value_source_value" IS NOT NULL WHERE "visit_occurrence_id" < 30 } TO { ?subject <http://api.stardog.com/drug_exposure#days_supply> ?days_supply . ?subject <http://api.stardog.com/drug_exposure#dose_unit_source_value> ?dose_unit_source_value . ?subject <http://api.stardog.com/drug_exposure#drug_concept_id> ?drug_concept_id . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_end_date> ?drug_exposure_end_date . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_end_datetime> ?drug_exposure_end_datetime . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_id> ?drug_exposure_id . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_start_date> ?drug_exposure_start_date . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_start_datetime> ?drug_exposure_start_datetime . ?subject <http://api.stardog.com/drug_exposure#drug_source_concept_id> ?drug_source_concept_id . ?subject <http://api.stardog.com/drug_exposure#drug_source_value> ?drug_source_value . ?subject <http://api.stardog.com/drug_exposure#drug_type_concept_id> ?drug_type_concept_id . ?s…

drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: omop drug_exposure table
is part of: cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

OMOP drug_exposure/prescription identifier source
type: NamedIndividual
type: identifier source

OMOP condition_occurrence/diagnosis identifier source
type: NamedIndividual

(denoter of the) OMOP condition_occurrence/diagnosis source
type: NamedIndividual
type: identifier source denoter
denotes: OMOP condition_occurrence/diagnosis identifier source

(denoter of the) OMOP drug_exposure/prescription identifier source
type: NamedIndividual
type: identifier source denoter
denotes: OMOP drug_exposure/prescription identifier source

condition_end_datetime column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: condition_end_datetime column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

condition_occurrence_id column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: condition_occurrence_id column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

condition_source_concept_id column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: condition_source_concept_id column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

condition_start_datetime column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: condition_start_datetime column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

condition_source_value column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: condition_source_value column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

verbatim_end_date column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: verbatim_end_date column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

person_id column from condition_occurrence in cdm_synthea10 schema
type: NamedIndividual
type: person_id column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

person_id column from drug_exposure query result
type: NamedIndividual
type: person_id column
is part of: drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_occurrence_id column from drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_occurrence_id column
is part of: drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

visit_occurrence_id column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
type: NamedIndividual
type: visit_occurrence_id column
is part of: condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432

drug_exposure_id column from omop drug_exposure plus vocabulary query result
type: NamedIndividual
type: drug_exposure_id column
is part of: omop drug_exposure plus vocabulary

drug_exposure_start_datetime column from omop drug_exposure plus vocabulary query result
type: NamedIndividual
type: drug_exposure_start_datetime column
is part of: omop drug_exposure plus vocabulary

drug_source_value column from omop drug_exposure plus vocabulary query result
type: NamedIndividual
type: drug_source_value column
is part of: omop drug_exposure plus vocabulary

PDS med order identfier source
type: NamedIndividual

denoter of the PDS med order identifier source
type: NamedIndividual
type: prescription identifier source denoter

patient_class
type: NamedIndividual
type: data column
is part of: patient_encounter

qualified cardinality: 1

Total Gleason Score for Prostate Cancer
alternative_term: GLEASON TOTAL SUM
definition: The value of the sum of the primary and secondary Gleason scores (range 2-10). If three patterns are identified, it is the sum of the primary pattern score and the score of the least well-differentiated pattern.
in_subset: NCIT C66830
in_subset: NCIT C61410
alternative_term: Total Gleason Score
alternative_term: Total Gleason Score for Prostate Cancer
in_subset: NCIT C125922

Primary Gleason Pattern
alternative_term: Primary Gleason Pattern
in_subset: NCIT C66830
definition: The most prevalent Gleason pattern in a prostate biopsy or prostatectomy specimen. The Gleason score is defined by adding the most prevalent (primary) and second most prevalent (secondary) patterns.
in_subset: NCIT C125922
alternative_term: GLEASON PRIMARY SCORE
in_subset: NCIT C61410

Secondary Gleason Pattern
in_subset: NCIT C66830
alternative_term: Secondary Gleason Pattern
definition: The second most prevalent Gleason pattern in a prostate biopsy or prostatectomy specimen. The Gleason score is defined by adding the most prevalent (primary) and second most prevalent (secondary) patterns.
alternative_term: GLEASON SECONDARY SCORE
in_subset: NCIT C61410
in_subset: NCIT C125922

Tertiary Gleason Pattern
alternative_term: Tertiary Gleason Pattern
definition: Prostate carcinoma patterns occupying less than 5% of the tumor.

geno.owl
comment: GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013

ido.owl
date: 2017-11-03T15:13:52
creator: Albert Goldfain
creator: Alexander Diehl
creator: Bjoern Peters
comment: The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, including terms such as 'pathogen', 'host', 'vector', and 'vaccine'. The structure of IDO adheres to the Basic Formal Ontology. Terms in IDO that are within the scope of other OBO Foundry ontologies, such as the Gene Ontology, are derived from those ontologies. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible. For more information, see http://www.infectiousdiseaseontology.org/Home.html.
creator: Alan Ruttenberg
default language: en
license: http://creativecommons.org/licenses/by/3.0/
creator: Barry Smith
version info: 2017-11-03
creator: Lindsay Cowell
Contributor: Jie Zheng

ogg.owl
version info: Vision Release: 1.0.59
description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
license: http://creativecommons.org/licenses/by/3.0/

The Ontology of Medically Related Social Entities
comment: 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
creator: William Hogan
creator: Mathias Brochhausen
creator: Amanda Hicks
creator: Swetha Garimalla
Contributor: Daniel Welch
version info: 2019-21-02
license: CC-BY 4.0
creator: Shariq Tariq

pdro.owl
creator: Jean-François Éthier
creator: Adrien Barton
comment: An ontology of drug prescriptions
comment: This is a merged version of the ontology.
creator: Ryeyan Taseen
creator: Paul Fabry

pr.owl
license: http://creativecommons.org/licenses/by/4.0/
has_obo_format_version: 1.2
date: 23:09:2019 10:14
comment: Use reasoner in OBO Edit to see the correct hierarchy.
comment: The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details.

ro.owl
license: https://creativecommons.org/publicdomain/zero/1.0/
source: ro
description: The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
comment: Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]

pno.owl
is allocated id range: IAO_0020000-IAO_0020999