ro_bfo_bridge
type: Ontology
label: relationship
label: The Ontology of Medically Related Social Entities
version info: $Revision: 80 $
version info: 1.1.1
Contributor: Alan Ruttenberg
comment: An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/
Contributor: Andrew Spear
Source: Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations"
Source: Barry Smith: "Against Fantology"
Source: Barry Smith: "Basic Tools of Formal Ontology"
Source: Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
title: Basic Formal Ontology (BFO)
creator: Holger Stenzhorn
publisher: Institute for Formal Ontology and Medical Information Science (IFOMIS)
Contributor: Pierre Grenon
Source: Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics"
Source: Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
Source: Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE"
Source: Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO"
Source: Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization"
Format: application/rdf+xml
language: en
default language: en
comment: obsolete classes from the information artifact ontology. see http://code.google.com/p/information-artifact-ontology/
creator: Richard Scheuermann
creator: Barry Smith
creator: Alan Ruttenberg
creator: Cornelius Rosse
date: 2009-08-07
creator: Amanda Hicks
creator: Anita Burgun
creator: Mark McGilchrist
creator: Shariq Tariq
creator: Swetha Garimalla
comment: The Clinical Data Integration Model serves as a global model in TRANSFoRm's unifiefd strutural/terminological interoperability mediation framework. It focuses on primary care research requirements.
comment: This file is the MIREOT specification file - see http://obi-ontology.org/page/MIREOT
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://ub2020.buffalo.edu/strategicstrengths/announcements/wp-content/uploads/2010/09/ehr-september-22.pdf)
Rights Management: http://creativecommons.org/licenses/by/3.0
has default namespace: relationship
comment: cvs version $Revision: 1.5 $
comment: This ontology is in early development. Expect it to change.
creator: Albert Goldfain
creator: Mathias Brochhausen
saved by: cjm
version info: 2012-06-24
comment: This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi
creator: Sivaram Arabandi
has date: 14:07:2006 00:00
comment: This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see http://genomebiology.com/2005/6/5/R46 or the OBO relations page hosted at http://obo.sourceforge.net/relationship
has default namespace: ro_bfo_bridge
version info: 2011-09-13
creator: Bill Hogan
creator: Anand Kumar
creator: Werner Ceusters
version info: $Revision$
comment: Domain and range constraints for OBO_REL, in terms of BFO
comment: release version 1.01
creator: Daniel Merico
creator: Adrien Barton
creator: Lindsay Cowell
comment: The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is always available at http://purl.obolibrary.org/obo/ogms.owl This is version 2011-09-20 aka '0.9' http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl The OGMS developer site is http://code.google.com/p/ogms/ The discussion group is http://groups.google.com/group/ogms-discuss If you are interested in participating in the development of OGMS, please send email to albertgoldfain@gmail.com. Be sure to include a google-account username with your request (this will be the username associated with a gmail address).
version info: 2011-09-20
version info: 2013-09-22
creator: Jean-Francois Ethier
creator: William Hogan
version IRI: cdim.2 1

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

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

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

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

in branch
type: AnnotationProperty
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
definition editor: GROUP:OBI
definition source: OBI_0000277
editor preferred term: in branch

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

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

editor note
type: AnnotationProperty
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 source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: ready for release

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

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

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

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

curator note
type: AnnotationProperty
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
editor preferred term: curator note
has curation status: ready for release

is denotator type
type: AnnotationProperty
definition editor: Alan Ruttenberg
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
definition: relates an class defined in an ontology, to the type of it's denotator
editor preferred term: is denotator type

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

expand expression to
type: AnnotationProperty
definition editor: Chris Mungall
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
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)"
editor preferred term: expand expression to

expand assertion to
type: AnnotationProperty
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
definition editor: Chris Mungall
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand assertion to

first order logic expression
type: AnnotationProperty
definition editor: PERSON:Alan Ruttenberg
editor preferred term: first order logic expression

antisymmetric property
type: AnnotationProperty
definition editor: Alan Ruttenberg
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: use boolean value xsd:true to indicate that the property is an antisymmetric property

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

has ID digit count
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition editor: Person:Alan Ruttenberg
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)

has ID range allocated to
type: AnnotationProperty
definition editor: Person:Alan Ruttenberg
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]

has ID policy for
type: AnnotationProperty
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
definition editor: Person:Alan Ruttenberg
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"

elucidation
type: AnnotationProperty
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
editor preferred term: elucidation
definition editor: person:Alan Ruttenberg

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

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

is allocated id range
type: AnnotationProperty
definition: Add as annotation triples in the granting ontology
definition editor: PERSON:Alan Ruttenberg
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"
editor preferred term: is allocated id range

has axiom label
type: AnnotationProperty
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
definition source: Person:Alan Ruttenberg
definition editor: Person:Alan Ruttenberg
editor preferred term: has axiom id

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

has_specified_input
type: AnnotationProperty
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: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
editor preferred term: has_specified_input
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: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
type: ObjectProperty
domain: planned process
sub property of: has_participant

has_specified_output
type: AnnotationProperty
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
editor preferred term: has_specified_output
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
type: ObjectProperty
domain: planned process
inverse of: is_specified_output_of
sub property of: has_participant

is_realized_by
type: AnnotationProperty
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungall
definition: Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
alternative term: executed_during
alternative term: has_realization
alternative term: is_realized_as
editor preferred term: is_realized_by
has curation status: ready for release
domain: realizable_entity
type: ObjectProperty
range: processual_entity

has ID prefix
type: AnnotationProperty
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
definition editor: Person:Alan Ruttenberg
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"

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

Coverage
type: AnnotationProperty
description: Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
comment: The extent or scope of the content of the resource.

Creator
type: AnnotationProperty
comment: An entity primarily responsible for making the content of the resource.
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.

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

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

Format
type: AnnotationProperty
comment: The physical or digital manifestation of the resource.
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).

Resource Identifier
type: AnnotationProperty
comment: An unambiguous reference to the resource within a given context.
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).

Language
type: AnnotationProperty
comment: A language of the intellectual content of the resource.
description: Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.

Publisher
type: AnnotationProperty
comment: An entity responsible for making the resource available
description: Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.

Relation
type: AnnotationProperty
description: 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 related resource.

Rights Management
type: AnnotationProperty
description: Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
comment: Information about rights held in and over the resource.

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

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

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

Resource Type
type: AnnotationProperty
comment: The nature or genre of the content of the resource.
description: Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.

inheres in
type: AnnotationProperty
editor note: This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant.
editor note: This relation belongs in BFO/RO, and will be in BFO 2
type: ObjectProperty
range: independent_continuant
domain: specifically_dependent_continuant

database_cross_reference
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

in_subset
type: AnnotationProperty

agent_in
type: AnnotationProperty
has_obo_namespace: relationship
has alternative id: OBO_REL:0000022
has_obo_namespace: ro_bfo_bridge
type: ObjectProperty
domain: continuant
range: occurrent
inverse of: has_agent
sub property of: participates_in

derived_into
type: AnnotationProperty
has alternative id: OBO_REL:0000016
has_obo_namespace: relationship
has_obo_namespace: ro_bfo_bridge
type: ObjectProperty
type: TransitiveProperty
range: continuant
domain: continuant
inverse of: derives_from

derives_from
type: AnnotationProperty
comment: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
has_obo_namespace: ro_bfo_bridge
has_obo_namespace: relationship
has alternative id: OBO_REL:0000015
has exact synonym: derived_from
has definition: Definition
  label: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: continuant
domain: continuant
has definition: Definition
  label: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

has_agent
type: AnnotationProperty
has alternative id: OBO_REL:0000021
has_obo_namespace: ro_bfo_bridge
has_obo_namespace: relationship
has definition: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
range: continuant
domain: occurrent
sub property of: has_participant
has definition: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

has_participant
type: AnnotationProperty
comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has alternative id: OBO_REL:0000019
has_obo_namespace: ro_bfo_bridge
has_obo_namespace: relationship
has definition: P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
range: continuant
domain: occurrent
inverse of: participates_in
has definition: P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

located_in
type: AnnotationProperty
comment: 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
has_obo_namespace: relationship
has alternative id: OBO_REL:0000008
has_obo_namespace: ro_bfo_bridge
has definition: Definition
  label: C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: continuant
domain: continuant
inverse of: location_of
has definition: Definition
  label: C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

location_of
type: AnnotationProperty
has_obo_namespace: ro_bfo_bridge
has alternative id: OBO_REL:0000009
has_obo_namespace: relationship
type: ObjectProperty
type: TransitiveProperty
domain: continuant
range: continuant

participates_in
type: AnnotationProperty
has_obo_namespace: relationship
has alternative id: OBO_REL:0000020
has_obo_namespace: ro_bfo_bridge
type: ObjectProperty
domain: continuant
range: occurrent

preceded_by
type: AnnotationProperty
comment: 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.
has_obo_namespace: ro_bfo_bridge
has alternative id: OBO_REL:0000017
has_obo_namespace: relationship
has definition: P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: occurrent
domain: occurrent
inverse of: precedes
has definition: P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

precedes
type: AnnotationProperty
has alternative id: OBO_REL:0000018
has_obo_namespace: relationship
has_obo_namespace: ro_bfo_bridge
type: ObjectProperty
type: TransitiveProperty
range: occurrent
domain: occurrent

transformation_of
type: AnnotationProperty
comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
has_obo_namespace: ro_bfo_bridge
has alternative id: OBO_REL:0000013
has_obo_namespace: relationship
has definition: Definition
  label: Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: continuant
domain: continuant
has definition: Definition
  label: Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

transformed_into
type: AnnotationProperty
comment: Obsoleted
has_obo_namespace: relationship
has alternative id: OBO_REL:0000014
has_obo_namespace: ro_bfo_bridge
type: ObjectProperty
sub property of: ObsoleteProperty
range: continuant
domain: continuant

inheres in
type: ObjectProperty
type: FunctionalProperty
alternative term: inheres_in
inverse of: is bearer of

is bearer of
type: ObjectProperty
alternative term: bearer of
alternative term: bearer_of

is aggregate of
type: ObjectProperty
alternative term: aggregate of
alternative term: aggregate_of
equivalent property: is-aggregate-of
sub property of: topObjectProperty

has temporal part
type: ObjectProperty
type: TransitiveProperty

temporal part of
type: ObjectProperty
type: TransitiveProperty
BFO OWL specification label: t-part-of
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]
has associated axiom(fol): (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
BFO CLIF specification label: temporalPartOf
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]
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])
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])
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
inverse of: has temporal part
imported from: bfo.owl

occupies temporal region
type: ObjectProperty
BFO CLIF specification label: occupiesTemporalRegion
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])
BFO OWL specification label: spans
inverse of: has temporal occupant
imported from: bfo.owl

has temporal occupant
type: ObjectProperty
BFO CLIF specification label: spanOf
BFO OWL specification label: span-of
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])
imported from: bfo.owl

has measurement unit label
type: ObjectProperty
type: FunctionalProperty
range: measurement unit label
sub property of: has_part

obsolete_specifically denotes
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
definition editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
definition: c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
has obsolescence reason: failed exploratory term
has curation status: pending final vetting
sub property of: ObsoleteProperty

is about
type: ObjectProperty
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 source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
definition editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting

mentions
type: ObjectProperty
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: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
definition editor: PERSON: Jonathan Rees
definition editor: Person: Alan Ruttenberg
has curation status: pending final vetting
sub property of: is about

denotes
type: ObjectProperty
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
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 source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
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
definition editor: person:Alan Ruttenberg
sub property of: is about

obsolete_materially denotes
type: ObjectProperty
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
has obsolescence reason: failed exploratory term
sub property of: ObsoleteProperty

is quality measurement of
type: ObjectProperty
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
definition editor: Alan Ruttenberg
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: 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
domain: measurement datum
sub property of: is about
range: quality

obsolete_describes
type: ObjectProperty
has obsolescence reason: failed exploratory term
sub property of: ObsoleteProperty

obsolete_represents
type: ObjectProperty
has obsolescence reason: failed exploratory term
sub property of: ObsoleteProperty

has coordinate unit label
type: ObjectProperty
type: FunctionalProperty
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
domain: cartesian spatial coordinate datum
range: length unit
sub property of: has_part

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

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

is quality specification of
type: ObjectProperty
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition: a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
has curation status: metadata complete
sub property of: is about

quality is specified as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition: inverse of the relation of is quality specification of
has curation status: metadata complete
inverse of: is quality specification of

has time stamp
type: ObjectProperty
type: FunctionalProperty
definition editor: Alan Ruttenberg
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has curation status: metadata incomplete
range: time measurement datum
domain: time stamped measurement datum
sub property of: has_part

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

is_concretization_of
type: ObjectProperty
definition: a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends
range: generically_dependent_continuant
domain: specifically_dependent_continuant

is_concretized_as
type: ObjectProperty
definition: a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends
inverse of: is_concretization_of
domain: generically_dependent_continuant
range: specifically_dependent_continuant

is_specified_output_of
type: ObjectProperty
definition editor: PERSON:Bjoern Peters
editor preferred term: is_specified_output_of
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
range: planned process
sub property of: participates_in

is member of organization
type: ObjectProperty
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
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
definition editor: Person:Helen Parkinson
definition: Relating a legal person to an organization in the case where the legal person has a role as member of the organization
editor preferred term: is member of organization
range: organization
inverse of: has organization member
domain: Class
  union of: Homo sapiens
  union of: organization

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization

is-aggregate-of
type: ObjectProperty
has obsolescence reason: BFO relation takes precedence.
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

is-component-of-aggregate
type: ObjectProperty
comment: At the instance level, this relation is the named inverse of is-aggregate-of. At the type level, however, not so. We expect BFO 2.0 to have this relation as well, and we will obsolete this property and declare it equivalent to BFO's version when BFO 2.0 comes out.

starts
type: ObjectProperty
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
has curation status: pending final vetting
sub property of: part_of

starts with
type: ObjectProperty
type: TransitiveProperty
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: a(y) = a(x) ? ?(y) < ?(x), where a is a function that maps a process to a start point, and ? is a function that maps a process to an end point.
alternative term: started by
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: pending final vetting
inverse of: starts
sub property of: has_part

Axiom
annotated target: started by
editor note: From Allen terminology
annotated property: alternative term
annotated source: starts with

ends
type: ObjectProperty
definition: inverse of ends with
has curation status: pending final vetting
inverse of: ends with
sub property of: part_of

ends with
type: ObjectProperty
type: TransitiveProperty
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: a(y) > a(x) ? ?(y) = ?(x), where a is a function that maps a process to a start point, and ? is a function that maps a process to an end point.
alternative term: finished by
has curation status: pending final vetting
sub property of: has_part

Axiom
annotated target: finished by
editor note: From Allen terminology
annotated property: alternative term
annotated source: ends with

is about
type: ObjectProperty
domain: information content entity

regulates
type: ObjectProperty
domain: processual_entity
range: Class
  union of: quality
  union of: processual_entity

towards
type: ObjectProperty
editor note: AG: Currently the only way to handle relational quality?
comment: relation binding a relational quality or disposition to the relevant type of entity

adjacent_to
type: ObjectProperty
comment: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
has alternative id: OBO_REL:0000012
has_obo_namespace: relationship
has definition: C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

contained_in
type: ObjectProperty
comment: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
has_obo_namespace: relationship
has alternative id: OBO_REL:0000010
inverse of: contains
has definition: Definition
  label: C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

contains
type: ObjectProperty
has_obo_namespace: relationship
has alternative id: OBO_REL:0000011

has_improper_part
type: ObjectProperty
type: TransitiveProperty
comment: See reasons for obsoletion of improper_part_of
has_obo_namespace: relationship
has alternative id: OBO_REL:0000024
sub property of: ObsoleteProperty
sub property of: has_part

has_integral_part
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: relationship
has alternative id: OBO_REL:0000005
sub property of: has_part
inverse of: integral_part_of

has_part
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: relationship
has alternative id: OBO_REL:0000003

has_proper_part
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: relationship
has alternative id: OBO_REL:0000007
sub property of: has_part

improper_part_of
type: ObjectProperty
type: TransitiveProperty
comment: OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
has_obo_namespace: relationship
has alternative id: OBO_REL:0000025
sub property of: ObsoleteProperty
inverse of: has_improper_part
sub property of: part_of
has definition: As for part_of, with the additional constraint that subject and object may be identical
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

integral_part_of
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000004
has_obo_namespace: relationship
sub property of: part_of
has definition: C integral_part_of C' if and only if: C part_of C' AND C' has_part C
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

part_of
type: ObjectProperty
type: TransitiveProperty
comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
has_obo_namespace: relationship
has alternative id: OBO_REL:0000002
editor note: There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
inverse of: has_part
has definition: Definition
  label: For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

proper_part_of
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000006
has_obo_namespace: relationship
inverse of: has_proper_part
sub property of: part_of
has definition: As for part_of, with the additional constraint that subject and object are distinct
  type: Definition
  database_cross_reference: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

relationship
type: ObjectProperty
comment: this relation was superfluous, so it has been obsoleted
has_obo_namespace: relationship
sub property of: ObsoleteProperty
has definition: A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
  type: Definition
  database_cross_reference: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

has measurement numeral
type: ObjectProperty
range: numeral
sub property of: has_part

measurement unit label of
type: ObjectProperty
sub property of: part_of

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: float

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

geographical location
type: Class
subclass of: site
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: GAZ

embryo development ending in birth or egg hatching
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: part_of
  some values from: life course
id: GO:0009792
definition: The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
has_obo_namespace: biological_process
has broad synonym: embryogenesis
imported from: go.owl

death
type: Class
subclass of: process_boundary
definition: A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
id: GO:0016265
comment: See also the biological process term 'apoptosis ; GO:0006915'.
database_cross_reference: Wikipedia:Death
has_obo_namespace: biological_process
imported from: go.owl
in_subset: goslim plant
in_subset: gosubset prok

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI branch derived
definition source: OBI_0000349
definition editor: PlanAndPlannedProcess Branch
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
editor preferred term: conditional specification
has curation status: metadata complete

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

objective specification
type: Class
subclass of: directive information entity
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: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
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 preferred term: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: pending final vetting

narrative object
type: Class
subclass of: information content entity
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition: A narrative object is an information content entity that is a set of propositions.
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
definition source: OBI_0000013
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition source: group:OBI
editor preferred term: narrative object
definition editor: person:Chris Stoeckert
has curation status: uncurated

action specification
type: Class
subclass of: directive information entity
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
has curation status: metadata incomplete

obsolete_artifact
type: Class
subclass of: ObsoleteClass
has obsolescence reason: failed exploratory term

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

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
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
editor preferred term: software
has curation status: metadata complete

obsolete2_digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000261
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
definition: A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
definition source: group:OBI
editor preferred term: obsolete_digital entity
definition editor: person:Chris Stoeckert
has obsolescence reason: failed exploratory term

journal article
type: Class
subclass of: report
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
definition source: OBI_0000159
definition: a report that is published in a journal
definition source: group:OBI
editor preferred term: journal article
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
has curation status: metadata complete

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: is_concretization_of
    some values from: information content entity
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
definition: A quality of an information bearer that imparts the information content
definition editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The pattern in ink on a page of a paperback novel.
editor preferred term: information carrier
has curation status: pending final vetting

model number
type: Class
subclass of: symbol
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: Person: Alan Ruttenberg
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
editor preferred term: model number
has curation status: pending final vetting

obsolete_material_entity
type: Class
subclass of: ObsoleteClass
has obsolescence reason: placeholder removed

obsolete2_binary digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000244
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
definition: A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
example of usage: MS Word document, ZIP file, DICOM file, JPEG file
editor preferred term: binary digital entity
editor note: digital_entity
definition source: group:OBI
definition editor: person:Chris Stoeckert
has obsolescence reason: failed exploratory term

obsolete_unit of measure
type: Class
subclass of: ObsoleteClass
definition editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The length of a ruler.
definition: a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
has obsolescence reason: failed exploratory term

programming language
type: Class
subclass of: plan specification
definition: A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition source: OBI_0000058
example of usage: R, Perl, Java
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: programming language
has curation status: metadata complete

data item
type: Class
subclass of: information content entity
definition source: OBO:imported "http://purl.obolibrary.org/obo/iao.owl"
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: 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: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition editor: PERSON: Alan Ruttenberg
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.
alternative term: data
has curation status: pending final vetting
IAO_0000412: iao.owl

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
definition editor: PERSON: Jonathan Rees
definition: a smallish, word-like datum...
editor preferred term: symbol

numeral
type: Class
subclass of: symbol
definition: A symbol that denotes a number.
definition editor: PERSON: Jonathan Rees
editor preferred term: numeral

information content entity
type: Class
subclass of: generically_dependent_continuant
subclass of: Restriction
  on property: is about
  some values from: entity
definition source: OBO:sourced "OBI:0000142"
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
definition editor: PERSON: Chris Stoeckert
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 preferred term: information content entity
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.
has curation status: pending final vetting

integer numeral
type: Class
subclass of: numeral
definition editor: PERSON: Jonathan Rees
definition: a numeral that denotes an integer
editor preferred term: integer numeral

scalar measurement datum
type: Class
subclass of: measurement datum
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.
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
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: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
has curation status: metadata complete

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

time trigger
type: Class
subclass of: conditional specification
definition source: OBI branch derived
definition source: OBI_0000331
definition editor: PlanAndPlannedProcess Branch
definition: revisit?
editor preferred term: time trigger
has curation status: uncurated

obsolete_study interpretation
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
editor note: 2009-03-16: work has been done on this term 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 source: OBI_0000005
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
alternative term: conclusion
definition: A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
definition editor: Lawrence Hunter
definition editor: PERSON: Jennifer Fostel
editor note: The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
editor preferred term: obsolete_study interpretation
has obsolescence reason: failed exploratory term
has curation status: pending final vetting

dot plot
type: Class
subclass of: graph
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
example of usage: Dot plot of SSC-H and FSC-H.
definition source: OBI_0000123
editor preferred term: dot plot
definition source: group:OBI
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

graph
type: Class
subclass of: diagram
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition source: OBI_0000240
definition editor: PERSON: Lawrence Hunter
editor preferred term: graph
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
has curation status: pending final vetting

obsolete2_text based digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000132
definition source: group:OBI
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
definition: A text based digital entity is a digital entity that is encoded so that it only contains text characters.
example of usage: XML file, C++ source code file
editor note: digital_entity
definition editor: person:Chris Stoeckert
editor preferred term: text based digital entity
has obsolescence reason: failed exploratory term

rule
type: Class
subclass of: conditional specification
editor note: MSI
definition source: OBI_0500021
definition source: PRS
definition editor: PRS
definition: a rule is an executable which guides, defines, restricts actions
example of usage: example to be added
editor preferred term: rule
has curation status: uncurated

contour plot
type: Class
subclass of: graph
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
definition source: OBI_0000246
editor preferred term: contour plot
editor note: generically_dependent_continuants
definition source: group:Flow Cytometry community
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

obsolete2_report figure
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000027
definition: A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
editor note: I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
editor note: Replaced by defined version of figure
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
editor preferred term: report figure
has obsolescence reason: failed exploratory term
has curation status: uncurated

algorithm
type: Class
subclass of: plan specification
definition: A plan specification which describes inputs, 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 source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: metadata complete

software interpreter
type: Class
subclass of: algorithm
definition: A software interpreter is a software application that executes some specified input software.
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition source: OBI_0000199
example of usage: R program, Perl interpreter, Java virtual machine
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: software interpreter
has curation status: metadata complete

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

density plot
type: Class
subclass of: graph
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
example of usage: Density plot of SSC-H and FSC-H.
definition source: OBI_0000179
editor preferred term: density plot
definition source: group:Flow Cytometry community
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

report
type: Class
subclass of: document
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term 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.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
definition source: GROUP: OBI
definition source: OBI_0000099
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Chris Stoeckert
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
editor preferred term: report
has curation status: pending final vetting

obsolete_report element
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: needs some more work (clarify relations).
editor note: 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
editor note: 2009-03-16: work has been done on this term 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.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000001
definition editor: PERSON: Melanie Courtot
editor note: Replaced by textual entity and figure
definition: A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
definition source: GROUP:OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Allyson Lister
editor note: There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
editor preferred term: report element
has obsolescence reason: failed exploratory term
has curation status: metadata complete

obsolete2_binary executable
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000222
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'
definition: Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
editor preferred term: binary executable
definition source: group:OBI
definition editor: person:Jennifer Fostel
has obsolescence reason: failed exploratory term

source code module
type: Class
subclass of: directive information entity
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition source: OBI_0000039
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: source code module
has curation status: uncurated

obsolete_report table
type: Class
subclass of: ObsoleteClass
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000265
definition: A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
editor preferred term: report table
has curation status: example to be eventually removed
has obsolescence reason: failed exploratory term

data format specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
definition source: OBI branch derived
definition source: OBI_0000187
definition editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: metadata incomplete

data set
type: Class
subclass of: data item
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
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.
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).
definition source: OBI_0000042
editor preferred term: data set
definition source: group:OBI
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: metadata complete

image
type: Class
subclass of: figure
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 source: OBI_0000030
definition source: group:OBI
editor preferred term: image
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
has curation status: ready for release

data about an ontology part
type: Class
subclass of: data item
definition editor: Person:Alan Ruttenberg
definition: data about an ontology part is a data item about a part of an ontology, for example a term

plan specification
type: Class
subclass of: directive information 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
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
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.
definition editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
editor preferred term: plan specification
has curation status: metadata complete

obsolete2_digital document
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000195
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
definition: A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
editor preferred term: digital document
definition source: group:OBI
definition editor: person:Jennifer Fostel
has obsolescence reason: failed exploratory term

measurement datum
type: Class
subclass of: data item
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,}.
editor preferred term: measurement datum
editor note: 2/2/2009 is_specified_output of some assay?
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 source: OBI_0000305
definition source: group:OBI
definition editor: person:Chris Stoeckert
has curation status: metadata complete
IAO_0000412: iao.owl

obsolete_identifier
type: Class
subclass of: ObsoleteClass
editor note: _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
has curation status: organizational term
has obsolescence reason: placeholder removed

version number
type: Class
subclass of: symbol
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.
definition editor: GROUP: IAO
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
editor preferred term: version number
has curation status: uncurated

serial number
type: Class
subclass of: symbol
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
editor preferred term: serial number
has curation status: uncurated

lot number
type: Class
subclass of: symbol
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
alternative term: batch number
editor preferred term: lot number
has curation status: uncurated

setting datum
type: Class
subclass of: data item
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
has curation status: uncurated

obsolete_digital quality
type: Class
subclass of: ObsoleteClass
editor note: Need to rework digital entity. Digital quality was suggested by Barry.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
has obsolescence reason: failed exploratory term

conclusion textual entity
type: Class
subclass of: textual entity
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: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
definition editor: Person:Alan Ruttenberg
editor preferred term: 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

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: is_concretization_of
      some values from: information content entity
definition: An information bearer is a material_entity in which a concretization of an information content entity inheres.
definition editor: GROUP: IAO
example of usage: a hard drive, a piece of paper with writing on it, a brain
editor preferred term: material information bearer
has curation status: metadata complete

histogram
type: Class
subclass of: graph
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: histogram
has curation status: ready for release

heatmap
type: Class
subclass of: graph
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: heatmap
has curation status: ready for release

Venn diagram
type: Class
subclass of: graph
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: Venn diagram
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram
has curation status: ready for release

obsolete_survival curve
type: Class
subclass of: ObsoleteClass
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
editor preferred term: obsolete_survival curve
has obsolescence reason: failed exploratory term
has curation status: ready for release

dendrogram
type: Class
subclass of: graph
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: dendrogram
has curation status: ready for release

scatter plot
type: Class
subclass of: graph
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
editor preferred term: scatter plot
alternative term: scattergraph
has curation status: ready for release

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
has curation status: ready for release

photographic print
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: bearer of
    some values from: Restriction
      on property: is_concretization_of
      some values from: photograph
definition: A photographic print is a material entity upon which a photograph generically depends.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
editor preferred term: photographic print
has curation status: pending final vetting

obsolescence reason specification
type: Class
equivalent class: Class
  one of: terms merged
  one of: term imported
  one of: placeholder removed
  one of: failed exploratory term
  one of: term split
subclass of: data about an ontology part
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
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: 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 preferred term: obsolescence reason specification
has curation status: pending final vetting

textual entity
type: Class
subclass of: information content entity
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
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
alternative term: text
editor preferred term: textual entity

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
definition editor: PERSON: Lawrence Hunter
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication
editor preferred term: citation
has curation status: pending final vetting

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

institutional identification
type: Class
subclass of: textual entity
definition: A textual entity intended to identify a particular institution
definition editor: PERSON: Lawrence Hunter
example of usage: University of Colorado Denver School of Medicine
editor preferred term: institutional identification
has curation status: pending final vetting

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
definition: A textual entity that describes a figure
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
definition editor: PERSON: Lawrence Hunter
editor preferred term: caption
has curation status: pending final vetting

document title
type: Class
subclass of: textual entity
definition: A textual entity that names a document
definition editor: PERSON: Lawrence Hunter
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
editor preferred term: document title
has curation status: pending final vetting

table
type: Class
subclass of: textual entity
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
definition editor: PERSON: Lawrence Hunter
editor preferred term: table
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting

table of abbreviations
type: Class
subclass of: table
definition: A table where the constituent texts are abbreviations and their expansions
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
definition editor: PERSON: Lawrence Hunter
editor preferred term: table of abbreviations
has curation status: pending final vetting

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

diagram
type: Class
subclass of: figure
definition: A figure that expresses one or more propositions
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
definition editor: PERSON: Lawrence Hunter
editor preferred term: diagram
has curation status: metadata complete

document
type: Class
subclass of: information content entity
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
definition editor: PERSON: Lawrence Hunter
editor preferred term: document
has curation status: metadata complete

publication
type: Class
subclass of: document
definition: A document that has been accepted by a publisher
example of usage: A journal article or book
definition editor: PERSON: Lawrence Hunter
editor preferred term: publication
has curation status: metadata complete

publication about an investigation
type: Class
subclass of: publication
subclass of: Restriction
  on property: is about
  some values from: investigation
definition: A publication that is about an investigation
example of usage: Most scientific journal articles
definition editor: PERSON: Lawrence Hunter
editor preferred term: publication about an investigation
alternative term: scientific publication
has curation status: metadata complete

patent
type: Class
subclass of: document
definition: A document that has been accepted by a patent authority
definition editor: PERSON: Lawrence Hunter
example of usage: US Patent 6,449,603
editor preferred term: patent
has curation status: metadata complete

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

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
definition editor: PERSON: Lawrence Hunter
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
editor preferred term: abstract
has curation status: metadata complete

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
definition editor: PERSON: Lawrence Hunter
example of usage: Section labelled 'introduction' of a typical scientific journal article
alternative term: introduction
editor preferred term: introduction to a publication about an investigation
has curation status: metadata complete

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
editor preferred term: methods section
has curation status: metadata complete

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design execution
definition: A part of a publication about an investigation that is about a study design execution
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'results' in a typical scientific journal article
editor preferred term: results section
has curation status: metadata complete

discussion section of a publication about an investigation
type: Class
subclass of: document part
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: discussion section
editor preferred term: discussion section of a publication about an investigation
has curation status: metadata complete

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: citation
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
editor preferred term: references section
has curation status: metadata complete

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: author identification
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
definition editor: PERSON: Lawrence Hunter
editor preferred term: author list
definition: part of a document that enumerates the authors of the document
has curation status: metadata complete

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: institutional identification
definition editor: PERSON: Lawrence Hunter
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
editor preferred term: institution list
definition: part of a document that has parts that are institution identifications associated with the authors of the document
has curation status: metadata complete

author contributions section
type: Class
subclass of: document part
definition: A part of a publication that is about the specific contributions of each author
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
definition editor: PERSON: Lawrence Hunter
editor preferred term: author contributions section
has curation status: metadata complete

acknowledgements section
type: Class
subclass of: document part
definition editor: PERSON: Lawrence Hunter
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
editor preferred term: acknowledgements section
has curation status: metadata complete

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
definition editor: PERSON: Lawrence Hunter
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
alternative term: endnote
editor preferred term: footnote
has curation status: metadata complete

supplementary material to a document
type: Class
subclass of: document part
definition editor: PERSON: Lawrence Hunter
alternative term: appendix
definition: part of a document that is segregated from the rest of the document due to its size
alternative term: supplementary material
editor preferred term: supplementary material to a document
has curation status: metadata complete

table of contents
type: Class
subclass of: table
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter
editor preferred term: table of contents
has curation status: pending final vetting

table of figures
type: Class
subclass of: table
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter
editor preferred term: table of figures
has curation status: pending final vetting

running title
type: Class
subclass of: document title
definition: A shorter version of a document title
definition editor: PERSON: Lawrence Hunter
editor preferred term: running title
has curation status: pending final vetting

copyright section
type: Class
subclass of: document part
definition: A document part that describes legal restrictions on making or distributing copies of the document
definition editor: PERSON: Lawrence Hunter
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
editor preferred term: copyright section
has curation status: metadata complete

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: zero_dimensional_region
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
definition editor: Alan Ruttenberg
has curation status: metadata complete

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero_dimensional_region
    intersection of: Restriction
      on property: part_of
      some values from: one_dimensional_region
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero_dimensional_region
    intersection of: Restriction
      on property: part_of
      some values from: two_dimensional_region
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero_dimensional_region
    intersection of: Restriction
      on property: part_of
      some values from: three_dimensional_region
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

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
definition: A scalar measurement datum that is the result of measurement of length quality
definition editor: Alan Ruttenberg
has curation status: metadata incomplete

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
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
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.

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
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality
definition editor: Person:Alan Ruttenberg
has curation status: metadata incomplete

hypothesis textual entity
type: Class
subclass of: textual entity
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A textual entity that expresses an assertion that is intended to be tested.
definition editor: Person:Alan Ruttenberg
editor preferred term: hypothesis 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

time measurement datum
type: Class
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
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measuring a temporal interval
definition editor: Person:Alan Ruttenberg
has curation status: metadata incomplete

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical location
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59

email address
type: Class
subclass of: information content entity
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
definition editor: Person:Alan Ruttenberg
definition editor: Person:Chris Stoeckart
editor preferred term: email address
has curation status: metadata incomplete

author role
type: Class
subclass of: role
definition: A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor preferred term: author role
has curation status: pending final vetting

data item extraction from journal article
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: journal article
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
definition: a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
definition editor: Person:Alan Ruttenberg
has curation status: metadata complete

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
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
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
definition: a planned process in which a document is created or added to by including the specified input in it.
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has curation status: pending final vetting

line graph
type: Class
subclass of: graph
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
alternative term: line chart
editor preferred term: line graph
has curation status: ready for release

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_participant
  some values from: CRID registry
subclass of: Restriction
  on property: has_participant
  some values from: CRID symbol
example of usage: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition editor: Person:Melanie Courtot
definition: a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
has curation status: metadata complete

associating information with a CRID in the CRID registry
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_participant
  some values from: CRID registry
subclass of: Restriction
  on property: has_specified_output
  some values from: CRID symbol
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
definition editor: PERSON:Alan Ruttenberg
has curation status: metadata complete

obsolete_establishing a CRID registry
type: Class
subclass of: ObsoleteClass
definition: a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
editor note: MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
has obsolescence reason: failed exploratory term

CRID symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part_of
  some values from: CRID
definition: A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
editor note: IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
definition source: Original proposal from Bjoern, discussions at IAO calls
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
example of usage: PMID:12345, 12345 in a database column which has header "pubmedID"

CRID
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has_part
  some values from: CRID symbol
imported from: http://purl.obolibrary.org/obo/iao.owl
alternative term: Centrally Registered IDentifier
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
example of usage: Entries in a Column of which the header is "Pubmed ID"
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 source: Original proposal from Bjoern, discussions at IAO calls
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
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".

CRID registry
type: Class
subclass of: data set
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.
editor note: IAO call, 20101124: PubMed registry is an instance of CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
has curation status: metadata incomplete

looking up a CRID
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_participant
  some values from: CRID registry
subclass of: Restriction
  on property: has_specified_input
  some values from: CRID symbol
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
has curation status: metadata complete

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

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has_part
  some values from: time stamped measurement datum
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
definition editor: Alan Ruttenberg
alternative term: experimental time series
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete

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

software method
type: Class
subclass of: software
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software module
type: Class
subclass of: software
definition: A software module is software composed of a collection of software methods.
definition editor: PERSON: Melanei Courtot
definition editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software library
type: Class
subclass of: software
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software application
type: Class
subclass of: software
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: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software script
type: Class
subclass of: software
definition: A software script is software whose instructions can be executed using a software interpreter.
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

Teleostomi
type: Class
subclass of: Gnathostomata
editor preferred term: Teleostomi
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Teleostomi
editor preferred term: Euteleostomi
imported from: ncbitaxon.owl

Homo/Pan/Gorilla group
type: Class
subclass of: Hominidae
editor preferred term: Homo/Pan/Gorilla group
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Eutheria
editor preferred term: Euarchontoglires
imported from: ncbitaxon.owl

Simiiformes
type: Class
subclass of: Haplorrhini
editor preferred term: Simiiformes
imported from: ncbitaxon.owl

Hominoidea
type: Class
subclass of: Catarrhini
editor preferred term: Hominoidea
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Sarcopterygii
editor preferred term: Tetrapoda
imported from: ncbitaxon.owl

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

Theria
type: Class
subclass of: Mammalia
editor preferred term: Theria
imported from: ncbitaxon.owl

Fungi/Metazoa group
type: Class
subclass of: Eukaryota
editor preferred term: Fungi/Metazoa group
imported from: ncbitaxon.owl

Metazoa
type: Class
subclass of: Fungi/Metazoa group
editor preferred term: Metazoa
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Eumetazoa
editor preferred term: Bilateria
imported from: ncbitaxon.owl

Coelomata
type: Class
subclass of: Bilateria
editor preferred term: Coelomata
imported from: ncbitaxon.owl

Deuterostomia
type: Class
subclass of: Coelomata
editor preferred term: Deuterostomia
imported from: ncbitaxon.owl

Haplorrhini
type: Class
subclass of: Primates
editor preferred term: Haplorrhini
imported from: ncbitaxon.owl

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

Eumetazoa
type: Class
subclass of: Metazoa
editor preferred term: Eumetazoa
imported from: ncbitaxon.owl

Chordata
type: Class
subclass of: Deuterostomia
editor preferred term: Chordata
imported from: ncbitaxon.owl

Vertebrata
type: Class
subclass of: Craniata
editor preferred term: Vertebrata
imported from: ncbitaxon.owl

Gnathostomata
type: Class
subclass of: Vertebrata
editor preferred term: Gnathostomata
imported from: ncbitaxon.owl

Sarcopterygii
type: Class
subclass of: Euteleostomi
editor preferred term: Sarcopterygii
imported from: ncbitaxon.owl

Craniata
type: Class
subclass of: Chordata
editor preferred term: Craniata
imported from: ncbitaxon.owl

Eutheria
type: Class
subclass of: Theria
editor preferred term: Eutheria
imported from: ncbitaxon.owl

Primates
type: Class
subclass of: Euarchontoglires
editor preferred term: Primates
imported from: ncbitaxon.owl

Catarrhini
type: Class
subclass of: Simiiformes
editor preferred term: Catarrhini
imported from: ncbitaxon.owl

Hominidae
type: Class
subclass of: Hominoidea
editor preferred term: Hominidae
imported from: ncbitaxon.owl

Homo
type: Class
subclass of: Homo/Pan/Gorilla group
editor preferred term: Homo
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Homo
alternative term: human being
editor preferred term: Homo sapiens
imported from: ncbitaxon.owl

planned process
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: has_participant
  some values from: patient
editor preferred term: planned process
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
imported from: obi.owl
IAO_0000412: obi.owl

investigation
type: Class
subclass of: planned process
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred term: investigation
imported from: obi.owl

study subject role
type: Class
subclass of: role in human social processes
subclass of: role
definition source: OBI
definition: study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about.
definition editor: GROUP: Role Branch
editor preferred term: study subject role
has curation status: ready for release
imported from: obi.owl

specimen role
type: Class
subclass of: role
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.
definition editor: GROUP: Role Branch
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 source: OBI
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.
editor preferred term: specimen role
definition: a role borne by a material entity that is gained during a specimen creation process and that can be realized by use of the specimen in an investigation
has curation status: ready for release
imported from: obi.owl

organization
type: Class
subclass of: material_entity
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
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.
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.
editor preferred term: organization
has curation status: ready for release

study design execution
type: Class
subclass of: planned process
definition: a planned process that realizes the concretization of a study design
editor preferred term: study design execution
imported from: obi.owl

individual organism identifier
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: is about
  some values from: organism
subclass of: Restriction
  on property: part_of
  some values from: individual organism CRID
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_169 Individual
definition: a CRID symbol used to distinguish one individual organism from another.
editor preferred term: individual organism identifier
has curation status: metadata complete
imported from: obi.owl

specimen identifier
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: denotes
  all values from: specimen
definition: A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation.
definition source: Penn Group
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: specimen ID
editor preferred term: specimen identifier
has curation status: metadata complete
imported from: obi.owl

organism
type: Class
subclass of: material_entity
subclass of: object
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.
definition editor: GROUP: OBI Biomaterial Branch
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 source: WEB: http://en.wikipedia.org/wiki/Organism
example of usage: animal
example of usage: fungus
editor preferred term: organism
example of usage: plant
example of usage: virus
has curation status: organizational term
imported from: obi.owl

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
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores 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.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition: A material entity that has the specimen role.
definition source: GROUP: OBI Biomaterial Branch
editor preferred term: specimen
has curation status: ready for release
imported from: obi.owl

study design
type: Class
subclass of: plan specification
definition: A study design is 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 preferred term: study design
imported from: obi.owl

obsolete_representation
type: Class
subclass of: ObsoleteClass
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T10:17:44Z

clinical finding
type: Class
subclass of: data item
definition: A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:02Z

clinical history
type: Class
subclass of: clinical finding
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:59Z

clinical picture
type: Class
subclass of: data item
curator note: creation date: 2010-07-19T10:20:20Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A representation of the clinically significant bodily components and/or bodily processes of a human being that is inferred from the totality of relevant clinical findings.

image finding
type: Class
subclass of: clinical finding
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T10:21:10Z
definition: A representation of an image that supports an inference to an assertion about some quality of a patient.

laboratory finding
type: Class
subclass of: clinical finding
curator note: creation date: 2009-06-23T10:21:58Z
definition: A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

preclinical finding
type: Class
subclass of: data item
definition editor: Albert Goldfain
definition: A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination.
curator note: creation date: 2009-06-23T10:22:44Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

symptom
type: Class
subclass of: entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:02:10Z
definition: A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease.
editor note: note: defined class

obsolete_bodily feature of a patient
type: Class
subclass of: ObsoleteClass
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:09:37Z

manifestation of a disease
type: Class
subclass of: quality
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:12:33Z
definition editor: Albert Goldfain
definition: A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable.

phenotype
type: Class
subclass of: quality
curator note: creation date: 2010-07-19T11:13:49Z
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.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

sign
type: Class
subclass of: entity
definition editor: Albert Goldfain
editor note: note: defined class
definition: A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in that is observed in a physical examination and is deemed by the clinician to be of clinical significance.
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 source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-11-18T11:14:36Z
editor preferred term: sign
IAO_0000412: ogms.owl

clinical manifestation of a disease
type: Class
subclass of: manifestation of a disease
curator note: creation date: 2009-06-23T11:15:43Z
definition: A manifestation of a disease that is detectable in a clinical history taking or physical examination.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

preclinical manifestation of a disease
type: Class
subclass of: manifestation of a disease
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination.
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:16:50Z

clinical phenotype
type: Class
subclass of: phenotype
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A clinically abnormal phenotype.
curator note: creation date: 2009-06-23T11:18:05Z

disease phenotype
type: Class
subclass of: phenotype
definition: A clinically abnormal phenotype that is characteristic of a single disease.
curator note: creation date: 2009-06-23T11:18:39Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

vital sign
type: Class
subclass of: sign
editor preferred term: vital sign
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
curator note: creation date: 2009-06-23T11:19:17Z
IAO_0000412: ogms.owl

predisposition to disease of type X
type: Class
subclass of: disposition
definition: A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X.
curator note: creation date: 2009-06-23T11:20:25Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

disease
type: Class
subclass of: disposition
subclass of: Restriction
  on property: inheres in
  some values from: organism
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:21:20Z
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

homeostasis
type: Class
subclass of: disposition
curator note: creation date: 2009-06-23T11:22:01Z
definition editor: Albert Goldfain

genetic predisposition to disease of type X
type: Class
subclass of: predisposition to disease of type X
definition: A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:23:07Z

acquired genetic disease
type: Class
subclass of: disease
definition: A disease whose physical basis is an acquired genetic disorder.
curator note: creation date: 2009-06-23T11:24:05Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

constitutional genetic disease
type: Class
subclass of: disease
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:24:59Z
definition: A disease whose physical basis is a constitutional genetic disorder.
definition editor: Albert Goldfain

obsolete_infectious disease
type: Class
subclass of: ObsoleteClass
definition: A disease whose physical basis is an infectious disorder.
curator note: creation date: 2009-06-23T11:25:51Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

abnormal homeostasis
type: Class
subclass of: homeostasis
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment.
curator note: creation date: 2009-06-23T11:26:44Z

normal homeostasis
type: Class
subclass of: homeostasis
definition: Homeostasis of a type that is not clinically abnormal.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:27:28Z

configuration
type: Class
subclass of: quality
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:36:24Z
definition editor: Albert Goldfain
definition: A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region.

pathological physical configuration
type: Class
subclass of: configuration
definition: A configuration which deviates in some way from a canonical configuration for a particular organism.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:36:58Z

disorder
type: Class
subclass of: material_entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
curator note: creation date: 2009-06-23T11:39:44Z

epigenetic disorder
type: Class
subclass of: disorder
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:40:27Z
definition: A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

genetic disorder
type: Class
subclass of: disorder
curator note: creation date: 2009-06-23T11:41:14Z
definition editor: Albert Goldfain
definition: A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

obsolete_infectious disorder
type: Class
subclass of: ObsoleteClass
curator note: creation date: 2009-06-23T11:41:45Z
definition: A disorder whose etiology includes the presence of a pathogenic organism within a host organism or an abnormal imbalance in the normal resident organismal flora.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

obsolete_secondary infection
type: Class
subclass of: ObsoleteClass
definition: A disorder consisting in the presence of a pathogenic organism within a host organism that occurs due to the disposition established by a prior infection with a pathogenic organism of a different kind.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:42:20Z
definition editor: Albert Goldfain

acquired genetic disorder
type: Class
subclass of: genetic disorder
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder.
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:43:09Z

constitutional genetic disorder
type: Class
subclass of: genetic disorder
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A genetic disorder inherited during conception that is part of all cells in the organism.
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:43:44Z

obsolete_standardized clinical process
type: Class
subclass of: ObsoleteClass
definition: A fiat process part which involves the execution of a standardized protocol for measuring qualities of a patient.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:47:06Z

clinical history taking
type: Class
subclass of: processual_entity
definition: An interview in which a clinician elicits a clinical history from a patient or from a third party who is reporting on behalf of the patient.
curator note: creation date: 2009-06-23T11:49:16Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

laboratory test
type: Class
subclass of: planned process
subclass of: processual_entity
subclass of: Restriction
  on property: has_specified_input
  some values from: specimen
subclass of: Restriction
  on property: starts with
  some values from: laboratory test ordering
subclass of: Restriction
  on property: has_specified_output
  some values from: laboratory finding
subclass of: Restriction
  on property: has_participant
  some values from: Class
    union of: patient
    union of: human study subject
subclass of: Restriction
  on property: has_specified_output
  some values from: normal value
definition: A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen.
curator note: creation date: 2009-06-23T11:49:49Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain

physical examination
type: Class
subclass of: processual_entity
curator note: creation date: 2010-07-19T11:50:18Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
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

etiological process
type: Class
subclass of: processual_entity
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:53:07Z
definition editor: Albert Goldfain
definition: A process in an organism that leads to a subsequent disorder.

bodily process
type: Class
subclass of: processual_entity
curator note: creation date: 2009-06-23T11:53:49Z
definition editor: Albert Goldfain

pathological bodily process
type: Class
subclass of: bodily process
curator note: creation date: 2009-06-23T11:54:29Z
definition: A bodily process that is clinically abnormal.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

disease course
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: realizes
  some values from: disease
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:55:44Z
definition: The totality of all processes through which a given disease instance is realized.

chronic disease course
type: Class
subclass of: disease course
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range.
curator note: creation date: 2009-06-23T11:56:26Z
definition editor: Albert Goldfain

progressive disease course
type: Class
subclass of: disease course
curator note: creation date: 2009-06-23T11:57:09Z
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis.

transient disease course
type: Class
subclass of: disease course
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
definition: A disease course that terminates in a return to normal homeostasis.
curator note: creation date: 2009-06-23T11:57:44Z

_undefined primitive term
type: Class
subclass of: entity
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:58:22Z

obsolete_bodily feature
type: Class
subclass of: ObsoleteClass
curator note: creation date: 2009-06-23T11:58:39Z
definition editor: Albert Goldfain

clinically abnormal
type: Class
subclass of: _undefined primitive term
curator note: creation date: 2009-06-23T11:59:24Z
definition editor: Albert Goldfain

physical basis
type: Class
subclass of: _undefined primitive term
curator note: creation date: 2009-06-23T12:00:09Z
definition editor: Albert Goldfain

realization
type: Class
subclass of: _undefined primitive term
curator note: creation date: 2009-06-23T12:00:39Z
definition editor: Albert Goldfain

diagnosis
type: Class
subclass of: data item
definition editor: Albert Goldfain
definition: The representation of a conclusion of a diagnostic process.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T12:42:23Z

normal value
type: Class
subclass of: generically_dependent_continuant
definition: A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population.
curator note: creation date: 2009-06-26T10:31:34Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

obsolete_infection
type: Class
subclass of: ObsoleteClass
definition editor: Albert Goldfain
curator note: creation date: 2009-07-08T12:20:49Z

pathological formation
type: Class
subclass of: material_entity
definition editor: Albert Goldfain
definition: TODO: Define, relate to disorder, and place in the OGMS hierarchy.
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
curator note: creation date: 2009-07-13T02:14:59Z

pathological anatomical structure
type: Class
subclass of: material_entity
curator note: creation date: 2009-07-13T02:14:05Z
definition editor: Albert Goldfain
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 source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf

portion of pathological body substance
type: Class
subclass of: material_entity
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition editor: Albert Goldfain
curator note: creation date: 2009-07-13T02:15:17Z
definition: TODO: Define, relate to disorder, and place in the OGMS hierarchy.

pathological transformation
type: Class
subclass of: pathological bodily process
curator note: creation date: 2009-07-13T02:17:07Z
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition: A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure.

pathological derivation
type: Class
subclass of: pathological bodily process
curator note: creation date: 2009-07-13T02:17:24Z
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition: A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier.
definition editor: Albert Goldfain

pathological invasion
type: Class
subclass of: pathological bodily process
definition editor: Albert Goldfain
curator note: creation date: 2009-07-13T02:17:47Z
definition source: http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
definition: TODO: Define.

physical examination finding
type: Class
subclass of: clinical finding
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
definition: TODO: Define.
curator note: creation date: 2009-11-24T04:51:11Z

organism population
type: Class
subclass of: object_aggregate
definition: An aggregate of organisms of the same type.
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2009-11-24T04:51:11Z
definition editor: Albert Goldfain

pain
type: Class
subclass of: symptom
definition: TODO: Define.
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2009-11-24T04:51:11Z
definition editor: Albert Goldfain

syndrome
type: Class
subclass of: quality
definition source: http://code.google.com/p/ogms/issues/detail
definition: A pattern of signs and symptoms that typically co-occur.
curator note: creation date: 2009-11-24T04:51:11Z
definition editor: Albert Goldfain

extended organism
type: Class
subclass of: object_aggregate
definition editor: Albert Goldfain
definition: An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-01-25T04:51:11Z

patient symptom report
type: Class
subclass of: information content entity
curator note: creation date: 2010-01-25T04:51:11Z
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
definition: A communication from a patient about something they perceive as being abnormal about their body or life.

congenital malformation
type: Class
subclass of: material_entity
definition source: http://code.google.com/p/ogms/issues/detail
definition: A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism.
definition editor: Albert Goldfain
curator note: creation date: 2010-03-31T04:51:11Z

treatment
type: Class
subclass of: processual_entity
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z
definition editor: Albert Goldfain
definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder

convalescence
type: Class
subclass of: processual_entity
definition: A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course.
definition editor: Albert Goldfain
curator note: creation date: 2010-03-31T04:51:11Z
definition source: http://code.google.com/p/ogms/issues/detail

life course
type: Class
subclass of: processual_entity
curator note: creation date: 2010-03-31T04:51:11Z
definition: A processual entity which has as parts all the processes in which a given organism is participant.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail

prognosis
type: Class
subclass of: data item
curator note: creation date: 2010-03-31T12:42:23Z
definition: A hypothesis about the course of a disease.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail

acute disease course
type: Class
subclass of: disease course
curator note: creation date: 2010-07-19T11:57:44Z
definition source: http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
definition editor: Albert Goldfain
definition: a disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset.

inflammation process
type: Class
subclass of: processual_entity
definition source: http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
definition: A process which is a response by an organism's tissues that is generally identified by swelling or localized pain
curator note: creation date: 2010-07-19T11:57:44Z
definition editor: Albert Goldfain

health care process
type: Class
subclass of: processual_entity
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
curator note: creation date: 2011-02-21T09:57:44Z
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6

health care encounter
type: Class
subclass of: health care process
subclass of: Restriction
  on property: part_of
  some values from: health care episode
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
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

hospitalization
type: Class
subclass of: health care encounter
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
definition editor: Albert Goldfain
definition: TODO

outpatient encounter
type: Class
subclass of: health care encounter
curator note: creation date: 2011-02-21T09:57:44Z
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
definition editor: Albert Goldfain
definition: TODO

inpatient encounter
type: Class
subclass of: health care encounter
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
definition editor: Albert Goldfain
definition: TODO

ED encounter
type: Class
subclass of: health care encounter
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
definition: TODO
curator note: creation date: 2011-02-21T09:57:44Z

injury
type: Class
subclass of: material_entity
definition: A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure.
definition editor: Albert Goldfain
curator note: creation date: 2011-09-20T09:57:44Z
editor note: At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5

prophylaxis
type: Class
subclass of: processual_entity
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e
definition: A planned process that has the objective to reduce the risk of acquiring one or more disorders.
curator note: creation date: 2011-09-20T09:57:44Z
definition editor: Albert Goldfain
editor note: Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.

diagnostic process
type: Class
subclass of: planned process
subclass of: processual_entity
subclass of: Restriction
  on property: has_specified_output
  some values from: diagnosis
subclass of: Restriction
  on property: part_of
  some values from: health care process
subclass of: Restriction
  on property: has_agent
  some values from: health care provider
subclass of: Restriction
  on property: has_participant
  some values from: patient
subclass of: Restriction
  on property: ends with
  some values from: diagnostic process conclusion
curator note: creation date: 2011-09-20T09:57:44Z
definition: An interpretive process that has as input a clinical picture of a given patient and as output an assertion (diagnostic statement) to the effect that the patient has a disease of such and such a type.
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
definition editor: Albert Goldfain

social security number
type: Class
subclass of: CRID
creator: Cheng Chen(cxchen1@ualr.edu)
alternative term: SSN
definition: Social Security Number(SSN) is a Centrally Registered IDentifier that is a nine-digit number issued to U.S. citizens, permanent residents, and temporary (working) residents under section 205(c) of the Social Security Act, codified as 42 U.S.C. § 405(c). The number is issued to an individual by the Social Security Administration, an independent agency of the United States government. Its primary purpose is to track individuals for Social Security purposes.
definition source: http://en.wikipedia.org/wiki/Social_Security_number

human social role
type: Class
equivalent class: Class
  intersection of: organism social role
  intersection of: Restriction
    on property: inheres in
    all values from: Homo sapiens
subclass of: organism social role
definition: A social role inhering in a human being.
definition editor: Mathias Brochhausen William R. Hogan

party to a legal entity
type: Class
subclass of: role in human social processes

party to a legal proceeding
type: Class
subclass of: party to a legal entity

party to a legal agreement
type: Class
subclass of: party to a legal entity

party to a marriage contract
type: Class
subclass of: party to a legal agreement

party to a power of attorney
type: Class
subclass of: party to a legal entity

gender role
type: Class
subclass of: role in human social processes
definition: A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Gender_role

male gender role
type: Class
subclass of: gender role
definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
definition editor: Mathias Brochhausen
alternative term: male gender

female gender role
type: Class
subclass of: gender role
definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
definition editor: Mathias Brochhausen
alternative term: female gender

human health care role
type: Class
subclass of: role in human social processes
definition: A human social role 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: 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 Mathias Brochhausen
alternative term: health care role

patient role
type: Class
subclass of: Class
  intersection of: human health care role
  intersection of: Restriction
    on property: inheres in
    all values from: organism
definition: A human health care role that inheres in an organism [human?] as the recipient of a health care service.
definition: A role borne by an organism being as the recipient of a health care service.
definition editor: Amanda Hicks
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Patient
alternative term: patient

health care provider role
type: Class
subclass of: human health care role
subclass 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 William R. Hogan

physician role
type: Class
subclass of: health care provider role
definition: A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Physician
alternative term: physician

nurse role
type: Class
subclass of: health care provider role
definition: A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.
definition editor: Mathias Brochhausen
definition source: based on: http://en.wikipedia.org/wiki/Nursing
alternative term: nurse

health care provider organization role
type: Class
subclass of: organization health care role
comment: Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division).

person health care provider role
type: Class
subclass of: human social role

physician practice
type: Class
subclass of: health care provider organization role

hospital role
type: Class
subclass of: health care provider role
definition: A role borne by an organization and realized by providing healthcare services by healthcare professionals of multiple different disciplines of medicine and enabling stationary treatment.
definition editor: Mathias Brochhausen
alternative term: hospital

integrated delivery network
type: Class
subclass of: health care provider organization role

collection of organisms
type: Class
equivalent class: Restriction
  on property: is-aggregate-of
  some values from: organism
subclass of: object_aggregate
definition: An object aggregate of organisms.
comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class.

collection of humans
type: Class
equivalent class: Restriction
  on property: is-aggregate-of
  some values from: Homo sapiens
subclass of: collection of organisms
comment: An object aggregate all of whose components are human beings.

role in human social processes
type: Class
subclass of: role
definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
comment: Previous definition: A role played by an entity in human social processes.

organization social role
type: Class
subclass of: role in human social processes
definition: A role in human social processes that inheres in an organization.
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
definition editor: William R. Hogan

organism social role
type: Class
equivalent class: Class
  intersection of: role in human social processes
  intersection of: Restriction
    on property: inheres in
    all values from: organism
subclass of: role in human social processes
definition: A role in human social processes that inheres in an organism.
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc.
comment: Previous definition: A role in human social processes played by an organism.
definition editor: William R. Hogan Mathias Brochhausen

organization health care role
type: Class
subclass of: organization social role
definition: An organization social role that is realized by a health care process.
comment: Previous definition: An organization social role played by an organization in health care processes.

geopolitical organization
type: Class
subclass of: ObsoleteClass
definition: An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii).
definition editor: William R. Hogan

major administrative subdivision
type: Class
equivalent class: Restriction
  on property: is member of organization
  on class: sovereign state
  qualified cardinality: 1
subclass of: subnational entity
definition: A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation.
comment: example: Northern Ireland

geopolitical dependency
type: Class
subclass of: subnational entity
definition: A subnational entity that does not possess full political independence or sovereignty as a sovereign state, but remains politically outside of the controlling state and controls a geographical region that is outside the controlling state's integral region.
comment: Typically, the common feature is that the dependency does not conduct foreign affairs, and relegates this authority to the sovereign state. BUt otherwise, it is largely or completely autonomous relative to the administrative subdivisions. Examples include Puerto Rico (U.S.), Guam (U.S.), Greenland (Denmark), French Polynesia (France), and Falkland Islands (United Kingdom).

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
    on class: organization
    min qualified cardinality: 2
subclass of: object_aggregate
definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.
definition editor: William R. Hogan Amanda Hicks

aggregate of sovereign states
type: Class
equivalent class: Class
  intersection of: Class
    complement of: sovereign state
  intersection of: Restriction
    on property: is-aggregate-of
    all values from: sovereign state
  intersection of: Restriction
    on property: is-aggregate-of
    on class: sovereign state
    min qualified cardinality: 2
subclass of: aggregate of geopoli organizations
definition editor: An aggregate of geopoli organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common
definition: An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them.
definition editor: William R. Hogan

aggregate of geopoli organizations
type: Class
equivalent class: Class
  intersection of: Class
    complement of: geopolitical organization
  intersection of: Restriction
    on property: is-aggregate-of
    all values from: geopolitical organization
  intersection of: Restriction
    on property: is-aggregate-of
    on class: geopolitical organization
    min qualified cardinality: 2
subclass of: aggregate of organizations
definition: An object aggregate that is not itself a geopolitical organization and whose members are only geopolitical organizations that have some feature in common
definition editor: William R. Hogan Amanda Hicks

aggregate of dependencies
type: Class
equivalent class: Class
  intersection of: Class
    complement of: geopolitical dependency
  intersection of: Restriction
    on property: is-aggregate-of
    all values from: geopolitical dependency
  intersection of: Restriction
    on property: is-aggregate-of
    on class: geopolitical dependency
    min qualified cardinality: 2
subclass of: aggregate of geopoli organizations
definition editor: Amanda Hicks
definition: An aggregate of geopoli organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.

aggregate of major administrative subdivisions
type: Class
equivalent class: Class
  intersection of: Class
    complement of: major administrative subdivision
  intersection of: Restriction
    on property: is-aggregate-of
    all values from: major administrative subdivision
  intersection of: Restriction
    on property: is-aggregate-of
    on class: major administrative subdivision
    min qualified cardinality: 2
subclass of: aggregate of geopoli organizations
definition editor: Amanda Hicks
definition: An aggregate of geopoli organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common

legal person role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: collection of humans
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
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
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.

intergovernmental organization
type: Class
subclass of: geopolitical organization
definition: an intergovernmental organization that has at least three member states, that has activies in at least three states, and that is unified by some formal intergovernmental agreement
definition source: "IGOs are organizations whose memebers include at lesat three states, that have activities in several states, and whose members are held together by a formal intergovernmental agreement ... These organizations range in size from three members (North American Free Trade Argreement [NAFTA]) to more than 190 memembers (Universal Postal Union (UPU)]. Memebers may come from primarily one georgraphic regioni (Oragnaization of American States [OAS]) or from all geographic regions (World Bank). although soem IGOs are designed to achieve a single purpose (Organization of Petroleum exporting countries [OPEC]), others have been developed for multiple tasks (United Nations [UN}). ... IGOs are recognized subjects of international law with separate standing fromt heir member states." Karns and Mingst I(2004) p. 7
definition editor: Amanda Hicks
Contributor: Katrina Donovan
comment: examples: North American Free Trade Argreement [NAFTA] , Universal Postal Union [UPU], Oragnaization of American States [OAS], World Bank), Organization of Petroleum exporting countries [OPEC] United Nations [UN[, The World Trade Organization [WTO], The World Health Organization [WHO], UNICEF

nongovernmental organizations
type: Class
subclass of: geopolitical organization
comment: Examples: Internaltion Federation of Red Cross and Red Crescent Societies, Oxfam, CARE, Doctors Without Borders, World Wildlife Fund, Transparency International, Human Rights Watch, Amnesty International, and Save the Children.
Contributor: Katrina Donovan
definition source: NGOs are private voluntary organizations whose members are individuals or associations that come together to acheive a common purpose. Some organizations are formed to advocate a particular cause such as human rights, peace, or envirnomental projetion. Others are established to provide services such as disaster relief, humantarian aid in war-torn socieities, or development assistance. ... National level groups are often called interest or pressure groups, and many of them are now linked to counterpart groups in other countries through transnational networks or federations. International NGOs, like IGOs, may draw their members from one region or several regions, and they may have very specific functions or be multi-functional. Karns and Mingst (2004) p. 10f.
definition: a geopolitical organization that is voluntary and private, whose members are individual persons or organizations that come together to acheive a common purpose.

private governance organizations
type: Class
subclass of: geopolitical organization
definition source: "Although the very meaning of the term is controversial, it involves authoritative decsionmaking in areas that once were part of national legal frameworks, the government, the sovereign state, or the public sector." Karns and Mingst (2004) p. 14.
definition editor: Amanda Hicks
comment: Examples: private bond-rating agencies such as Moody's Investors Service, International Chamber of Commerce, Worldwide Responsible Apparel Manufacturing Principles, Forest Stewardship
Contributor: Katrina Donovan

governmental organization
type: Class
subclass of: organization
definition editor: Amanda Hicks
definition: An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). Note: this definition was taken over from "geopolitical organization".
comment: IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.

sovereign state
type: Class
subclass of: governmental organization
definition: A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states.
comment: Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam".
definition editor: William R. Hogan
definition source: http://en.wikipedia.org/wiki/Sovereign_state
alternative term: nation
alternative term: nation state

subnational entity
type: Class
equivalent class: Restriction
  on property: is member of organization
  on class: sovereign state
  qualified cardinality: 1
subclass of: governmental organization
definition editor: Amanda Hicks
definition editor: William R. Hogan
definition: a governmental organization that has a local, regional, or territorial government that recognizes a sovereign state as its higher political authority

supranational entity
type: Class
subclass of: governmental organization
definition editor: Amanda Hicks
comment: e.g., the EU

biological sex
type: Class
subclass of: quality
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.
editor preferred term: biological sex
imported from: obi.owl
imported from: pato.owl

auscultatory blood pressure measurement process
type: Class
subclass of: noninvasive blood pressure measurement process

auscultatory pulse rate measurement process
type: Class
subclass of: pulse rate measurement process

axillary temperature
type: Class
equivalent class: Class
  intersection of: body temperature
  intersection of: Restriction
    on property: inheres in
    some values from: Axillary fossa
subclass of: body temperature
definition: The temperature of the axillary fossa.

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
definition: The pressure exerted by circulating blood on the walls of blood vessels.
editor preferred term: blood pressure
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
definition source: http://en.wikipedia.org/wiki/Blood_pressure

blood pressure measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: blood pressure
subclass of: scalar measurement datum
subclass of: measurement datum

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
subclass of: vital sign measurement process

body temperature
type: Class
equivalent class: Class
  intersection of: temperature
  intersection of: Restriction
    on property: inheres in
    all values from: Restriction
      on property: part_of
      some values from: Human body
subclass of: vital sign
definition editor: Albert Goldfain
definition: The temperature of a part of the human body

body temperature measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: body temperature
subclass of: scalar measurement datum
subclass of: measurement datum

body temperature measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: body temperature measurement datum
subclass of: planned process
subclass of: vital sign measurement process

brachial pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Brachial artery
subclass of: pulse rate
definition: The pulse rate of the brachial artery.

cardiac cycle phase
type: Class
subclass of: processual_entity
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 .

carotid pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Common carotid artery
subclass of: pulse rate
definition: The pulse rate of the carotid artery.

core body temperature
type: Class
subclass of: body temperature

diastole
type: Class
subclass of: cardiac cycle phase
definition: The phase of the cardiac cycle in which the heart fills with blood.

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.

diastolic central venous pressure
type: Class
equivalent class: Class
  intersection of: diastolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Class
      union of: Wall of superior vena cava
      union of: Wall of inferior vena cava
subclass of: diastolic blood pressure
definition: The diastolic blood pressure in the thoracic vena cava.

diastolic left ventricular pressure
type: Class
equivalent class: Class
  intersection of: diastolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Wall of left ventricle
subclass of: diastolic blood pressure
definition: The left ventricular pressure during diastole.

diastolic pulmonary artery pressure
type: Class
equivalent class: Class
  intersection of: diastolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Wall of pulmonary artery
subclass of: diastolic blood pressure
definition: The pulmonary artery pressure during diastole.

diastolic right ventricular pressure
type: Class
equivalent class: Class
  intersection of: diastolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Wall of right ventricle
subclass of: diastolic blood pressure
definition: The right ventricular pressure during diastole.

dorsalis pedis pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Dorsalis pedis artery
subclass of: pulse rate
definition: The pulse rate of the dorsalis pedis artery.

facial pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Facial artery
subclass of: pulse rate
definition: The pulse rate of the facial artery.

femoral pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Femoral artery
subclass of: pulse rate
definition: The pulse rate of the femoral artery.

invasive blood pressure measurement process
type: Class
subclass of: blood pressure measurement process

noninvasive blood pressure measurement process
type: Class
subclass of: blood pressure measurement process

oral temperature
type: Class
equivalent class: Class
  intersection of: body temperature
  intersection of: Restriction
    on property: inheres in
    some values from: Oral cavity
subclass of: body temperature
definition: The temperature of the oral cavity.

oscillometric blood pressure measurement process
type: Class
subclass of: noninvasive blood pressure measurement process

popliteal pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Popliteal artery
subclass of: pulse rate
definition: The pulse rate of the popliteal artery.

pulse rate
type: Class
subclass of: vital sign
subclass of: rate
subclass of: Restriction
  on property: inheres in
  some values from: Artery
definition editor: Albert Goldfain
definition: The rate at which an artery pulses (i.e., participates in expansion-contraction cycles) as blood passes through it.

pulse rate measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: pulse rate
subclass of: scalar measurement datum
subclass of: measurement datum

pulse rate measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: pulse rate measurement datum
subclass of: planned process
subclass of: vital sign measurement process

radial pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Radial artery
subclass of: pulse rate
definition: The pulse rate of the radial artery.

rectal temperature
type: Class
equivalent class: Class
  intersection of: body temperature
  intersection of: Restriction
    on property: inheres in
    some values from: Lumen of rectum
subclass of: body temperature
definition: The temperature of the lumen of the rectum.

respiratory rate
type: Class
subclass of: vital sign
subclass of: rate
definition: The rate at which an organism breathes.

respiratory rate measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: respiratory rate
subclass of: measurement datum

respiratory rate measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: respiratory rate measurement datum
subclass of: planned process
subclass of: vital sign measurement process

systole
type: Class
subclass of: cardiac cycle phase
definition: The phase of the cardiac cycle in which the heart contracts.

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.

systolic central venous pressure
type: Class
equivalent class: Class
  intersection of: systolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Class
      union of: Wall of superior vena cava
      union of: Wall of inferior vena cava
subclass of: systolic blood pressure
definition: The systolic blood pressure in the thoracic vena cava.

systolic left ventricular pressure
type: Class
equivalent class: Class
  intersection of: systolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Wall of left ventricle
subclass of: systolic blood pressure
definition: The left ventricular pressure during systole.

systolic pulmonary artery pressure
type: Class
equivalent class: Class
  intersection of: systolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Wall of pulmonary artery
subclass of: systolic blood pressure
definition: The pulmonary artery pressure during systole.

systolic right ventricular pressure
type: Class
equivalent class: Class
  intersection of: systolic blood pressure
  intersection of: Restriction
    on property: towards
    all values from: Wall of right ventricle
subclass of: systolic blood pressure
definition: The right ventricular pressure during systole.

temporal pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Superficial temporal artery
subclass of: pulse rate
definition: The pulse rate of the temporal artery.

tibialis posterior pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Posterior tibial artery
subclass of: pulse rate
definition: The pulse rate of the tibialis posterior artery.

tympanic temperature
type: Class
equivalent class: Class
  intersection of: body temperature
  intersection of: Restriction
    on property: inheres in
    some values from: External acoustic tube
subclass of: body temperature
definition: The temperature of the external acoustic tube.

ulnar pulse rate
type: Class
equivalent class: Class
  intersection of: pulse rate
  intersection of: Restriction
    on property: inheres in
    some values from: Ulnar artery
subclass of: pulse rate
definition: The pulse rate of the ulnar artery.

vaginal temperature
type: Class
equivalent class: Class
  intersection of: body temperature
  intersection of: Restriction
    on property: inheres in
    some values from: Lumen of vagina
subclass of: body temperature
definition: The temperature of the lumen of the vagina.

palpatory pulse rate measurement process
type: Class
subclass of: pulse rate measurement process

researcher role
type: Class
subclass of: role in human social processes
subclass of: role
definition: The role a human plays if he / she is involved in research activities.
editor preferred term: researcher role
imported from: biotop.owl

Wall of superior vena cava
type: Class
subclass of: Wall of blood vessel
IAO_0000412: FMA.owl

Wall of inferior vena cava
type: Class
subclass of: Wall of blood vessel
IAO_0000412: FMA.owl

Lumen of rectum
type: Class
subclass of: Anatomical entity
IAO_0000412: FMA.owl

Wall of pulmonary artery
type: Class
subclass of: Wall of blood vessel
IAO_0000412: FMA.owl

Lumen of vagina
type: Class
subclass of: Anatomical entity
IAO_0000412: FMA.owl

Oral cavity
type: Class
subclass of: Anatomical entity
IAO_0000412: FMA.owl

Human body
type: Class
subclass of: Anatomical entity
definition: Anatomical structure which is the aggregate material substance of an individual member of the human species.
IAO_0000412: FMA.owl

Brachial artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Radial artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Ulnar artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Common carotid artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Posterior tibial artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Dorsalis pedis artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Facial artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Superficial temporal artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Artery
type: Class
subclass of: Anatomical entity
definition: Subdivision of arterial tree (organ) which consists of branching sets of tubes (arterial trunk) that form a tree; together with other arterial trees (organ part), it constitutes an arterial tree (organ).
IAO_0000412: FMA.owl

Axillary fossa
type: Class
subclass of: Anatomical entity
IAO_0000412: FMA.owl

External acoustic tube
type: Class
subclass of: Anatomical entity
IAO_0000412: FMA.owl

Anatomical entity
type: Class
definition: Organismal continuant entity which is enclose\ d by the bona fide boundary of an organism or is an attribute of its structural\ organization. Examples: cell, heart, head, peritoneal cavity, apex of lung, an\ atomical term, sagittal plane.
IAO_0000412: FMA.owl

Wall of blood vessel
type: Class
subclass of: Anatomical entity
IAO_0000412: FMA.owl

Femoral artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Popliteal artery
type: Class
subclass of: Artery
IAO_0000412: FMA.owl

Wall of right ventricle
type: Class
subclass of: Wall of blood vessel
definition: Wall of ventricle which is continuous with the wall of pulmonary trunk.
IAO_0000412: FMA.owl

Wall of left ventricle
type: Class
subclass of: Wall of blood vessel
definition: Wall of ventricle which is continuous with the wall of aorta.
IAO_0000412: FMA.owl

Portion of blood
type: Class
subclass of: Anatomical entity
definition: Portion of body substance which consists of plasma and blood cells.
IAO_0000412: FMA.owl

regulation of temperature
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: body temperature
subclass of: regulation of biological quality
definition: A homeostatic process in which an organism modulates its internal body temperature.
IAO_0000412: GO.owl

regulation of heart rate
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: pulse rate
subclass of: regulation of biological quality
definition: Any process that modulates the frequency or rate of heart contraction.
IAO_0000412: GO.owl

blood circulation
type: Class
subclass of: processual_entity
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.
IAO_0000412: GO.owl

regulation of blood pressure
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: blood pressure
subclass of: regulation of biological quality
definition: Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
IAO_0000412: GO.owl

regulation of biological quality
type: Class
subclass of: processual_entity
definition: Any process that modulates the frequency, rate or extent of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
IAO_0000412: GO.owl

length
type: Class
subclass of: quality
editor preferred term: length
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: PATO

mass
type: Class
subclass of: quality
editor preferred term: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: PATO

temperature
type: Class
subclass of: quality
definition: A physical quality of the thermal energy of a system.
IAO_0000412: PATO.owl

rate
type: Class
subclass of: quality
definition: A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
IAO_0000412: PATO.owl

pressure
type: Class
subclass of: quality
definition: A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
IAO_0000412: PATO.owl

length unit
type: Class
subclass of: measurement unit label
editor preferred term: length unit
imported from: UO

mass unit
type: Class
subclass of: measurement unit label
editor preferred term: mass unit
imported from: UO

time unit
type: Class
subclass of: measurement unit label
editor preferred term: time unit
imported from: UO

entity
type: Class
equivalent class: Class
  union of: continuant
  union of: occurrent

continuant
type: Class
equivalent class: Class
  union of: dependent_continuant
  union of: independent_continuant
  union of: spatial_region
subclass of: entity
disjoint with: occurrent
comment: Definition: An entity [bfo: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.
comment: Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
comment: Synonyms: endurant

dependent_continuant
type: Class
equivalent class: Class
  union of: generically_dependent_continuant
  union of: specifically_dependent_continuant
subclass of: continuant
disjoint with: independent_continuant
disjoint with: spatial_region
comment: Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.

disposition
type: Class
subclass of: realizable_entity
disjoint with: function
disjoint with: role
comment: Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
comment: Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity.

fiat_object_part
type: Class
subclass of: material_entity
disjoint with: object
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
comment: Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso
comment: Synonyms: fiat substance part

function
type: Class
subclass of: realizable_entity
disjoint with: role
comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
comment: Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law

generically_dependent_continuant
type: Class
subclass of: dependent_continuant
disjoint with: specifically_dependent_continuant
comment: Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
comment: Examples: a certain PDF file that exists in different and in several hard drives

independent_continuant
type: Class
equivalent class: Class
  union of: material_entity
  union of: object_boundary
  union of: site
subclass of: continuant
disjoint with: spatial_region
comment: Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
comment: Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
comment: Synonyms: substantial entity

material_entity
type: Class
equivalent class: Class
  union of: fiat_object_part
  union of: object
  union of: object_aggregate
subclass of: independent_continuant
disjoint with: object_boundary
disjoint with: site
comment: Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
comment: Examples: collection of random bacteria, a chair, dorsal surface of the body

object
type: Class
subclass of: material_entity
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
comment: Examples: an organism, a heart, a chair, a lung, an apple
comment: Synonyms: substance

object_aggregate
type: Class
subclass of: material_entity
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
comment: Synonyms: substance aggregate

object_boundary
type: Class
subclass of: independent_continuant
disjoint with: site
comment: Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
comment: Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
comment: Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
comment: Synonyms: substance boundary

one_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: three_dimensional_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with one dimension.
comment: Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space

quality
type: Class
subclass of: specifically_dependent_continuant
disjoint with: realizable_entity
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
comment: Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee

realizable_entity
type: Class
subclass of: specifically_dependent_continuant
comment: Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap: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.
comment: Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity

role
type: Class
subclass of: realizable_entity
comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
comment: Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university

site
type: Class
subclass of: independent_continuant
comment: Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
comment: Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
comment: Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.

spatial_region
type: Class
equivalent class: Class
  union of: one_dimensional_region
  union of: three_dimensional_region
  union of: two_dimensional_region
  union of: zero_dimensional_region
subclass of: continuant
comment: Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
comment: Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
comment: Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
comment: Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
comment: Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe

specifically_dependent_continuant
type: Class
equivalent class: Class
  union of: quality
  union of: realizable_entity
subclass of: dependent_continuant
comment: Definition: A continuant [snap: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.
comment: Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
comment: Synonyms: property, trope, mode

three_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with three dimensions.
comment: Examples: a cube-shaped part of space, a sphere-shaped part of space

two_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with two dimensions.
comment: Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space

zero_dimensional_region
type: Class
subclass of: spatial_region
comment: Definition: A spatial region [snap:SpatialRegion] with no dimensions.
comment: Examples: a point

connected_spatiotemporal_region
type: Class
equivalent class: Class
  union of: spatiotemporal_instant
  union of: spatiotemporal_interval
subclass of: spatiotemporal_region
disjoint with: scattered_spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].
comment: Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus

connected_temporal_region
type: Class
equivalent class: Class
  union of: temporal_instant
  union of: temporal_interval
subclass of: temporal_region
disjoint with: scattered_temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
comment: Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis

fiat_process_part
type: Class
subclass of: processual_entity
disjoint with: process
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life

occurrent
type: Class
equivalent class: Class
  union of: processual_entity
  union of: spatiotemporal_region
  union of: temporal_region
subclass of: entity
comment: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
comment: Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
comment: Synonyms: perdurant

process
type: Class
subclass of: processual_entity
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: the life of an organism, the process of sleeping, the process of cell-division

process_aggregate
type: Class
subclass of: processual_entity
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
comment: Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together

process_boundary
type: Class
subclass of: processual_entity
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
comment: Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery

processual_context
type: Class
subclass of: processual_entity
comment: Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
comment: Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
comment: Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.

processual_entity
type: Class
equivalent class: Class
  union of: fiat_process_part
  union of: process
  union of: process_aggregate
  union of: process_boundary
  union of: processual_context
subclass of: occurrent
disjoint with: spatiotemporal_region
disjoint with: temporal_region
comment: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
comment: Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird

scattered_spatiotemporal_region
type: Class
subclass of: spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
comment: Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair

scattered_temporal_region
type: Class
subclass of: temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
comment: Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair

spatiotemporal_instant
type: Class
subclass of: connected_spatiotemporal_region
disjoint with: spatiotemporal_interval
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
comment: Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process

spatiotemporal_interval
type: Class
subclass of: connected_spatiotemporal_region
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
comment: Examples: the spatiotemporal region occupied by a process or by a fiat processual part

spatiotemporal_region
type: Class
equivalent class: Class
  union of: connected_spatiotemporal_region
  union of: scattered_spatiotemporal_region
subclass of: occurrent
disjoint with: temporal_region
comment: Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.
comment: Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.
comment: Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.
comment: Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
comment: Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis

temporal_instant
type: Class
subclass of: connected_temporal_region
disjoint with: temporal_interval
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
comment: Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death

temporal_interval
type: Class
subclass of: connected_temporal_region
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
comment: Examples: any continuous temporal duration during which a process occurs

temporal_region
type: Class
equivalent class: Class
  union of: connected_temporal_region
  union of: scattered_temporal_region
subclass of: occurrent
comment: Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
comment: Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
comment: Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
comment: Definition: An occurrent [span:Occurrent] that is part of time.
comment: Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death

patient
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: patient role
subclass of: Homo sapiens
definition: a human that has a patient role

individual organism CRID
type: Class
subclass of: CRID
subclass of: Restriction
  on property: is about
  all values from: organism
definition: a CRID that denotes an individual organism.

patient CRID symbol
type: Class
subclass of: individual organism identifier
subclass of: Restriction
  on property: is about
  some values from: patient
definition: a CRID symbol denoting a patient

birth
type: Class
subclass of: process_boundary
comment: the expulsion of a fetus out of the body of its mother

human intra-uterine life course
type: Class
subclass of: embryo development ending in birth or egg hatching
subclass of: Restriction
  on property: part_of
  some values from: human life course
subclass of: Restriction
  on property: has_participant
  some values from: Homo sapiens
definition: a processual entity which has as parts all the processes in which a given human is a participant occurring before its birth

human extra-uterine life course
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: preceded_by
  some values from: human intra-uterine life course
subclass of: Restriction
  on property: part_of
  some values from: human life course
subclass of: Restriction
  on property: starts with
  some values from: human birth
subclass of: Restriction
  on property: has_participant
  some values from: Homo sapiens
subclass of: Restriction
  on property: ends with
  some values from: human death
definition: a processual entity which has as parts all the processes in which a given human is a participant occurring after its birth

human birth instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: human birth
definition: a moment at which a human birth occurs

human death instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: human death
definition: a moment at which a human death occurs

physician
type: Class
subclass of: health care provider
definition: a health care provider that has a physician role

diagnostic process conclusion
type: Class
subclass of: process_boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: diagnostic process conclusion instant
definition: the end of a diagnostic process

diagnostic process conclusion instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: diagnostic process conclusion
definition: a moment at which a diagnostic conclusion occurs

health care provider
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: health care provider role
subclass of: Homo sapiens
definition: a human that has a health care provider role

researcher
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: researcher role
subclass of: Homo sapiens
definition: a human that has a researcher role

return to normal homeostasis
type: Class
subclass of: process_boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: return to normal homeostasis instant
subclass of: Restriction
  on property: realizes
  some values from: normal homeostasis
definition: the process boundary at which an abnormal homeostasis is replaced by a normal homeostasis for a given organism

return to normal homeostasis instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: return to normal homeostasis
definition: a moment at which a return to normal homeostasis occurs

patient CRID
type: Class
subclass of: individual organism CRID
subclass of: Restriction
  on property: is about
  all values from: patient
definition: a CRID that denotes a patient

human life course
type: Class
subclass of: life course
subclass of: Restriction
  on property: has_participant
  some values from: Homo sapiens
definition: a life course which has as parts all the processes in which a given human is participant

human study subject
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: has role
    some values from: study subject role
subclass of: Homo sapiens
definition: a human that has a study subject role

past status diagnostic process
type: Class
subclass of: diagnostic process
example of usage: A diagnostic process evaluating if a patient had a hip fracture in the past or not.
definition: a diagnostic process which aims at establishing a diagnosis regarding the presence or absence of disease at a point in time anterior to the diagnostic process

current status diagnostic process
type: Class
subclass of: diagnostic process
example of usage: A diagnostic process evaluating if a patient currently has a hip fracture or not.
definition: a diagnostic process which aims at establishing a diagnosis regarding the presence or absence of disease at a point in time during the diagnostic process

disease course instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: disease course
example of usage: Anyone of the instants during which a person has a cancer
definition: a moment at which a disease course occurs

laboratory test ordering instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: laboratory test ordering
definition: a moment at which a laboratory test ordering occurs

laboratory test ordering
type: Class
subclass of: process_boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: laboratory test ordering instant
comment: A laboratory test ordering is formalized as an instantaneous event that occurs at the end of the process during which all the specifications for the laboratory test are given.
definition: the ordering of a laboratory test

specimen creation confirmation
type: Class
subclass of: process_boundary
subclass of: Restriction
  on property: has_participant
  some values from: specimen
subclass of: Restriction
  on property: occupies temporal region
  some values from: specimen creation confirmation instant
example of usage: The confirmation that a blood test tube has been drawn from Mr. Smith
definition: the confirmation of a specimen creation

specimen creation confirmation instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: specimen creation confirmation
definition: a moment at which a specimen creation confirmation occurs

laboratory test result confirmation
type: Class
subclass of: process_boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: laboratory test result confirmation instant
comment: A laboratory test result confirmation is formalized as an instantaneous event that occurs at the end of the process during which the laboratary test result is confirmed by the laboratory team.
example of usage: The validation of an automatically generated serum sodium measurement by the laboratory team.
definition: the confirmation of a laboratary test result

laboratory test result confirmation instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: laboratory test result confirmation
definition: a moment at which a laboratory test result confirmation occurs

lower bound of normal value range
type: Class
subclass of: normal value
definition: the lower bound of a range of normal values for a given quality

upper bound of normal value range
type: Class
subclass of: normal value
definition: the upper bound of a range of normal values for a given quality

scalar measurement datum laboratory finding
type: Class
subclass of: laboratory finding
subclass of: Restriction
  on property: has measurement unit label
  on class: laboratory measurement unit label
  min qualified cardinality: 1
subclass of: Restriction
  on property: has measurement numeral
  on class: numeral
  min qualified cardinality: 1
definition: a laboratory finding that is measured by a scalar measurement datum

human birth
type: Class
subclass of: birth
subclass of: Restriction
  on property: occupies temporal region
  some values from: human birth instant
comment: A human birth is the process boundary between the intra-uterine life course and the extra-uterine life course of a given human.
definition: the birth of a human

human death
type: Class
subclass of: death
subclass of: Restriction
  on property: occupies temporal region
  some values from: human death instant
comment: the death of a human

unique normal value
type: Class
subclass of: normal value
definition: The unique normal value for a given quality which has only one normal value.

formulated pharmaceutical data item
type: Class
subclass of: data item
definition: a data item that is about a formulated pharmaceutical

strength data item
type: Class
subclass of: atomic formulated pharmaceutical data item
subclass of: Restriction
  on property: has measurement numeral
  some values from: numeral
subclass of: Restriction
  on property: has measurement unit label
  some values from: formulated pharmaceutical strength unit label
definition: an atomic formulated pharmaceutical data item that is about a strength

dose form data item
type: Class
subclass of: atomic formulated pharmaceutical data item
definition: an atomic formulated pharmaceutical data item that is about a dose form

active ingredient data item
type: Class
subclass of: atomic formulated pharmaceutical data item
definition: an atomic formulated pharmaceutical data item that is about an active ingredient

formulated pharmaceutical category data item
type: Class
subclass of: atomic formulated pharmaceutical data item
definition: an atomic formulated pharmaceutical data item that is about a formulated pharmaceutical category

health care instruction set
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has_part
  some values from: health care instruction item
definition: A plan specification composed of health care instruction items that when concretized is realized in a process in which the bearer tries to achieve health care-related objectives
example of usage: The part of a prescription detailing the pain medications a patient should take and physiotheray he should follow after a hip fracture.

formulated pharmaceutical instruction item
type: Class
subclass of: health care instruction item
subclass of: Restriction
  on property: has_part
  some values from: posological information item
subclass of: Restriction
  on property: has_part
  on class: Class
    union of: active ingredient data item
    union of: brand name data item
  min qualified cardinality: 1
definition: a health care instruction item that describes how to use a formulated pharmaceutical
example of usage: The part of a prescription detaillling how to take a specific pain medication after a hip fracture.

health care instruction item
type: Class
subclass of: action specification
example of usage: The part of a prescription detailling specific physiotherapy a patient should follow after a hip fracture.
definition: an action specification that describes an action related to health care

written creation date
type: Class
subclass of: textual entity
definition: a textual entity denoting a creation date

health care prescription
type: Class
subclass of: document
subclass of: Restriction
  on property: has_part
  some values from: written creation date
subclass of: Restriction
  on property: has_part
  some values from: health care provider author identification
subclass of: Restriction
  on property: has_part
  some values from: patient identification
subclass of: Restriction
  on property: has_part
  some values from: health care instruction item
definition: a document authored by a health care provider that includes health care instructions for a patient
example of usage: A document authored by Dr Dupont detailling the pain medications Mr Smith. should take and the physiotherapy he should follow after a hip fracture.

health care provider author identification
type: Class
subclass of: author identification
subclass of: Restriction
  on property: denotes
  on class: health care provider
  max qualified cardinality: 1
definition: an author identification denoting a particular health care provider

patient identification
type: Class
subclass of: written name
subclass of: Restriction
  on property: denotes
  on class: patient
  max qualified cardinality: 1
definition: a written name denoting a particular patient

atomic formulated pharmaceutical data item
type: Class
subclass of: formulated pharmaceutical data item
definition: a data item that is about an atomic formulated pharmaceutical

composite formulated pharmaceutical data item
type: Class
subclass of: formulated pharmaceutical data item
definition: a data item that is about a composite formulated pharmaceutical

brand name data item
type: Class
subclass of: atomic formulated pharmaceutical data item
definition: an atomic formulated pharmaceutical data item that is about a brand

posological information item
type: Class
subclass of: directive information entity part
definition: a directive information entity part that is about the dosage of a formulated pharmaceutical

total dose per administration item
type: Class
subclass of: posological information item
definition: a posological information item that is about the total dose of a formulated pharmaceutical per administration

number of formulated pharmaceutical unit per administration item
type: Class
subclass of: posological information item
definition: a posological information item that is about the number of formulated pharmaceutical unit per administration

mode of administration item
type: Class
subclass of: posological information item
definition: a posological information item that is about the mode of administration of a formulated pharmaceutical

administration frequency item
type: Class
subclass of: posological information item
definition: a posological information item that is about the administration frequency of a formulated pharmaceutical

total of formulated pharmaceutical unit per treatment period item
type: Class
subclass of: posological information item
definition: a posological information item that is about the total of formulated pharmaceutical unit per treatment period

duration of treatment period item
type: Class
subclass of: posological information item
definition: a posological information item that is about the duration of administration of a formulated pharmaceutical

directive information entity part
type: Class
subclass of: information content entity
definition: an information content entity that is a proper part of a directive information entity

vital sign measurement process
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: vital sign measurement datum
subclass of: planned process
definition: a measurement process of a vital sign

vital sign measurement process instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: vital sign measurement process
definition: a moment at which a vital sign measurement process occurs

blood pressure measurement process instant
type: Class
equivalent class: Class
  intersection of: vital sign measurement process instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: blood pressure measurement process
definition: a moment at which a blood pressure measurement process occurs

body temperature measurement process instant
type: Class
equivalent class: Class
  intersection of: vital sign measurement process instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: body temperature measurement process
definition: a moment at which a body temperature measurement process occurs

pulse rate measurement process instant
type: Class
equivalent class: Class
  intersection of: vital sign measurement process instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: pulse rate measurement process
definition: a moment at which a pulse rate measurement process occurs

respiratory rate measurement process instant
type: Class
equivalent class: Class
  intersection of: vital sign measurement process instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: respiratory rate measurement process
definition: a moment at which a respiratory rate measurement process occurs

human mass measurement process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: human mass measurement datum
subclass of: Restriction
  on property: has_specified_input
  some values from: Homo sapiens
definition: a measurement process of a human's mass

human mass measurement process instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: human mass measurement process
definition: a moment at which a human mass measurement process occurs

human mass measurement datum
type: Class
subclass of: mass measurement datum
subclass of: Restriction
  on property: is about
  some values from: human mass
subclass of: Restriction
  on property: has measurement unit label
  on class: measurement unit label
  min qualified cardinality: 1
subclass of: Restriction
  on property: has measurement numeral
  on class: numeral
  min qualified cardinality: 1
definition: a mass measurement datum that is the result of measurement of a human mass quality

human height measurement 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_specified_output
  some values from: human height measurement datum
definition: a measurement process of a human's height

human height measurement process instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: human height measurement process
definition: a moment at which a human height measurement process occurs

human height measurement datum
type: Class
subclass of: length measurement datum
subclass of: Restriction
  on property: is about
  some values from: human height
subclass of: Restriction
  on property: has measurement unit label
  on class: measurement unit label
  min qualified cardinality: 1
subclass of: Restriction
  on property: has measurement numeral
  on class: numeral
  min qualified cardinality: 1
definition: a length measurement datum that is the result of measurement of human height

systolic blood pressure measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: systolic blood pressure
subclass of: blood pressure measurement datum
definition: a blood pressure measurement datum that is about a systolic blood pressure

diastolic blood pressure measurement datum
type: Class
equivalent class: Restriction
  on property: is about
  some values from: diastolic blood pressure
subclass of: blood pressure measurement datum
definition: a blood pressure measurement datum that is about a diastolic blood pressure

human mass
type: Class
subclass of: mass
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
definition: the total mass of a human
comment: Altough mass and weight formally designate different (yet related) concepts, when clinicans refer to weight, they do refer to the mass of the patient, not its weight in newton.

human height
type: Class
subclass of: length
subclass of: Restriction
  on property: inheres in
  some values from: Homo sapiens
definition: the length from the bottom of the feet to the top of the head of a human body, standing erect

vital sign measurement datum
type: Class
equivalent class: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: vital sign
subclass of: measurement datum
definition: a measurement datum that is a recording of the output of a vital sign measurement

reason for health care encounter role
type: Class
subclass of: role
example of usage: The role played by hip pain in bringing a patient to seek a health care encounter.
definition: the role played by a disorder (or a sign, a symptom etc.) that is realized by an encounter of the organism having the disorder (or the sign, the symptom, etc.) with a health care provider

health care encounter instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: health care encounter
subclass of: temporal_instant
definition: a moment at which a health care encounter occurs

health care episode
type: Class
subclass of: health care process
subclass of: Restriction
  on property: has_part
  some values from: health care encounter
definition: Health care process that is composed by one or more healthcare encounters focusing on the same health issue.

laboratory measurement unit label
type: Class
equivalent class: Class
  intersection of: measurement unit label
  intersection of: Restriction
    on property: measurement unit label of
    some values from: scalar measurement datum laboratory finding
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a laboratory finding

diastolic bp measurement unit label
type: Class
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a diastolic blood pressure

systolic bp measurement unit label
type: Class
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a systolic blood pressure

body temperature measurement unit label
type: Class
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a body temperature

pulse rate measurement label
type: Class
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a pulse rate

respiratory rate measurement label
type: Class
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a respiratory rate

human height measurement label
type: Class
equivalent class: Class
  intersection of: length unit
  intersection of: Restriction
    on property: part_of
    some values from: human height measurement datum
subclass of: length unit
definition: a measurement unit label that denotes a unit of measure of a human height

formulated pharmaceutical strength unit label
type: Class
equivalent class: Class
  intersection of: measurement unit label
  intersection of: Restriction
    on property: measurement unit label of
    some values from: strength data item
subclass of: measurement unit label
definition: a measurement unit label that denotes a unit of measure of a formulated pharmaceutical strength

reason for health care encounter
type: Class
subclass of: entity
subclass of: Restriction
  on property: has role
  some values from: reason for health care encounter role
definition: An entity playing a role of a reason for encounter.
comment: Given that a sign or a symptom can be a reason for encounter, and given that these two categories are currently classified as direct subclasses of ‘entity’, we had to classify ‘reason for encounter’ as a subclass of ‘entity’.
example of usage: a cough; a hip pain; a red eye

imaging test
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: image finding
subclass of: Restriction
  on property: has_participant
  some values from: Class
    union of: patient
    union of: human study subject
definition: A medical examination that has as specified output an image finding

surgical intervention
type: Class
subclass of: planned process
definition: A planned process during which operative manual and instrumental techniques are used on a patient to investigate and/or treat a pathological condition, or to help improve bodily function or appearance.

health care encounter conclusion
type: Class
subclass of: process_boundary
definition: The end of a health care encounter process

health care encounter beginning
type: Class
subclass of: process_boundary
definition: The beginning of a health care encounter process

health care encounter conclusion instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: health care encounter conclusion
definition: A moment at which a health care encounter conclusion occurs

health care encounter beginning instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: health care encounter beginning
definition: A moment at which a health care encounter conclusion occurs

surgical intervention instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: surgical intervention
definition: a moment at which a surgical intervention occurs

imaging test instant
type: Class
equivalent class: Class
  intersection of: temporal_instant
  intersection of: Restriction
    on property: has temporal occupant
    some values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: temporal part of
        some values from: imaging test
definition: a moment at which an imaging test occurs

physician practice
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: physician practice
subclass of: organization
editor note: This entity has the same label than the OMRSE entity "physician practice". Their entity being a role, it might benefit from being renamed "physician practice role"

human mass measurement label
type: Class
equivalent class: Class
  intersection of: mass unit
  intersection of: Restriction
    on property: part_of
    some values from: human mass measurement datum
subclass of: mass unit
definition: a measurement unit label that denotes a unit of measure of a human mass

diastolic blood pressure measurement process instant
type: Class
subclass of: blood pressure measurement process instant

systolic blood pressure measurement process instant
type: Class
subclass of: blood pressure measurement process instant

diastolic blood presure measurement process
type: Class
equivalent class: Class
  intersection of: blood pressure measurement process
  intersection of: Restriction
    on property: has_specified_output
    some values from: diastolic blood pressure measurement datum
subclass of: blood pressure measurement process

systolic blood pressure measurement process
type: Class
equivalent class: Class
  intersection of: blood pressure measurement process
  intersection of: Restriction
    on property: has_specified_output
    some values from: systolic blood pressure measurement datum
subclass of: blood pressure measurement process

health care prescription date
type: Class
equivalent class: Class
  intersection of: written creation date
  intersection of: Restriction
    on property: part_of
    some values from: health care prescription
subclass of: written creation date

active ingredient
type: Class
equivalent class: Class
  intersection of: pharmaceutical ingredient
  intersection of: Restriction
    on property: has role
    some values from: active ingredient role
  intersection of: Restriction
    on property: part_of
    some values from: formulated pharmaceutical
subclass of: pharmaceutical ingredient
database_cross_reference: HL7V3.0:ACTI
description: An active ingredient is a pharmaceutical ingredient that has the disposition to treat a certain disease.

formulated pharmaceutical
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has_proper_part
  some values from: pharmaceutical ingredient
database_cross_reference: NCIt:Pharmaceutical_Formulation
database_cross_reference: UMLS:C1705957
description: A formulated pharmaceutical is a chemical substance whose granular parts include an active ingredient, an excipient, and possibly a stability regulator for the active ingredient.
database_cross_reference: drugbank:drugs
database_cross_reference: medicare:drugs
database_cross_reference: sider:drugs
database_cross_reference: pharmgkb:Drug
database_cross_reference: dailymed:drugs

inactive ingredient
type: Class
equivalent class: Class
  intersection of: pharmaceutical ingredient
  intersection of: Restriction
    on property: has role
    some values from: inactive ingredient role
  intersection of: Restriction
    on property: part_of
    some values from: formulated pharmaceutical
subclass of: pharmaceutical ingredient
database_cross_reference: HL7V3.0:IACT
description: An inactive ingredient is a pharmaceutical ingredient that is part of a pharmaceutical formulation but does not have the disposition to treat a certain disease.

molecular entity
type: Class
subclass of: material_entity
database_cross_reference: CHEBI:23367
database_cross_reference: GRO:MolecularEntity
description: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.

gene
type: Class
subclass of: DNA region
database_cross_reference: FMA:Structural_gene
database_cross_reference: GRO:Gene
database_cross_reference: Galen:Gene
database_cross_reference: LNC:LP32747-5
database_cross_reference: MSH:D005796
database_cross_reference: NCIt:Gene
database_cross_reference: NCIt:Gene_Object
database_cross_reference: NDFRT:C242394
database_cross_reference: PRO:Gene
database_cross_reference: SNOMEDCT:67271001
database_cross_reference: SO:0000704
database_cross_reference: UMLS:C0017337
database_cross_reference: pharmgkb:Gene
description: A gene is a part of DNA that encodes information about other molecular entities.
database_cross_reference: diseasome:genes

genotype with SNP
type: Class
subclass of: genotype
database_cross_reference: MSH:D020641
database_cross_reference: NCIt:Single_Nucleotide_Polymorphism
database_cross_reference: SO:0000694
database_cross_reference: UMLS:C0752046
description: A genotype with a single-nucleotide polymorphism (SNP). A SNP is a variation at a single nucleotide locus in the genomes of members of a species. For a variation to be considered a SNP, it must occur in at least 1% of the population.

genotype with copy number variation
type: Class
subclass of: genotype
database_cross_reference: SO:0001019
description: A genotype of which variants with a different number of copies of a sequence identifical region exist.

pharmaceutical ingredient role
type: Class
subclass of: role
description: A pharmaceutical ingredient role is a role played by a chemical substance that is part of a pharmaceutical formulation.

chemical substance
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: has_proper_part
  some values from: molecular entity
description: A chemical substance is a material entity consisting of many chemical entities and typically has connected boundaries.

active ingredient role
type: Class
subclass of: pharmaceutical ingredient role
description: An active ingredient role is a role played by a chemical substance which has the disposition to treat a certain disease and is part of a pharmaceutical formulation.

inactive ingredient role
type: Class
subclass of: pharmaceutical ingredient role
description: An inactive ingredient role is a role played by a chemical substance which is part of a pharmaceutical formulation but does not have the disposition to treat a certain disease.

pharmaceutical ingredient
type: Class
equivalent class: Class
  intersection of: chemical substance
  intersection of: Restriction
    on property: part_of
    some values from: formulated pharmaceutical
subclass of: chemical substance
subclass of: Restriction
  on property: part_of
  some values from: formulated pharmaceutical
database_cross_reference: dailymed:ingredients
description: A pharmaceutical ingredient is a chemical substance that is part of a formulated pharmaceutical that bears a pharmaceutical ingredient role.

genotype
type: Class
subclass of: molecular entity part
description: In this context, a genotype is a material entity made up of two DNA regions on two homologous chromosomes in a diploid cell. One chromosome is derived from the father and one is derived from the mother. The two DNA regions are located at the same genetic locus on each of the two chromosomes.

ethnicity
type: Class
subclass of: quality
editor preferred term: ethnicity
definition: Ethinicity is the quality of an organism that describes membership in a social group based on a common heritage.

chromosome
type: Class
subclass of: molecular complex
subclass of: Restriction
  on property: has_part
  some values from: DNA

dsDNA
type: Class
subclass of: molecular complex

molecular complex
type: Class
subclass of: molecular entity
disjoint with: DNA

DNA region
type: Class
subclass of: molecular entity part
comment: A DNA region is a part of a DNA molecule that is made up of a continous chain of deoxyribonucleotide residues.

DNA
type: Class
subclass of: molecular entity

genotype with indel variation
type: Class
subclass of: genotype
description: A genotype of which variants exist that differ though an insertion, deletion or a combination thereof.

genotype with short tandem repeat variation
type: Class
subclass of: genotype

genotype with multiple nucleotide polymorphism
type: Class
subclass of: genotype
description: A genotype with a multiple-nucleotide polymorphism (MNP). An MNP is a variation of several adjacent nucleotides in the genomes of members of a species. For a variation to be considered an MNP, it must occur in at least 1% of the population.

molecular entity part
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: part_of
  some values from: molecular entity
comment: A part of a molecular entity or a set of molecular entities. It can be made up of several non-connected sub-parts, potentially on separate molecular entities.

genotype with allele
type: Class
subclass of: genotype
description: A genotype containing one matching allele on each chromosome (e.g., CYP2C9*1/*3)

example to be eventually removed
type: NamedIndividual
type: curation status specification

failed exploratory term
type: Thing
type: obsolescence reason specification
type: NamedIndividual
definition editor: Person:Alan Ruttenberg
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job

metadata complete
type: Thing
type: curation status specification
type: NamedIndividual
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: NamedIndividual
type: curation status specification
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
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: NamedIndividual
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
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.

core
type: NamedIndividual
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

placeholder removed
type: Thing
type: obsolescence reason specification
type: NamedIndividual

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
deprecated: true
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.

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
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.

defined class
type: NamedIndividual
type: denotator type
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: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a 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.
definition editor: Alan Ruttenberg
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

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
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