Informed Consent Ontology (ICO)
type: Ontology
version IRI: ico.owl
Contributor: Anna Maria Masci
Contributor: Chris Stoeckert
Contributor: Cui Tao
Contributor: Helena Ellis
Contributor: Jian Guan
Contributor: Jihad Obeid
Contributor: Jonathan Bona
Contributor: Mathias Brochhausen
Contributor: William Duncan
creator: Alla Karnovsky
creator: Asiyah Yu Lin
creator: Christoph Brochhausen
creator: Cooper Stansbury
creator: Elizabeth Eisenhauer
creator: Elizabeth Umberfield
creator: Frank Manion
creator: J. Neil Otte
creator: Jie Zheng
creator: Jonathan Vajda
creator: Kathleen Ford
creator: Marcy Harris
creator: Yongqun "Oliver" He
description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.
license: http://creativecommons.org/licenses/by/4.0/
comment: Terms were identified from a sample of informed consent templates, and definitions were selected based on concordance between the defintion and the use of the term in the source informed consent template document. We preferentially selected defintioins from the NCI thesuarus.
version info: 2025-03-15

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only
sub property of: label

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

DUO_preferred_label
type: AnnotationProperty

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

example of usage
type: AnnotationProperty
editor preferred label: example of usage
has curation status: ready for release
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

in branch
type: AnnotationProperty
editor preferred label: in branch
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

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

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has exact synonym: DEFINITION
label: textual definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
database_cross_reference: IAO:0000116
has_obo_namespace: uberon
id: editor_note
is metadata tag: 1
shorthand: editor_note

definition editor
type: AnnotationProperty
editor preferred label: term editor
has curation status: ready for release
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred label: alternative label
editor preferred label: alternative term
has curation status: pending final vetting
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: OBO Operations committee
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: alternative label

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: ready for release
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

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

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

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

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

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

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

expand assertion to
type: AnnotationProperty
editor preferred label: expand assertion to
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)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
definition editor: Chris Mungall

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

antisymmetric property
type: AnnotationProperty
editor preferred label: 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
definition editor: Alan Ruttenberg

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

has ID digit count
type: AnnotationProperty
editor preferred label: has ID digit count
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: 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)
definition editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
editor preferred label: has ID range allocated
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
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
definition editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
editor preferred label: has ID policy for
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: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
definition editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
editor preferred label: has ID prefix
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: 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

elucidation
type: AnnotationProperty
editor preferred label: elucidation
definition editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

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

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

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

retired from use as of
type: AnnotationProperty
editor preferred label: retired from use as of
definition: relates a class of CRID to the date after which further instances should not be made, according to the central authority
editor note: In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp
definition editor: Alan Ruttenberg

has ontology root term
type: AnnotationProperty
editor preferred label: has ontology root term
definition: Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
definition editor: Nicolas Matentzoglu

may be identical to
type: AnnotationProperty
editor preferred label: may be identical to
definition: A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged.
definition editor: David Osumi-Sutherland
term tracker item: #40
ontology term requester: VFB
comment: Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance.

scheduled for obsoletion on or after
type: AnnotationProperty
editor preferred label: scheduled for obsoletion on or after
definition: Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.
definition editor: Chris Mungall, Jie Zheng
term tracker item: https://github.com/geneontology/go-ontology/issues/15532
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/32
ontology term requester: GO ontology
range: dateTime

has axiom label
type: AnnotationProperty
editor preferred label: has axiom id
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
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

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

term_mapping_to_UMLS
type: AnnotationProperty
sub property of: seeAlso

term_mapping_to_NCIT
type: AnnotationProperty
sub property of: seeAlso

term_mapping_to_HL7v3
type: AnnotationProperty
sub property of: seeAlso

RUBRIC
type: AnnotationProperty
definition editor: Cooper Stansbury
curator note: This annotation property specifies classes that were developed as part of an alignment effort between the Common Rule Ontology and the Informed Consent Ontology in the Summer of 2018. These classes represent entities that are necessary for understanding the regularatory frameworks that influence informed consent, often at a different level of granularity than individual consent processes. These classes were created to be compatible with regulatory frameworks outside the Unitied States, hence they are general.

PICO CLASS
type: AnnotationProperty
comment: All classes and properties with this annotation are members of the PICO grammar.

Merriam-Webster Definition
type: AnnotationProperty

code
type: AnnotationProperty
read only: true
definition: A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus.
code: NHC0
Semantic_Type: Conceptual Entity
Preferred_Name: code
has exact synonym: code

Semantic_Type
type: AnnotationProperty
definition: A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
code: P106
Semantic_Type: Conceptual Entity
Display_Name: Semantic Type
Preferred_Name: Semantic_Type
DesignNote: In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
has exact synonym: Semantic_Type

Display_Name
type: AnnotationProperty
definition: A property representing an alternative Preferred Name for use in some NCI systems.
code: P107
Semantic_Type: Conceptual Entity
Display_Name: Display Name
Preferred_Name: Display_Name
has exact synonym: Display Name
has exact synonym: Display_Name

Preferred_Name
type: AnnotationProperty
definition: A property representing the word or phrase that NCI uses by preference to refer to the concept.
code: P108
Semantic_Type: Conceptual Entity
Display_Name: Preferred Name
Preferred_Name: Preferred_Name
has exact synonym: Preferred Name
has exact synonym: Preferred Term
has exact synonym: Preferred_Name

UMLS_CUI
type: AnnotationProperty
definition: A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
code: P207
Semantic_Type: Conceptual Entity
Display_Name: UMLS CUI
Preferred_Name: UMLS_CUI
has exact synonym: UMLS_CUI

Contributing_Source
type: AnnotationProperty
definition: A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
code: P322
Semantic_Type: Conceptual Entity
Display_Name: Contributing Source
Preferred_Name: Contributing_Source
has exact synonym: Contributing_Source

ALT_DEFINITION
type: AnnotationProperty
definition: A property representing the English language definition of a concept from a source other than NCI.
code: P325
Semantic_Type: Conceptual Entity
Display_Name: [source] Definition
Preferred_Name: ALT_DEFINITION
has exact synonym: ALT_DEFINITION

Legacy Concept Name
type: AnnotationProperty
read only: true
definition: A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
code: P366
Semantic_Type: Conceptual Entity
Preferred_Name: Legacy Concept Name
has exact synonym: Legacy Concept Name
has exact synonym: Legacy_Concept_Name

DesignNote
type: AnnotationProperty
definition: A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
code: P98
Semantic_Type: Conceptual Entity
Display_Name: DesignNote
Preferred_Name: DesignNote
has exact synonym: DesignNote

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

NIAID GSCID-BRC alternative term
type: AnnotationProperty
editor preferred label: NIAID GSCID-BRC alternative term
has curation status: ready for release
definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
sub property of: alternative term

temporal interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.

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

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

Date
type: AnnotationProperty
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
comment: An account of the content of the resource.

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

Source
type: AnnotationProperty
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
comment: The topic of the content of the resource.

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

database_cross_reference
type: AnnotationProperty

has exact synonym
type: AnnotationProperty
definition: A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has exact synonym: FULL_SYN
has exact synonym: Synonym with Source Data
label: has_exact_synonym

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in subset
type: AnnotationProperty
definition: An association that connects the concept defining a particular terminology subset with concepts that belong to this subset.
has exact synonym: Concept_In_Subset
label: in_subset

shorthand
type: AnnotationProperty

label
type: AnnotationProperty
editor preferred label: label

part of
type: ObjectProperty
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: Ontology for Biomedical Investigations
temporal interpretation: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
imported from: iao.owl
imported from: Ontology for Biomedical Investigations
temporal interpretation: RO_0001901

realized in
type: ObjectProperty
sub property of: topObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: Ontology for Biomedical Investigations
imported from: http://purl.obolibrary.org/obo/ro.owl
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
sub property of: topObjectProperty
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: Ontology for Biomedical Investigations
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded_by
type: ObjectProperty
type: TransitiveProperty
label: preceded by

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred label: occurs in
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred label: site of
definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

is restricted to
type: ObjectProperty
DUO_preferred_label: is_restricted_to
definition: A is restricted to B iff A is a consent code and B is an investigation and A may only participate in instances of a class C, of which B is an instance.
definition editor: J. Neil Otte
curator note: E.g. A dataset is restricted to an instance of an investigation for a specific disease or at geographical location.
id: DUO:0000010

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

obsolete_specifically denotes
type: ObjectProperty
sub property of: ObsoleteProperty
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
has curation status: pending final vetting
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: 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
editor note: see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
definition editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
has obsolescence reason: failed exploratory term
deprecated: true

is about
type: ObjectProperty
domain: information content entity
editor preferred label: is about
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: A (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

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

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
editor preferred label: denotes
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: A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
definition editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

obsolete_materially denotes
type: ObjectProperty
sub property of: ObsoleteProperty
editor note: see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote
has obsolescence reason: failed exploratory term
deprecated: true

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

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

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

denoted by
type: ObjectProperty
domain: entity
range: information content entity
definition: inverse of the relation 'denotes'
definition editor: Person: Jie Zheng, Chris Stoeckert, Mike Conlon
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/206

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

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

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

is quality specification of
type: ObjectProperty
sub property of: is about
inverse of: quality is specified as
has curation status: metadata complete
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.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters

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

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

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

legally revokes
type: ObjectProperty
sub property of: has participant
type: FunctionalProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: deontic declaration
range: deontic role
definition: d socio-legally revokes s if s participates in d and at the end of d s no longer exists. It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question.
definition editor: Mathias Brochhausen

obsolete_legally transfers
type: ObjectProperty
sub property of: ObsoleteProperty
type: FunctionalProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical.
definition editor: Mathias Brochhausen
has obsolescence reason: failed exploratory term
deprecated: true

obsolete form signed by
type: ObjectProperty
sub property of: ObsoleteProperty
definition: An object property that represents a relation between a form and the person or organization who acts as a signer and signs the form.
definition editor: Yongqun He, Elizabeth Eisenhauer
deprecated: true

obsolete is associated with review board approval number
type: ObjectProperty
sub property of: ObsoleteProperty
domain: informed consent form
range: review board approval number
definition: A relation that links an informed consent form to an associated IRB number.
definition editor: Elizabeth Eisenhauer, Yongqun He, Asiyah Yu Lin, Alla Karnovsky, Marcy Harris
deprecated: true

obsolete is assigned by organization
type: ObjectProperty
sub property of: ObsoleteProperty
definition: An object property that represents a relation between a unique identifier (ID) and an organization that assigns the ID.
definition editor: Yongqun He, Elizabeth Eisenhauer, Asiyah Yu Lin, Alla Karnovsky, Marcy Harris
deprecated: true

permits
type: ObjectProperty
sub property of: realized in
definition: A relation holding between an instance of a deontic role and an instance of an intentional action when the deontic role bearer participates in the intentional action and is allowed to do so.

has agent
type: ObjectProperty
sub property of: has participant
inverse of: agent in
definition editor: J. Neil Otte, Jonathan Vajda, Cooper Stansbury
comment: A relation between an instance of Process and an instance of Continuant, where the continuant is a causal participant in the process.

agent in
type: ObjectProperty
sub property of: participates in
definition: A relation between a continuant and a process, where the continuant is a causal participant in the process.
definition editor: J. Neil Otte, Jonathan Vajda, Cooper Stansbury

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
editor preferred label: is_supported_by_data
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has curation status: ready for release
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
definition editor: OBI
definition source: OBI
definition source: Philly 2011 workshop
imported from: Ontology for Biomedical Investigations

has specified input
type: ObjectProperty
equivalent property:
  inverse of: is specified input of
sub property of: has participant
inverse of: is specified input of
domain: planned process
editor preferred label: has specified input
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition: The inverse property of is specified input of
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: Ontology for Biomedical Investigations
label: has_specified_input

is specified input of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is specified input of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: Ontology for Biomedical Investigations
label: is_specified_input_of

has specified output
type: ObjectProperty
equivalent property:
  inverse of: is specified output of
sub property of: has participant
inverse of: is specified output of
domain: planned process
editor preferred label: has specified output
editor preferred label: has_specified_output
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition: The inverse property of is specified output of
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
imported from: Ontology for Biomedical Investigations
label: has_specified_output

is specified output of
type: ObjectProperty
sub property of: participates in
range: planned process
editor preferred label: is specified output of
editor preferred label: is_specified_output_of
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: Ontology for Biomedical Investigations
label: is_specified_output_of

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: metadata complete
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: Ontology for Biomedical Investigations

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: metadata complete
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
definition editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: Ontology for Biomedical Investigations

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

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

is-aggregate-of
type: ObjectProperty
sub property of: topObjectProperty
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.

characteristic of
type: ObjectProperty
inverse of: bearer of
type: FunctionalProperty
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this fragility is a characteristic of this vase
example of usage: this red color inheres in this apple
example of usage: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
imported from: Ontology for Biomedical Investigations
temporal interpretation: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
label: inheres in

bearer of
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: Inverse of characteristic_of
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
imported from: Ontology for Biomedical Investigations
temporal interpretation: RO_0001901
label: bearer_of
label: has characteristic

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: Ontology for Biomedical Investigations

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
imported from: Ontology for Biomedical Investigations
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
range: Class
  union of: process
  union of: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
imported from: Ontology for Biomedical Investigations

concretizes
type: ObjectProperty
domain: specifically dependent continuant
domain: Class
  union of: process
  union of: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
definition: A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.
imported from: Ontology for Biomedical Investigations

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
imported from: Ontology for Biomedical Investigations
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function
imported from: Ontology for Biomedical Investigations

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality
imported from: Ontology for Biomedical Investigations

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role
imported from: Ontology for Biomedical Investigations

has disposition
type: ObjectProperty
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

derives from
type: ObjectProperty
sub property of: topObjectProperty
inverse of: derives into
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
imported from: Ontology for Biomedical Investigations
imported from: ro.owl

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative term: derives_into
imported from: Ontology for Biomedical Investigations

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of
temporal interpretation: RO_0001901

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
imported from: Ontology for Biomedical Investigations
temporal interpretation: RO_0001901
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

Axiom
annotated source: located in
annotated property: domain
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

Axiom
annotated source: located in
annotated property: range
annotated target: independent continuant
editor note: This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.

2D boundary of
type: ObjectProperty
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: 2D_boundary_of
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of
temporal interpretation: RO_0001901

has 2D boundary
type: ObjectProperty
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: has boundary
alternative term: has_2D_boundary
temporal interpretation: RO_0001901

has component
type: ObjectProperty
sub property of: has part
has curation status: pending final vetting
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator note: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
imported from: Ontology for Biomedical Investigations
temporal interpretation: RO_0001901

has active participant
type: ObjectProperty
sub property of: has participant
example of usage: 'heart development' has active participant some Shh protein
has curation status: pending final vetting
definition: x has participant y if and only if x realizes some active role that inheres in y
editor note: This may be obsoleted and replaced by the original 'has agent' relation
definition editor: Chris Mungall
alternative term: has agent
imported from: http://purl.obolibrary.org/obo/ro.owl
in subset: ro-eco

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
temporal interpretation: RO_0001901

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
temporal interpretation: RO_0001901

DEPRECATED inheres in
type: ObjectProperty
comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
deprecated: true

DEPRECATED bearer of
type: ObjectProperty
deprecated: true

designated by
type: ObjectProperty
definition: The inverse of designates, which relates an Entity to some Information Content Entity.
curator note: Note on modification: Changed relation to hold between an IAO: Information Content Entity instead of a Designative Information Content Entity.
date: Imported 08.09.2018
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

has familial relationship to
type: ObjectProperty
definition: A relationship between persons by virtue of ancestry or legal union.
definition source: https://github.com/CommonCoreOntology/CommonCoreOntologies/blob/master/AgentOntology.ttl
date: Retrieved from Common Core Ontologies 2/06/2019
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

prescribed by
type: ObjectProperty
inverse of: prescribes
definition: The inverse of presecribes, which relates an Entity to some Directive Information Content Entity.
date: Imported 08.09.2018
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

prescribes
type: ObjectProperty
sub property of: is about
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
comment: For all types T1 and T2, if T1 prescribes T2, then there is some instance of T1, t1, that serves as a rule or guide to some instance of T2, t2 (if T2 is a type of bfo:Occurrent) or that serves as a model for some instance of T2, t2 (if T2 is a type of bfo:Continuant).

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

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

obsolete_deontic document act
type: Class
subclass of: Obsolete Class
example of usage: my filling in an immigration form, a judge's signing and stamping a court order
definition: A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

software development
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      union of: software
      union of: source code module
subclass of: planned process
definition: A planned process that has specified output a software product and that involves the creation of source code.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan
definition source: http://en.wikipedia.org/wiki/Software_development
elucidation: A planned process resulting in a software product involving the creation of source code.

count
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is specified output of
    some values from: counting
subclass of: measurement datum
definition: A measurement datum that is the output of counting.
definition editor: Mathias Brochhausen
elucidation: A measurement datum that is the output of counting.

counting
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has specified output
    some values from: count
subclass of: planned process
definition: The planned process of finding the number of elements in a finite set of objects.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Counting
elucidation: The planned process of finding the number of elements in a finite set of objects.

source code repository
type: Class
subclass of: document
subclass of: Restriction
  on property: has part
  some values from: source code module
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: source code module
editor preferred label: software source code version control repository
definition: A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
definition editor: William R. Hogan
comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based

compiling software
type: Class
subclass of: software development
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      union of: software
      union of: source code module
  intersection of: Restriction
    on property: has specified output
    some values from: software
editor preferred label: process of compiling software
definition: A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
definition editor: William R. Hogan
comment: It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).
comment: Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code.

dataset creating
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has specified output
    some values from: data set
subclass of: planned process
editor preferred label: creating a data set
definition: A planned process that has a data set as its specified output.
definition editor: William R. Hogan
alternative term: data set creation
alternative term: dataset creation

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
imported from: bfo.owl
imported from: Ontology for Biomedical Investigations
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
comment: from BFO

Axiom
annotated source: entity
annotated property: editor note
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: bfo.owl
imported from: Ontology for Biomedical Investigations
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: editor note
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
imported from: bfo.owl
imported from: Ontology for Biomedical Investigations
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
imported from: bfo.owl
imported from: Ontology for Biomedical Investigations
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

obsolete dependent continuant
type: Class
subclass of: Obsolete Class
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
deprecated: true

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

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
imported from: bfo.owl
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

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

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
imported from: Ontology for Biomedical Investigations
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
imported from: Ontology for Biomedical Investigations
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
imported from: Ontology for Biomedical Investigations
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: Ontology for Biomedical Investigations
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: Ontology for Biomedical Investigations
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
imported from: Ontology for Biomedical Investigations
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

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

Axiom
annotated source: fiat object part
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object part
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

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

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
imported from: bfo.owl
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: Ontology for Biomedical Investigations
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
imported from: Ontology for Biomedical Investigations
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

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

Axiom
annotated source: process boundary
annotated property: definition
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
imported from: bfo.owl
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
editor preferred label: material entity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: ido.owl
imported from: Ontology for Biomedical Investigations
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
imported from: bfo.owl
imported from: Ontology for Biomedical Investigations

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: a marriage bond, an instance of requited love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: elucidation
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigations

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

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: Ontology for Biomedical Investigations

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl
imported from: Ontology for Biomedical Investigations

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

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative term: polymer
imported from: chebi.owl
imported from: Ontology for Biomedical Investigations

material disposal
type: Class
subclass of: waste management
definition: A planned process in which materials are removed permanently from the laboratory or repository.
imported from: chmo.owl
id: CHMO:0002832
comment: makes no judgement about whether this is a good way to do it, or a bad way such as tipping down the sink.

waste management
type: Class
subclass of: planned process
definition: A planned process that involves all aspects of dealing with the waste produced in experiments.
imported from: chmo.owl
id: CHMO:0002845

cell
type: Class
subclass of: material entity
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl
imported from: Ontology for Biomedical Investigations

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

erythrocyte
type: Class
subclass of: cell
editor preferred label: erythrocyte
definition: A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
imported from: cl.owl
imported from: Ontology for Biomedical Investigations

reticulocyte
type: Class
subclass of: cell
editor preferred label: reticulocyte
definition: An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.
imported from: cl.owl
imported from: Ontology for Biomedical Investigations

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

leukocyte
type: Class
subclass of: cell
editor preferred label: leukocyte
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
imported from: cl.owl
imported from: Ontology for Biomedical Investigations

mononuclear cell
type: Class
subclass of: cell
editor preferred label: mononuclear cell
definition: A leukocyte with a single non-segmented nucleus in the mature form.
imported from: cl.owl
imported from: Ontology for Biomedical Investigations

peripheral blood mononuclear cell
type: Class
subclass of: mononuclear cell
editor preferred label: peripheral blood mononuclear cell
definition: A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood.
imported from: cl.owl
imported from: Ontology for Biomedical Investigations

data use permission
type: Class
subclass of: data item
definition: A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
alternative term: consent code
id: DUO:0000001

obsolete consent code primary category
type: Class
subclass of: Obsolete Class
definition: A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.
has obsolescence reason: This term was depreacted as it is not used to tag datasets but instead as patterns for DUO codes capture. This is an archive specific requirement, e.g. "one code from a primary category and one or more from a second category' This is better done by Schemablocks and constraining the pattern of usage of DUO terms at each archive level.
id: DUO:0000002
deprecated: true

obsolete consent code secondary category
type: Class
subclass of: Obsolete Class
definition: A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.
has obsolescence reason: This term was depreacted as it is not used to tag datasets but instead as patterns for DUO codes capture. This is an archive specific requirement, e.g. "one code from a primary category and one or more from a second category' This is better done by Schemablocks and constraining the pattern of usage of DUO terms at each archive level.
id: DUO:0000003
deprecated: true

no restriction
type: Class
subclass of: data use permission
definition: This data use permission indicates there is no restriction on use.
id: DUO:0000004
shorthand: NRES
comment: 20180907, Meeting Moran Melanie: This is to be thought about more carefully - what is the intent when using 'no restriction' as usually users still need to be researchers.
comment: Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service

population origins or ancestry research prohibited
type: Class
subclass of: data use modifier
definition: This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited.
id: DUO:0000044
shorthand: NPOA

obsolete general research use and clinical care
type: Class
subclass of: Obsolete Class
definition: This data use limitation indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
term replaced by: General Research Use, DUO_0000042 Clinical Care USe, DUO_0000043
id: DUO:0000005
shorthand: GRU-CC
comment: This term includes clinical care, which was not defined in the original consent codes paper. This term does not have a usage in our current use cases and we recommend using DUO:0000042, General Research Use, instead
comment: This term was made obsolete as per https://github.com/EBISPOT/DUO/issues/45

health or medical or biomedical research
type: Class
subclass of: general research use
definition: This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
id: DUO:0000006
shorthand: HMB

disease specific research
type: Class
subclass of: health or medical or biomedical research
subclass of: Restriction
  on property: is restricted to
  some values from: disease or disorder
definition: This data use permission indicates that use is allowed provided it is related to the specified disease.
id: DUO:0000007
shorthand: DS
comment: This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms.

population origins or ancestry research only
type: Class
subclass of: data use permission
definition: This data use permission indicates that use of the data is limited to the study of population origins or ancestry.
alternative term: population origins/ancestry research
id: DUO:0000011
shorthand: POA

research specific restrictions
type: Class
subclass of: data use modifier
subclass of: Restriction
  on property: is restricted to
  some values from: Topic
definition: This data use modifier indicates that use is limited to studies of a certain research type.
id: DUO:0000012
shorthand: RS

obsolete research use only
type: Class
subclass of: Obsolete Class
definition: This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care).
id: DUO:0000014
shorthand: RU
comment: Deprecated as GRU-CC was split into GRU and CC, so this is not applicable anymore as a qualifier of GRU-CC

no general methods research
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).
id: DUO:0000015
shorthand: NMDS

genetic studies only
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively)
id: DUO:0000016
shorthand: GSO

data use modifier
type: Class
subclass of: data item
definition: Data use modifiers indicate additional conditions for use.
id: DUO:0000017

not for profit, non commercial use only
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
id: DUO:0000018
shorthand: NPUNCU

publication required
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
id: DUO:0000019
shorthand: PUB

collaboration required
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).
id: DUO:0000020
shorthand: COL
comment: This could be coupled with a string describing the primary study investigator(s).

ethics approval required
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.
id: DUO:0000021
shorthand: IRB

geographical restriction
type: Class
subclass of: data use modifier
subclass of: Restriction
  on property: is restricted to
  some values from: geographic location
definition: This data use modifier indicates that use is limited to within a specific geographic region.
id: DUO:0000022
shorthand: GS
comment: This should be coupled with an ontology term describing the geographical location the restriction applies to.

publication moratorium
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.
alternative term: publication embargo
id: DUO:0000024
shorthand: MOR
comment: This should be coupled with a date specified as ISO8601

time limit on use
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is approved for a specific number of months.
id: DUO:0000025
shorthand: TS
comment: This should be coupled with an integer value indicating the number of months.

user specific restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to use by approved users.
id: DUO:0000026
shorthand: US

project specific restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to use within an approved project.
id: DUO:0000027
shorthand: PS

institution specific restriction
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is limited to use within an approved institution.
id: DUO:0000028
shorthand: IS

return to database or resource
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that the requestor must return derived/enriched data to the database/resource.
id: DUO:0000029
shorthand: RTN

method development
type: Class
subclass of: investigation
DUO_preferred_label: method development
definition: An investigation concerning development of methods, algorithms, software or analytical tools.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000031

population research
type: Class
subclass of: investigation
DUO_preferred_label: population research
definition: An investigation concerning a specific population group.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000032
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

ancestry research
type: Class
subclass of: investigation
DUO_preferred_label: ancestry research
definition: An investigation concerning ancestry or population origins.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000033

age category research
type: Class
subclass of: investigation
DUO_preferred_label: age category research
definition: An investigation concerning specific age categories.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000034
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

gender category research
type: Class
subclass of: investigation
DUO_preferred_label: gender category research
definition: An investigation concerning specific gender categories.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000035
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

research control
type: Class
subclass of: investigation
DUO_preferred_label: research control
definition: An investigation concerning use of data as reference or control material.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000036

biomedical research
type: Class
subclass of: investigation
DUO_preferred_label: biomedical research
definition: An investigation concerning health, medical, or biomedical research.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000037

genetic research
type: Class
subclass of: biomedical research
DUO_preferred_label: genetic research
definition: Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity).
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000038

drug development research
type: Class
subclass of: biomedical research
DUO_preferred_label: drug development research
definition: Biomedical research concerning drug development.
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000039

disease category research
type: Class
subclass of: biomedical research
DUO_preferred_label: disease category research
definition: Biomedical research research concerning specific disease/s
curator note: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000040

general research use
type: Class
subclass of: data use permission
definition: This data use permission indicates that use is allowed for general research use for any research purpose.
id: DUO:0000042
shorthand: GRU
comment: This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.

clinical care use
type: Class
subclass of: data use modifier
definition: This data use modifier indicates that use is allowed for clinical use and care.
id: DUO:0000043
shorthand: CC
comment: Clinical Care is defined as Health care or services provided at home, in a healthcare facility or hospital. Data may be used for clinical decision making.

not for profit organisation use only
type: Class
subclass of: not for profit, non commercial use only
definition: This data use modifier indicates that use of the data is limited to not-for-profit organizations.
id: DUO:0000045
shorthand: NPU

non-commercial use only
type: Class
subclass of: not for profit, non commercial use only
definition: This data use modifier indicates that use of the data is limited to not-for-profit use.
id: DUO:0000046
shorthand: NCU
comment: This indicates that data can be used by commercial organisations for research purposes, but not commercial purposes.

environmental material
type: Class
subclass of: material entity
editor preferred label: environmental material
definition: A material entity which other material entities in an environmental system are primarily or partially composed of.
imported from: envo.owl
imported from: Ontology for Biomedical Investigations

video
type: Class
subclass of: data format specification
definition: Data containing moving pictures stored in digital and analog formats.

geographic location
type: Class
subclass of: site
type: NamedIndividual
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: gaz.owl
id: GAZ:00000448

governmental organization
type: Class
subclass of: organization
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".

female pregnancy
type: Class
subclass of: process
definition: The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
imported from: go.owl
database_cross_reference: Wikipedia:Gestation
has exact synonym: gestation
has_obo_namespace: biological_process
has_related_synonym: carrying of young
id: GO:0007565
in subset: goslim chembl

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

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: pending final vetting
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

narrative object
type: Class
subclass of: information content entity
editor preferred label: narrative object
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
has curation status: metadata incomplete
definition: A narrative object is an information content entity that is a set of propositions.
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
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 editor: person:Chris Stoeckert
definition source: OBI_0000013
definition source: group:OBI

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

obsolete_artifact
type: Class
subclass of: Obsolete Class
has obsolescence reason: failed exploratory term
deprecated: true

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: metadata incomplete
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
definition editor: GROUP: IAO
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.

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

obsolete2_digital entity
type: Class
subclass of: Obsolete Class
editor preferred label: obsolete_digital entity
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.
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 editor: person:Chris Stoeckert
definition source: OBI_0000261
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

journal article
type: Class
subclass of: report
subclass of: publication
subclass of: Restriction
  on property: is specified output of
  some values from: publishing process
subclass of: Restriction
  on property: is specified output of
  all values from: publishing process
editor preferred label: journal article
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.
has curation status: metadata complete
definition: A report that is published in a journal.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000159
definition source: group:OBI

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
editor preferred label: information carrier
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
has curation status: pending final vetting
definition: A quality of an information bearer that imparts the information content
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'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
definition editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

model number
type: Class
subclass of: symbol
editor preferred label: model number
has curation status: pending final vetting
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.
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
definition editor: Person: Alan Ruttenberg

obsolete_material_entity
type: Class
subclass of: Obsolete Class
has obsolescence reason: placeholder removed
deprecated: true

obsolete2_binary digital entity
type: Class
subclass of: Obsolete Class
editor preferred label: binary digital entity
example of usage: MS Word document, ZIP file, DICOM file, JPEG file
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.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
editor note: digital_entity
definition editor: person:Chris Stoeckert
definition source: OBI_0000244
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

obsolete_unit of measure
type: Class
subclass of: Obsolete Class
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.
definition editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
has obsolescence reason: failed exploratory term
deprecated: true

programming language
type: Class
subclass of: plan specification
editor preferred label: programming language
example of usage: R, Perl, Java
has curation status: metadata complete
definition: A language in which source code is written that is intended to be 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 editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000058
definition source: group:OBI

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: iao.owl
imported from: Ontology for Biomedical Investigations
imported from: ogms.owl

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
has curation status: pending final vetting
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
definition editor: PERSON: James A. Overton
definition editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary

numeral
type: Class
subclass of: symbol
editor preferred label: numeral
has curation status: metadata incomplete
definition: A symbol that denotes a number.
definition editor: PERSON: Jonathan Rees

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl
imported from: Ontology for Biomedical Investigations
imported from: ogms.owl

integer numeral
type: Class
subclass of: numeral
editor preferred label: integer numeral
has curation status: metadata incomplete
definition: A numeral that denotes an integer
definition editor: PERSON: Jonathan Rees

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.
has curation status: metadata complete
definition: A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor preferred label: directive information entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

time trigger
type: Class
subclass of: conditional specification
editor preferred label: time trigger
has curation status: uncurated
definition editor: PlanAndPlannedProcess Branch

obsolete_study interpretation
type: Class
subclass of: Obsolete Class
editor preferred label: obsolete_study interpretation
has curation status: pending final vetting
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
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.
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.
definition editor: Lawrence Hunter
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
alternative term: conclusion
definition source: OBI_0000005
has obsolescence reason: failed exploratory term
deprecated: true

dot plot
type: Class
subclass of: graph
editor preferred label: dot plot
example of usage: Dot plot of SSC-H and FSC-H.
has curation status: example to be eventually removed
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.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI

graph
type: Class
subclass of: diagram
editor preferred label: graph
has curation status: pending final vetting
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 editor: PERSON: Lawrence Hunter
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI

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

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

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

obsolete2_report figure
type: Class
subclass of: Obsolete Class
editor preferred label: report figure
has curation status: uncurated
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 editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000027
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

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

software interpreter
type: Class
subclass of: algorithm
editor preferred label: software interpreter
example of usage: R program, Perl interpreter, Java virtual machine
has curation status: metadata complete
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 editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000199
definition source: group:OBI

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

density plot
type: Class
subclass of: graph
editor preferred label: density plot
example of usage: Density plot of SSC-H and FSC-H.
has curation status: example to be eventually removed
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.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000179
definition source: group:Flow Cytometry community

report
type: Class
subclass of: document
editor preferred label: report
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.
has curation status: pending final vetting
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: 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
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition source: GROUP: OBI
definition source: OBI_0000099

obsolete_report element
type: Class
subclass of: Obsolete Class
editor preferred label: report element
has curation status: metadata complete
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).
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
editor note: Replaced by textual entity and figure
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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Allyson Lister
definition editor: PERSON: Melanie Courtot
definition source: GROUP:OBI
definition source: OBI_0000001
has obsolescence reason: failed exploratory term
deprecated: true

obsolete2_binary executable
type: Class
subclass of: Obsolete Class
editor preferred label: binary executable
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 note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'
definition editor: person:Jennifer Fostel
definition source: OBI_0000222
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

source code module
type: Class
subclass of: directive information entity
editor preferred label: source code module
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.
has curation status: metadata incomplete
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
definition source: OBI_0000039
definition source: group:OBI

obsolete_report table
type: Class
subclass of: Obsolete Class
editor preferred label: report table
has curation status: example to be eventually removed
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
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 editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
definition source: OBI_0000265
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

data format specification
type: Class
subclass of: directive information entity
editor preferred label: data format specification
has curation status: metadata incomplete
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
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 editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000187

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI

image
type: Class
subclass of: figure
editor preferred label: image
has curation status: ready for release
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI

data about an ontology part
type: Class
subclass of: data item
editor preferred label: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
definition editor: Person:Alan Ruttenberg
imported from: Ontology for Biomedical Investigations

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
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
definition: A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: iao.owl
imported from: Ontology for Biomedical Investigations
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

obsolete2_digital document
type: Class
subclass of: Obsolete Class
editor preferred label: digital document
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 note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
definition editor: person:Jennifer Fostel
definition source: OBI_0000195
definition source: group:OBI
has obsolescence reason: failed exploratory term
deprecated: true

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: pending final vetting
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

obsolete_identifier
type: Class
subclass of: Obsolete Class
has curation status: organizational term
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 obsolescence reason: placeholder removed
deprecated: true

version number
type: Class
subclass of: symbol
editor preferred label: version number
has curation status: metadata incomplete
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
definition editor: GROUP: IAO

serial number
type: Class
subclass of: symbol
editor preferred label: serial number
has curation status: metadata incomplete
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.
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 :-)
definition editor: GROUP: IAO

lot number
type: Class
subclass of: symbol
editor preferred label: lot number
has curation status: metadata incomplete
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

setting datum
type: Class
subclass of: data item
has curation status: metadata incomplete
definition: A settings datum is a datum that denotes some configuration of an instrument.
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.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.

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

conclusion textual entity
type: Class
subclass of: textual entity
editor preferred label: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
definition editor: Person:Alan Ruttenberg

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

histogram
type: Class
subclass of: graph
editor preferred label: histogram
has curation status: ready for release
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 editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

heatmap
type: Class
subclass of: graph
editor preferred label: heatmap
has curation status: ready for release
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 editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI

Venn diagram
type: Class
subclass of: graph
editor preferred label: Venn diagram
has curation status: ready for release
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
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram

obsolete_survival curve
type: Class
subclass of: Obsolete Class
editor preferred label: obsolete_survival curve
has curation status: ready for release
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
has obsolescence reason: failed exploratory term
deprecated: true

dendrogram
type: Class
subclass of: graph
editor preferred label: dendrogram
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
has curation status: ready for release
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.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram

scatter plot
type: Class
subclass of: graph
editor preferred label: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
has curation status: ready for release
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.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
alternative term: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot

photograph
type: Class
subclass of: image
has curation status: ready for release
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

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

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

textual entity
type: Class
subclass of: information content entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: metadata incomplete
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
definition editor: PERSON: Lawrence Hunter
alternative term: text
imported from: iao.owl
imported from: Ontology for Biomedical Investigations

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred label: citation
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.
has curation status: pending final vetting
definition: A textual entity intended to identify a particular publication.
definition editor: PERSON: Lawrence Hunter

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

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

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
editor preferred label: caption
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.
has curation status: pending final vetting
definition: A textual entity that describes a figure
definition editor: PERSON: Lawrence Hunter

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

table
type: Class
subclass of: textual entity
editor preferred label: table
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting
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

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

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

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

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

publication
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is specified output of
    all values from: publishing process
subclass of: document
editor preferred label: publication
example of usage: journal article, newspaper story, book, etc.
has curation status: metadata complete
definition: A document that is the output of a publishing process.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition editor: PERSON: Lawrence Hunter
alternative term: published document
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
comment: Revisit the term in Octorber 2020. Improve the defintion.

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

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

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

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred label: abstract
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.
has curation status: metadata complete
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
alternative term: precis
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

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
editor preferred label: introduction to a publication about an investigation
example of usage: Section labelled 'introduction' of a typical scientific journal article
has curation status: metadata complete
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
alternative term: background
alternative term: introduction
alternative term: overview
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred label: methods section
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
has curation status: metadata complete
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: experimental
alternative term: experimental methods
alternative term: experimental procedures
alternative term: experimental section
alternative term: method
alternative term: methodology
alternative term: methods
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

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

discussion section of a publication about an investigation
type: Class
subclass of: document part
editor preferred label: discussion section of a publication about an investigation
has curation status: metadata complete
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
alternative term: discussion section
alternative term: discussions
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: citation
editor preferred label: references section
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"
has curation status: metadata complete
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter
alternative term: literature cited
alternative term: reference
alternative term: reference list
alternative term: references
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

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

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

author contributions section
type: Class
subclass of: document part
editor preferred label: author contributions section
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.
has curation status: metadata complete
definition: A part of a publication that is about the specific contributions of each author
definition editor: PERSON: Lawrence Hunter
alternative term: author contributions
alternative term: authors' contribution
alternative term: authors' contributions
alternative term: authors' roles
alternative term: contributions by the authors
alternative term: contributorship
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

acknowledgements section
type: Class
subclass of: document part
editor preferred label: acknowledgements section
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
has curation status: metadata complete
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
definition editor: PERSON: Lawrence Hunter
alternative term: acknowledgement
alternative term: acknowledgements
alternative term: acknowledgment
alternative term: acknowledgments
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
editor preferred label: footnote
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.
has curation status: metadata complete
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
alternative term: endnote
alternative term: footnotes
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

supplementary material to a document
type: Class
subclass of: document part
editor preferred label: supplementary material to a document
has curation status: metadata complete
definition: A part of a document that is segregated from the rest of the document due to its size
definition editor: PERSON: Lawrence Hunter
alternative term: additional file
alternative term: additional files
alternative term: additional information
alternative term: appendix
alternative term: electronic supplementary material
alternative term: electronic supplementary materials
alternative term: supplemental data
alternative term: supplemental information
alternative term: supplemental material
alternative term: supplementary data
alternative term: supplementary files
alternative term: supplementary information
alternative term: supplementary material
alternative term: supplementary materials
alternative term: supporting information
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

table of contents
type: Class
subclass of: table
editor preferred label: table of contents
has curation status: pending final vetting
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

table of figures
type: Class
subclass of: table
editor preferred label: table of figures
has curation status: pending final vetting
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

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

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

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: zero-dimensional spatial region
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
has curation status: metadata complete
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
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 editor: Alan Ruttenberg
curator note: AR notes: We need to discuss whether it should include site.

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

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

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

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

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

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

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

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

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographic location
has curation status: metadata incomplete
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 https://github.com/information-artifact-ontology/IAO/issues/59

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

author role
type: Class
subclass of: role
editor preferred label: author role
has curation status: pending final vetting
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

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
has curation status: metadata complete
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

publishing process
type: Class
subclass of: planned process
has curation status: metadata complete
definition: A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free.
definition editor: Person: Jie Zheng
definition source: https://en.wikipedia.org/wiki/Publishing
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
ontology term requester: VEuPathDB

document in preparation for publication
type: Class
subclass of: document
has curation status: metadata complete
definition: A document that is in preparation for submission to be published.
definition editor: PERSON: Jie Zheng
definition source: EFO_0001795 in preparation
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/232
ontology term requester: VEuPathDB

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 preferred label: documenting
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: pending final vetting
definition: A planned process in which a document is created or added to by including the specified input in it.
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
definition editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
imported from: iao.owl
imported from: Ontology for Biomedical Investigations
term_mapping_to_UMLS: C1548385
term_mapping_to_HL7v3: 11609

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

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified output
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
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.
has curation status: metadata complete
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
editor note: 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition editor: Person:Melanie Courtot
alternative term: assigning a CRID

associating information with a centrally registered identifier in its 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 specified input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
example of usage: Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them.
has curation status: metadata complete
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
definition editor: PERSON:Alan Ruttenberg
alternative term: associating information with a CRID in the CRID registry

obsolete_establishing a CRID registry
type: Class
subclass of: Obsolete Class
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
deprecated: true

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: centrally registered identifier
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: metadata complete
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: metadata complete
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls

looking up a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has specified output
  some values from: information content entity
subclass of: Restriction
  on property: has participant
  some values from: centrally registered identifier registry
example of usage: Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID.
has curation status: metadata complete
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
alternative term: looking up a CRID

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
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete
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

written name
type: Class
subclass of: textual entity
editor preferred label: written name
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
has curation status: pending final vetting
definition: A textual entity that denotes a particular in reality.
definition editor: PERSON: Bill Hogan
definition source: https://github.com/information-artifact-ontology/IAO/issues/114
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.

software method
type: Class
subclass of: software
has curation status: metadata incomplete
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: https://github.com/information-artifact-ontology/IAO/issues/80

software module
type: Class
subclass of: software
has curation status: metadata incomplete
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: https://github.com/information-artifact-ontology/IAO/issues/80

software library
type: Class
subclass of: software
has curation status: metadata incomplete
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: https://github.com/information-artifact-ontology/IAO/issues/80

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

software script
type: Class
subclass of: software
has curation status: metadata incomplete
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: https://github.com/information-artifact-ontology/IAO/issues/80

abbreviation textual entity
type: Class
subclass of: textual entity
editor preferred label: abbreviation textual entity
example of usage: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
definition: A textual entity listing abbreviations and their expansions that are used in a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

abbreviations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: abbreviation textual entity
editor preferred label: abbreviations section
example of usage: The section labelled 'abbreviations' in a typical scientific journal article.
definition: A part of a document where abbreviations and their long-forms used within the document are listed.
definition editor: PERSON: Bill Baumgartner
alternative term: abbreviation and acronyms
alternative term: abbreviation list
alternative term: abbreviations
alternative term: abbreviations and acronyms
alternative term: abbreviations list
alternative term: abbreviations used
alternative term: definitions for abbreviations
alternative term: list of abbreviations
alternative term: list of abbreviations used
alternative term: non-standard abbreviations
alternative term: nonstandard abbreviations
alternative term: nonstandard abbreviations and acronyms
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

author information section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author information textual entity
editor preferred label: author information section
example of usage: The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)
definition: A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: author information
alternative term: authors’ information
alternative term: biographies
alternative term: contributor information
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

author information textual entity
type: Class
subclass of: textual entity
editor preferred label: author information textual entity
example of usage: From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
definition: A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author summary section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: author summary textual entity
editor preferred label: author summary section
example of usage: The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)
definition: A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers.
definition editor: PERSON: Bill Baumgartner
alternative term: author summary
alternative term: summary
alternative term: synopsis
definition source: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

author summary textual entity
type: Class
subclass of: textual entity
editor preferred label: author summary textual entity
example of usage: From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX.
definition: A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
definition editor: PERSON: Bill Baumgartner
definition source: Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines).
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

availability section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: availability textual entity
editor preferred label: availability section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained.
definition editor: PERSON: Bill Baumgartner
alternative term: availability
alternative term: availability of data
alternative term: data archiving
alternative term: data availability
alternative term: data availability statement
alternative term: data sharing statement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

availability textual entity
type: Class
subclass of: textual entity
editor preferred label: availability textual entity
example of usage: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com
definition: A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

case report section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: case report textual entity
editor preferred label: case report section
example of usage: The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)
definition: A part of a document about the medical history of a specific patient as it relates to the topic of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: case presentation
alternative term: case report
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

case report textual entity
type: Class
subclass of: textual entity
editor preferred label: case report textual entity
example of usage: Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension.
definition: A textual entity that expresses a detailed account of a portion of the medical history for a specific patient.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conclusion section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: conclusion textual entity
editor preferred label: conclusion section
example of usage: The section labelled 'conclusion' in a typical scientific journal article.
definition: A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document.
definition editor: PERSON: Bill Baumgartner
alternative term: concluding remarks
alternative term: conclusion
alternative term: conclusions
alternative term: findings
alternative term: summary
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

conflict of interest section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: conflict of interest textual entity
editor preferred label: conflict of interest section
example of usage: The section labelled 'conflict of interest statement' in a typical scientific journal article.
definition: A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: authors' disclosures of potential conflicts of interest
alternative term: competing financial interests
alternative term: competing interests
alternative term: conflict of interest
alternative term: conflict of interest statement
alternative term: conflict of interests
alternative term: conflicts of interest
alternative term: declaration of competing interest
alternative term: declaration of competing interests
alternative term: declaration of interest
alternative term: declaration of interests
alternative term: disclosure of conflict of interest
alternative term: disclosure of potential conflicts of interest
alternative term: duality of interest
alternative term: statement of interest
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

conflict of interest textual entity
type: Class
subclass of: textual entity
editor preferred label: conflict of interest statement
example of usage: SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)]
definition: A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: consent textual entity
editor preferred label: consent section
example of usage: The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/)
definition: A part of a document about the consent process that was used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
alternative term: consent
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent textual entity
type: Class
subclass of: textual entity
editor preferred label: consent textual entity
example of usage: From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
definition: A textual entity that documents the consenting process used to enroll patients in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

ethical approval section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: ethical approval textual entity
editor preferred label: ethical approval section
example of usage: The section labelled 'ethical approval' in a typical scientific journal article.
definition: A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis.
definition editor: PERSON: Bill Baumgartner
alternative term: ethical approval
alternative term: ethical requirements
alternative term: ethics
alternative term: ethics statement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

ethical approval textual entity
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred label: ethical approval textual entity
example of usage: From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review.
definition: A textual entity that documents the ethical approval of some study design.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

figures section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: figure
editor preferred label: figures section
example of usage: The section labelled 'figures' in a typical scientific journal article.
definition: A part of a document that contains one or more figures.
definition editor: PERSON: Bill Baumgartner
alternative term: figures
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

funding source declaration section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: funding source declaration textual entity
editor preferred label: funding source declaration section
example of usage: The section labelled 'funding' in a typical scientific journal article.
definition: A part of a document used to detail information regarding the source of funding used in support of the generation of the document content.
definition editor: PERSON: Bill Baumgartner
alternative term: financial support
alternative term: funding
alternative term: funding information
alternative term: funding sources
alternative term: funding statement
alternative term: funding/support
alternative term: grants
alternative term: role of the funding source
alternative term: source of funding
alternative term: sources of funding
alternative term: study funding
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

funding source declaration textual entity
type: Class
subclass of: textual entity
editor preferred label: funding souce declaration textual entity
example of usage: From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication.
definition: A textual entity documenting the source of funding that supported some study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

future directions section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: future directions textual entity
editor preferred label: future directions section
example of usage: The section labelled 'future directions' in a typical scientific journal article.
definition: A part of a document detailing extensions of the described work that may be implemented at some future point in time.
definition editor: PERSON: Bill Baumgartner
alternative term: future challenges
alternative term: future considerations
alternative term: future developments
alternative term: future directions
alternative term: future outlook
alternative term: future perspectives
alternative term: future plans
alternative term: future prospects
alternative term: future research
alternative term: future research directions
alternative term: future studies
alternative term: future work
alternative term: outlook
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

future directions textual entity
type: Class
subclass of: textual entity
editor preferred label: future directions textual entity
example of usage: Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members.
definition: A textual entity expressing ideas regarding future work relevant to work described in a document that could be done.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: genome announcement textual entity
editor preferred label: genome announcement section
example of usage: The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)
definition: A document part announcing the publication of a novel draft genome sequence.
definition editor: PERSON: Bill Baumgartner
alternative term: genome announcement
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

genome announcement textual entity
type: Class
subclass of: textual entity
editor preferred label: genome announcement textual entity
example of usage: Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB).
definition: A textual entity that describes the generation and public release of a novel, draft genome sequence.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

keyword textual entity
type: Class
subclass of: textual entity
editor preferred label: keyword textual entity
example of usage: From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure.
definition: A textual entity listing keywords indicating the major theme(s) of a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

keywords section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: keyword textual entity
editor preferred label: keywords section
example of usage: The section labelled 'keywords' in a typical scientific journal article.
definition: A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed.
definition editor: PERSON: Bill Baumgartner
alternative term: keywords
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: study limitations textual entity
subclass of: Restriction
  on property: is about
  some values from: study design
editor preferred label: study limitations section
example of usage: The section labelled 'limitations' in a typical scientific journal article.
definition: A part of a document about biases or short comings related to the study design and execution.
definition editor: PERSON: Bill Baumgartner
alternative term: limitations
alternative term: study limitations
definition source: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

study limitations textual entity
type: Class
subclass of: textual entity
editor preferred label: study limitations textual entity
example of usage: Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out.
definition: A textual entity addressing a shortcoming or bias of a study design or execution.
definition editor: PERSON: Bill Baumgartner
definition source: Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

materials section
type: Class
subclass of: document part
editor preferred label: materials section
example of usage: The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)
definition: A part of a document about the materials required to reproduce the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: materials
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

notes section
type: Class
subclass of: document part
editor preferred label: notes section
example of usage: The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):
definition: A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc.
definition editor: PERSON: Bill Baumgartner
alternative term: notes
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

patients section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: patients textual entity
editor preferred label: patients section
example of usage: The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)
definition: A part of a document about the patients that participated in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

patients textual entity
type: Class
subclass of: textual entity
editor preferred label: patients textual entity
example of usage: Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred.
definition: A textual entity expressing information regarding the patients used in a study.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: pre-publication history textual entity
editor preferred label: pre-publication history section
example of usage: The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)
definition: A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors.
definition editor: PERSON: Bill Baumgartner
alternative term: notice of republication
alternative term: pre-publication history
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

pre-publication history textual entity
type: Class
subclass of: textual entity
editor preferred label: pre-publication history textual entity
example of usage: From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub
definition: A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

related work section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: related work textual entity
editor preferred label: related work section
example of usage: The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)
definition: A part of a document about work in other publications that is relevant to the content of the document.
definition editor: PERSON: Bill Baumgartner
alternative term: related literature
alternative term: related work
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

related work textual entity
type: Class
subclass of: textual entity
editor preferred label: related work textual entity
example of usage: Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
definition: A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: requirements textual entity
editor preferred label: requirements section
example of usage: The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/).
definition: A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource.
definition editor: PERSON: Bill Baumgartner
alternative term: requirements
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements textual entity
type: Class
subclass of: textual entity
editor preferred label: requirements textual entity
example of usage: From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None
definition: A textual entity that expresses the requirements necessary to use a resource, e.g. software.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis textual entity
type: Class
subclass of: textual entity
editor preferred label: statistical analysis textual entity
example of usage: From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant.
definition: A textual entity documenting statistical analysis tools and techniques employed.
definition editor: PERSON: Bill Baumgartner
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

statistical analysis section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: statistical analysis textual entity
editor preferred label: statistical analysis section
example of usage: The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)
definition: A part of the document used to describe the statistical methodologies employed in the work presented in the document.
definition editor: PERSON: Bill Baumgartner
alternative term: statistical analysis
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

tables section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has part
  some values from: table
editor preferred label: tables section
example of usage: The section labelled 'tables' in a typical scientific journal article.
definition: A part of a document that contains one or more tables.
definition editor: PERSON: Bill Baumgartner
alternative term: tables
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

postal code
type: Class
subclass of: identifier
definition: An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
definition editor: Mathias Brochhausen

Postal delivery route
type: Class
subclass of: plan specification
definition: A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region.
definition editor: Mathias Brochhausen

zone improvement plan code
type: Class
subclass of: postal code
definition: A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
definition editor: Mathias Brochhausen
alternative term: ZIP code

database extract, transform, and load process
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: information content entity
editor preferred label: database extract, transform, and load process
definition: A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
editor note: Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second
editor note: Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output.
definition editor: PERSON:Alan Ruttenberg
alternative term: ETL
definition source: WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/187

descriptive data section
type: Class
subclass of: document part
editor preferred label: descriptive data section
has curation status: metadata complete
definition: A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made.
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/prisma/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

additional results section
type: Class
subclass of: results section
editor preferred label: additional results section
has curation status: metadata complete
definition: A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/consort/
definition source: https://www.equator-network.org/reporting-guidelines/prisma/
definition source: https://www.equator-network.org/reporting-guidelines/strobe/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

research participants section
type: Class
subclass of: document part
editor preferred label: research participants section
has curation status: metadata complete
definition: A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.).
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/consort/
definition source: https://www.equator-network.org/reporting-guidelines/prisma/
definition source: https://www.equator-network.org/reporting-guidelines/strobe-nut/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

measurement methods section
type: Class
subclass of: methods section
editor preferred label: measurement methods section
has curation status: metadata complete
definition: A methods section that describes details of data assessment methods (data measurement).
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.equator-network.org/reporting-guidelines/strobe/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

research settings section
type: Class
subclass of: document part
editor preferred label: research settings section
has curation status: metadata complete
definition: A document part that describes the physical/social/cultural conditions around a research trial.
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: https://www.ncbi.nlm.nih.gov/books/NBK262175/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

study bias section
type: Class
subclass of: study limitations section
editor preferred label: study bias section
has curation status: metadata complete
definition: A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others.
definition editor: PERSON: Chen Yang
definition editor: PERSON: Jie Zheng
definition source: DOI: 10.1097/PRS.0b013e3181de24bc
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/235
ontology term requester: ONE ontology

graphical abstract
type: Class
subclass of: abstract
editor preferred label: graphical abstract
has curation status: metadata complete
definition: An abstract that is pictorial summary of the main findings described in the document.
definition editor: PERSON: Jie Zheng
definition editor: PERSON: Tim Beck
alternative term: visual abstract
definition source: https://www.elsevier.com/authors/journal-authors/graphical-abstract
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234
ontology term requester: Biomedical literature NLP project

identifier
type: Class
subclass of: information content entity
editor preferred label: identifier
definition: An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
imported from: pno.owl

identity document
type: Class
equivalent class: Class
  intersection of: document
  intersection of: Restriction
    on property: is about
    some values from: documented identity
  intersection of: Restriction
    on property: is concretized as
    some values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: characteristic of
        some values from: Restriction
  intersection of: Restriction
    on property: is concretized as
    all values from: Class
      intersection of: specifically dependent continuant
      intersection of: Restriction
        on property: characteristic of
        some values from: Restriction
subclass of: document
definition: A document that denotes some identity and is concretized by the bearer of some credential role.
definition editor: Amanda Hicks

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

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

credential role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: authentication
  intersection of: Restriction
    on property: characteristic of
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: identity document
subclass of: role
definition: A role that inheres in a concretization of an identity document and is realized by an authentication process.
definition editor: Amanda Hicks

obsolete_claim
type: Class
subclass of: Obsolete Class
has obsolescence reason: placeholder removed
deprecated: true

deontic document act
type: Class
equivalent class: Class
  intersection of: deontic declaration
  intersection of: Restriction
    on property: has specified input
    some values from: document act input document
  intersection of: Restriction
    on property: has specified output
    some values from: document
subclass of: deontic declaration
example of usage: my filling in an immigration form, a judge's signing and stamping a court order
definition: A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document.
definition editor: Mathias Brochhausen

obsolete_document act
type: Class
subclass of: Obsolete Class
example of usage: my filling in an immigration form, a judge's signing and stamping a court order
definition: A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document.
definition editor: Mathias Brochhausen
has obsolescence reason: failed exploratory term
term replaced by: obsolete_deontic document act
deprecated: true

social act
type: Class
subclass of: planned process
example of usage: Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
definition: A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that needs to be perceived.
definition editor: Mathias Brochhausen

obsolete_socio-legal generically dependent continuant
type: Class
subclass of: Obsolete Class
example of usage: the claim of a piece of land, the obligation to pay rent to the owner of a rental property
definition: Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities.
definition editor: Mathias Brochhausen
deprecated: true

obsolete_deontic declaration
type: Class
subclass of: Obsolete Class
editor preferred label: deontic declaration
example of usage: my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract.
definition: A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document.
definition editor: Mathias Brochhausen
alternative term: declaration
alternative term: status function declaration
has obsolescence reason: failed exploratory term
deprecated: true

obligee role
type: Class
subclass of: role
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements.
definition editor: Mathias Brochhausen

document act input document
type: Class
subclass of: document
definition: A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification).
definition editor: Mathias Brochhausen

deontic role
type: Class
subclass of: role
definition: A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave.
definition editor: Mathias Brochhausen
definition editor: Neil Otte

deontic declaration
type: Class
equivalent class: Class
  union of: Restriction
    on property: legally revokes
    some values from: deontic role
  union of: Restriction
    on property: has specified output
    some values from: deontic role
subclass of: social act
definition: A social act that creates or revokes a deontic role.
definition editor: Mathias Brochhausen

obsolete_obligation
type: Class
subclass of: Obsolete Class
has obsolescence reason: placeholder removed
deprecated: true

obsolete_declaration executive role
type: Class
subclass of: Obsolete Class
definition: The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

obsolete_document template creator role
type: Class
subclass of: Obsolete Class
example of usage: the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline
definition: The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
comment: not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants.
deprecated: true

obsolete_claimant role
type: Class
subclass of: Obsolete Class
definition: The role of a human being or an aggregate of human beings concretizing a claim.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

obsolete_obligator role
type: Class
subclass of: Obsolete Class
definition: The role of a human being or an aggregate of human beings concretizing an obligation.
definition editor: Mathias Brochhausen
has obsolescence reason: placeholder removed
deprecated: true

obsolete_declaration target
type: Class
subclass of: Obsolete Class
example of usage: me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act
definition: The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
definition editor: Mathias Brochhausen
has obsolescence reason: failed exploratory term
deprecated: true

document act template creator role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: Class
      union of: Homo sapiens
      union of: organization
      union of: collection of humans
      union of: aggregate of organizations
    intersection of: Restriction
      on property: realized in
      all values from: Class
        intersection of: planned process
        intersection of: Restriction
example of usage: The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified
definition: A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act.
definition editor: Mathias Brochhausen

deontic declaration performer role
type: Class
subclass of: role
definition: A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration.
definition editor: Mathias Brochhausen
alternative term: declaration performer role

obsoleted_document act target
type: Class
subclass of: Obsolete Class
definition: The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.
definition editor: Mathias Brochhausen
deprecated: true

document act performer role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: Class
      union of: Homo sapiens
      union of: organization
      union of: collection of humans
      union of: aggregate of organizations
  intersection of: Restriction
    on property: realized in
    all values from: obsolete_deontic document act
example of usage: a judge's role of signing a court order
definition: A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act.
definition editor: Mathias Brochhausen

standing declaration
type: Class
subclass of: social act
definition: A social act that postulates a socio-legal fact for a specified group of people or organizations.
definition editor: Mathias Brochhausen
alternative term: enactment

obligor role
type: Class
subclass of: role
definition: A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements.
definition editor: John Judkins
definition editor: Mathias Brochhausen

ontology module
type: Class
subclass of: data about an ontology part
editor preferred label: ontology module
editor note: I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
alternative term: ontology file
curator note: This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.

base ontology module
type: Class
subclass of: ontology module
editor preferred label: base ontology module
definition: An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.

editors ontology module
type: Class
subclass of: ontology module
editor preferred label: editors ontology module
definition: An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
alternative term: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred label: main release ontology module
definition: An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
editor note: TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module

bridge ontology module
type: Class
subclass of: ontology module
editor preferred label: bridge ontology module
definition: An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.

import ontology module
type: Class
subclass of: subset ontology module
editor preferred label: import ontology module
definition: A subset ontology module that is intended to be imported from another ontology.
editor note: TODO: add axioms that indicate this is the output of a module extraction process.
alternative term: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred label: subset ontology module
definition: An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
alternative term: ontology slim
alternative term: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: curation subset ontology module
definition: A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.

analysis subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: analysis ontology module
definition: An ontology module that is intended for usage in analysis or discovery applications.

single layer subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: single layer ontology module
definition: A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
alternative term: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: exclusion subset ontology module
definition: A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
alternative term: antislim

external import ontology module
type: Class
subclass of: import ontology module
editor preferred label: external import ontology module
definition: An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
alternative term: external import

species subset ontology module
type: Class
subclass of: subset ontology module
editor preferred label: species subset ontology module
definition: A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
alternative term: taxon subset

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred label: reasoned ontology module
definition: An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.

generated ontology module
type: Class
subclass of: ontology module
editor preferred label: generated ontology module
definition: An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
editor note: TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process

template generated ontology module
type: Class
subclass of: generated ontology module
editor preferred label: template generated ontology module
definition: An ontology module that is automatically generated from a template specification and fillers for slots in that template.

taxonomic bridge ontology module
type: Class
subclass of: bridge ontology module
editor preferred label: taxonomic bridge ontology module

ontology module subsetted by expressivity
type: Class
subclass of: subset ontology module
editor preferred label: ontology module subsetted by expressivity

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred label: obo basic subset ontology module
definition: A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports

ontology module subsetted by OWL profile
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred label: ontology module subsetted by OWL profile

EL++ ontology module
type: Class
subclass of: ontology module subsetted by OWL profile
editor preferred label: EL++ ontology module

informed consent form
type: Class
equivalent class: Class
  union of: incomplete informed consent form
  union of: complete informed consent form indicating consent
subclass of: document act input document
definition: A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.
editor note: The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. For instance, whereas the NCIt definition restricted informed consent forms to clinical trials, the present definition does not.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte
alternative term: informed consent document
definition source: NCIt C16468
curator note: See curator note for 'incomplete informed consent form'.
term_mapping_to_UMLS: C0009797
term_mapping_to_NCIT: C16468

designing an informed consent form
type: Class
subclass of: planned process
definition: A planned process that involves the design of an informed consent form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

validating an informed consent form
type: Class
subclass of: planned process
definition: A planned process that validates an informed consent form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He

approving an informed consent form
type: Class
subclass of: planned process
definition: A planned process that approves an informed consent form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He

signing an informed consent form
type: Class
subclass of: social act
definition: A social act that is a part of an informed consent process and has output of a signed informed consent form. The signing process leads to a legal obligation.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, Jihad Obeid, Chris Stoeckert, and Mathias Brochhausen
curator note: This class is under group discussion as of 03/26/2019.
comment: Signing here does not mean that we have to sign with a pen. It may happen in terms of signing a piece of a paper or an electronic form.

informed consent regulatory body
type: Class
subclass of: organization
definition: An organization charged with approving clinical study protocols and ensuring that applicable governing rules and laws are upheld.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

part of informed consent form
type: Class
subclass of: document part
definition: A document that is a part of an informed consent form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
alternative term: informed consent form element
curator note: This class is under group discussion as of 03/26/2019.

description of participation risk
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes potential harm or estimates the likelihood of harm.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, Cooper Stansbury

recontact method directive
type: Class
subclass of: directive information entity
definition: A document part that prescribes a method of contact in the future.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, Cooper Stansbury

option to check
type: Class
subclass of: user input directive
definition: An answer directive that is part of a document and whose filling in or leaving blank is incidental to the completion of the form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, J. Neil Otte

required informed consent element
type: Class
subclass of: document part
definition: A document part of an informed consent form for which an answer is required in order to complete the form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, J. Neil Otte
curator note: This class is under group discussion as of 03/26/2019.

optional informed consent element
type: Class
subclass of: document part
definition: A document part of an informed consent form for which an answer is not required in order to complete the form.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, J. Neil Otte
curator note: This class is under group discussion as of 03/26/2019.

informed consent form for human biospecimen collection
type: Class
subclass of: informed consent form
definition: An informed consent form that documents a voluntary decision to deposit a human biospecimen.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
definition source: WEB: http://www.irb.umich.edu/policies/consent/
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/
curator note: This class is under group discussion as of 03/26/2019.

informed consent form for human blood sample collection
type: Class
subclass of: informed consent form
definition: An informed consent form that is specifically for human blood sample collection.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He

signed informed consent form
type: Class
equivalent class: Class
  intersection of: informed consent form
  intersection of: Restriction
    on property: has part
    some values from: signature
subclass of: informed consent form
definition: An informed consent form that has been signed by at least one participant.
definition editor: Yongqun He
curator note: Note from J. Neil Otte (7.24.18): 'signed informed consent form' is not a synonym nor subclass of 'complete informed consent form indicating consent'. A signed informed consent form may bear the signature of a witness or doctor, but not yet be complete. Also, a complete informed consent form may need only have been stamped or witnessed by checking a box in an electronic form, and may not require a signature.

allowed research scope in informed consent form
type: Class
subclass of: directive information entity
definition: A directive information entity that specifies the scope of allowed research and is derived from a research protocol.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete fully signed informed consent form
type: Class
subclass of: Obsolete Class
definition: An informed consent form that has been signed by all participants.
definition editor: Yongqun He
deprecated: true

informed consent form signed by human subject
type: Class
subclass of: informed consent form
definition: An informed consent form that has been signed by a human subject
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

signature section
type: Class
subclass of: document part
definition: A document part that is specified as a place to receive a signature.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

human subject signature section in informed consent form
type: Class
subclass of: signature section
definition: A signature section in informed consent element that that is specified as a place to receive a signature from a human subject.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

investigator signature section in informed consent form
type: Class
subclass of: signature section
definition: A signature section in an informed consent form that is specified as a place to receive a signature from an investigator.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

temporal region identifier
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: temporal region
definition: A information content entity that designates a temporal region.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, J. Neil Otte
term tracker item: https://github.com/ICO-ontology/ICO/issues/36

completely filled informed consent form
type: Class
subclass of: informed consent form
definition: An informed consent form that has been filled with all required contents.
definition editor: Yongqun He

partially filled informed consent form
type: Class
subclass of: informed consent form
definition: An informed consent form that has been partially filled with required contents.
definition editor: Yongqun He

effective date specification in informed consent form
type: Class
subclass of: temporal region identifier
definition: A date specification in an informed consent form that specifies an effective date of an investigation.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete expiration date specification in informed consent form
type: Class
subclass of: Obsolete Class
definition: A date specification in an informed consent form that specifies the expiration date of an investigation.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
deprecated: true

starting date specification in informed consent form
type: Class
subclass of: temporal region identifier
definition: A date specification in an informed consent form that specifies the starting date of an investigation.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete human blood sample collection section
type: Class
subclass of: Obsolete Class
definition: A document part that describes and specifies human blood sample collection procedures.
definition editor: Yongqun He
deprecated: true

informed consent form for clinical study
type: Class
subclass of: informed consent form
definition: An informed consent form that is used for a clinical study.
definition editor: Yongqun He
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/
curator note: This class is under group discussion as of 03/26/2019.

informed consent form for storage and future use of unused samples
type: Class
subclass of: informed consent form
definition: An informed consent form that is used for a storage and future use of unused samples.
definition editor: Yongqun He
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/
curator note: This class is under group discussion as of 03/26/2019.

informed consent form for qualitative study
type: Class
subclass of: informed consent form
definition: An informed consent form that is used for a qualitative study.
definition editor: Yongqun He
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/
curator note: This class is under group discussion as of 03/26/2019.

informed assent form for child or minor
type: Class
subclass of: informed assent form
definition: An informed consent form that is adapted to the cognitive abilities and reading abilities child or minor.
definition editor: Yongqun He, Jonathan Vajda
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/

informed consent form for qualitative research involving children
type: Class
subclass of: informed consent form
definition: An informed consent form for qualitative study that involves children.
definition editor: Yongqun He
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/

informed consent form for clinical research involving children
type: Class
subclass of: informed consent form
definition: An informed consent form for clinical study that involves children.
definition editor: Yongqun He
definition source: WEB: http://www.who.int/rpc/research_ethics/informed_consent/en/

date specification in informed consent form
type: Class
subclass of: data item
definition: A data item that indicates a date that specified on an informed consent form.
editor note: 5/7/2014 Asiyah Yu Lin: It is the date specification that appears on the informed consent form, which is may different with the actual date.
definition editor: Yongqun He, Asiyah Yu Lin, J. Neil Otte
curator note: This class is under group discussion as of 03/26/2019.

informed consent form signing date
type: Class
subclass of: temporal region identifier
definition: A date specification that designates when an informed consent form was signed.
editor note: 5/7/2014 Asiyah Yu Lin: look at the OBI example of sample collection date http://purl.obolibrary.org/obo/OBI_0001619
definition editor: Yongqun He, J. Neil Otte

project duration specification
type: Class
subclass of: temporal region identifier
definition: A temporal region identifier that designates a project duration.
definition editor: Yongqun He, J. Neil Otte

project starting date specification
type: Class
subclass of: temporal region identifier
definition: A date specification that designates the date when a project begins.
definition editor: J. Neil Otte

project end date specification
type: Class
subclass of: temporal region identifier
definition: A date specification that designates the date when a project ends.
definition editor: J. Neil Otte

human subject consenter
type: Class
subclass of: Homo sapiens
definition: A human subject who provides informed consent without a legal guardian.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

informed consent rule specification
type: Class
subclass of: directive information entity
definition: A directive information entity that specifies the deontic roles that are produced, revoked, or modified following a process of informed consent, where those deontic roles inhere in the human subject consenter signing an informed consent form, and the investigator or organization leading a research study or providing health care.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obligation informed consent rule specification
type: Class
subclass of: informed consent rule specification
example of usage: An example is that the organization leading a study may be obliged to destroy a patient's biospecimens after 10 years as required in an informed consent form.
definition: An informed consent rule specification that specifies a course of action legally required to be taken.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

permission informed consent rule specification
type: Class
subclass of: informed consent rule specification
definition: An informed consent rule specification that specifies an optional course of action that is an option for a participant to take.
editor note: An example is that a human subject consenter is given the option to withdraw from a consented study any time as specified in an informed consent form.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

informed consent identification code
type: Class
subclass of: data item
definition: A data item consisting of a unique identification code designating an informed consent.
definition editor: Yongqun He

investigator role
type: Class
subclass of: role
definition: A role borne by an agent that, if realized, is realized in an investigation.
definition editor: J. Neil Otte

act of authorizing
type: Class
subclass of: social act
definition: A planned process of making the decision of the competent authorities in form of a letter, document, or verbal or electronic form, that confirms that somebody has permission to do something or be somewhere, e.g. to realize a given project.
editor note: The alternative term of 'permission' has semantic similarity with authorization in the sense of 'approval to do something' and 'the act of giving a formal (usualy written) authorization. The semnatic similarity measuremment of permission and authorization is done using WordNet::Similarity (http://marimba.d.umn.edu/cgi-bin/similarity/)
definition editor: Asiyah Yu Lin, Yongqun He, Elizabeth Umberfield
alternative term: permission
definition source: NCIt C41192

human population
type: Class
subclass of: population
definition: A population of human beings.
definition editor: Yongqun He

nonprofit organization
type: Class
subclass of: organization
definition: An organization that is operated without the principal goal of making a financial profit.
definition editor: Yongqun He

profit organization
type: Class
subclass of: organization
definition: An organization which has the principle goal of earning financial profit.
definition editor: Yongqun He

obsolete animal research investigation
type: Class
subclass of: Obsolete Class
definition: An investigation that involves animal research.
definition editor: Yongqun He
deprecated: true

cancer research investigation
type: Class
subclass of: investigation
definition: An investigation that targets cancer research.
definition editor: Yongqun He

obsolete metastatic melanoma research investigation
type: Class
subclass of: Obsolete Class
definition: A cancer research investigation that specifically targets metastatic melanoma research.
definition editor: Yongqun He
deprecated: true

drug testing investigation
type: Class
subclass of: investigation
definition: An investigation that targets drug testing.
definition editor: Yongqun He

human research investigation
type: Class
subclass of: investigation
definition: An investigation that involves human research.
definition editor: Yongqun He

obsolete genetic study
type: Class
subclass of: Obsolete Class
definition: An investigation that has process part some genetic analysis.
definition editor: Yongqun He
deprecated: true

nonprofit research investigation
type: Class
subclass of: investigation
subclass of: Restriction
  on property: has agent
  some values from: nonprofit organization
definition: An investigation that is conducted with a nonprofit purpose.
definition editor: Yongqun He

for-profit research investigation
type: Class
subclass of: investigation
subclass of: Restriction
  on property: has agent
  some values from: profit organization
definition: An investigation that is conducted with the purpose of earning a profit.
definition editor: Yongqun He

investigation period
type: Class
subclass of: one-dimensional temporal region
definition: A one-dimensional temporal region to which an investigation stands in the occupies_temporal_region relation.
definition editor: J. Neil Otte

ethics directive
type: Class
subclass of: directive information entity
definition: A directive information entity prescribes an ethical requirement.
definition editor: Yongqun He, Cooper Stansbury

act of storing a specimen
type: Class
subclass of: act of storing
subclass of: Restriction
  on property: has participant
  some values from: specimen
definition: A planned process that involves placing a specimen in some location in order to maintain possession of it.
definition editor: J. Neil Otte

informed consent form for genetic study
type: Class
subclass of: informed consent form
definition: An informed consent form that is designed for use in genetic studies.
definition editor: Asiyah Yu Lin, Marcy Harris, Alla Karnovsky, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

human subject unable to give informed consent
type: Class
subclass of: Homo sapiens
definition: A human subject who is unable to give informed consent. In this case, another person is generally authorized to give consent on his behalf, e.g., parents or legal guardians of a child, though in this circumstance the child may be required to provide informed assent, and conservators for the mentally ill.
definition editor: Yongqun He
definition source: web: http://en.wikipedia.org/wiki/informed_consent
curator note: This class is under group discussion as of 03/26/2019.

obsolete informed consent form for quantitative study
type: Class
subclass of: Obsolete Class
definition editor: Marcy Harris
deprecated: true

study requiring informed consent
type: Class
subclass of: investigation
definition: An investigation that requires an informed consent process.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

clinical trial
type: Class
subclass of: investigation
definition: A study that is a clinical trial that requires an informed consent process.
definition editor: Elizabeth Eisenhauer, Yongqun He
curator note: Based on NCI/PT, a clinical trial is a type of research study that tests how well new medical approaches work in people. These studies test new methods of screening, prevention, diagnosis, or treatment of a disease.
curator note: Needs work. Best fit is to rely on SIO_0001000, which has a fine-grained hierarchy. Parent is 'intervention study' (SIO_0000994) which is an investigation (SIO_0000747). However, we have investigation already defined in OBI_0000066.
see also: UMLS: C0008976

clinical trial title
type: Class
subclass of: investigation title
subclass of: Restriction
  on property: denotes
  some values from: clinical trial
definition: An investigation title that designates a clinical trial study, briefly identifying the purpose or design of the investigation.
definition editor: Elizabeth Eisenhauer, Yongqun He
term tracker item: https://github.com/ICO-ontology/ICO/issues/36

obsolete general requirement for informed consent
type: Class
subclass of: Obsolete Class
see also: §46.116 General requirements for informed consent
deprecated: true

contact person for questions about research
type: Class
subclass of: Homo sapiens
definition: A person who is the contact for questions about research.
definition editor: Marcy Harris, Alla Karnovsky, Frank Manion, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

contact person for questions about research subject rights
type: Class
subclass of: Homo sapiens
definition: A person who is the contact for questions about research subject right.
definition editor: Marcy Harris, Alla Karnovsky, Frank Manion, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete contact person in the event of a research-related injury to the subject
type: Class
subclass of: Obsolete Class
definition: A person who is the contact for questions in the event of a research-related injury to the subject
definition editor: Marcy Harris, Alla Karnovsky, Frank Manion, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
deprecated: true

contact person in informed consent process
type: Class
subclass of: Homo sapiens
definition: A person who can be contacted during an informed consent process.
definition editor: Marcy Harris, Alla Karnovsky, Frank Manion, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

research subject role
type: Class
subclass of: role
definition: A role that inheres in human being and is an output of some participation in a research study.
editor note: The term definition is adapted from the definition of the NCIt term 'Human Study Subject' with modification.
definition editor: Yongqun He, Elizabeth Eisenhauer, Asiyah Yu Lin, Asiyah Yu Lin, Marcy Harris
alternative term: human patient
term_mapping_to_UMLS: C2349001
term_mapping_to_NCIT: C70665

authorization for release of confidential health information
type: Class
subclass of: act of authorizing
definition: An act of authorizing that is signed by a patient, or his legal representative, or clinical study participant for the use or disclosure of oral, written, or electronic form of confidential health information that identifies the individual and relates to the medical history, diagnosis, treatment, or prognosis of his condition.
definition editor: Asiyah Yu Lin, Yongqun He
definition source: NCIt C70679
curator note: This class is under group discussion as of 03/26/2019.

obsolete authorization document
type: Class
subclass of: Obsolete Class
definition: A document that is the output of an authorization process.
definition editor: Asiyah Yu Lin
curator note: JV: This probably belongs in D-Acts
deprecated: true

obsolete authorization for medical records release
type: Class
subclass of: Obsolete Class
definition: An authorization process aims to release the medical record.
definition editor: Asiyah Yu Lin
see also: UMLS CUI: C2921556
deprecated: true

obsolete benefit
type: Class
subclass of: Obsolete Class
definition: A benefit is a disposition or the potential positive effects that may arise from participating in a study.
editor note: This term definition is adopted from the NCIt definiton of "benefit" (C25387) with modification.
definition editor: Asiyah Yu Lin, Marcy Harris, Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Frank Manion, J. Neil Otte, Cooper Stansbury
term_mapping_to_UMLS: C0814225
term_mapping_to_NCIT: C25387
comment: Note that a payment is not a benefit of a study.
deprecated: true

risk
type: Class
subclass of: disposition
definition: A risk is a disposition or the potential future harm that may arise from some present action. It is often combined or confused with the probability of an event which is seen as undesirable.
editor note: This term definition is adapted from the NCIt definiton of "Risk" (C17102) . The following source is alos referenced: BMEO(Biomedical Ethics Ontology) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725426/
definition editor: Asiyah Yu Lin, Marcy Harris, Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Frank Manion
definition source: NCIt: C17102
curator note: This class is under group discussion as of 03/26/2019.
term_mapping_to_UMLS: C0035647
term_mapping_to_NCIT: C17102

institutional review board
type: Class
subclass of: organization
definition: A specially constituted organization comprised of medical, scientific and non-scientific members established and designated by an entity to ensure the protection of the rights, safety and well-being of human subjects recruited to participate in biomedical or behavioral research according to the requirements outlined in Title 38, part 16 (same as Title 45, part 46 and Title 21, part 56) of the U.S. Code of Federal Regulations. IRB responsibility include but not limited to the reviewing, approving, and providing continuing review of trial protocol and amendments and of the methods and material to be used in obtaining and documenting informed consent of the trial. Other equivalent committees with the same or similar functions are also considered to be IRBs.
definition editor: Asiyah Yu Lin
alternative term: IRB
definition source: NCIT C16741
term_mapping_to_UMLS: C0086911

research assistant role
type: Class
subclass of: role
definition: a role inhering in a homo sapiens that, if realized, is realized in assisting with a research process.
definition editor: Asiyah Yu Lin, J. Neil Otte

legal guardian role
type: Class
subclass of: role
definition: A role that inheres in an individual who is authorized under applicable State or local law to consent on behalf of a child or incapable person to general medical care including participation in clinical research.
editor note: Yongqun He: Based on the definition, may be better to label it as consent legal guardian role
definition editor: Asiyah Yu Lin, Yongqun He
alternative term: legally authorized representative role
definition source: NCTI C51828
curator note: This class is under group discussion as of 03/26/2019.

obsolete legal guardian
type: Class
subclass of: Obsolete Class
editor note: Yongqun He: Based on the definition of 'legal guardian role', it may be better to label the term as 'consent legal guardian' of 'legal guardian of consent'.
definition editor: Asiyah Yu Lin, Yongqun He
alternative term: legally authorized representative
deprecated: true

individually identifiable health information entity
type: Class
subclass of: protected health information entity
definition: A protected health information entity which identifies an individual; or with respect to which there is a reasonable basis to believe the information can be used to identify an individual.
definition editor: Cooper Stansbury, Jonathan Vajda, J. Neil Otte
curator note: Individually identifiable health information includes many common identifiers such as name, address, birth date, Social Security Number.
curator note: This is adapted from HIPAA.

informed consent process with assent
type: Class
equivalent class: Class
  intersection of: informed consent process
  intersection of: Restriction
    on property: has part
    some values from: act of communicating assent
subclass of: informed consent process
definition: An informed consent process that has an act of communicating assent as a process part, where the person who provides the assent does not bear a competency to consent.
definition editor: Asiyah Yu Lin, Yongqun He, Frank Manion, Chris Stoeckert, Jihad Obeid, Jonathan Bona, Mathias Brochhausen
definition editor: J. Neil Otte, Jonathan Vajda
definition source: http://www.hopkinsmedicine.org/institutional_review_board/guidelines_policies/guidelines/informed_consent_i.html
definition source: https://www.cancer.gov/about-cancer/treatment/clinical-trials/patient-safety/childrens-assent

informed assent form
type: Class
subclass of: document
definition: A document that explains relevant information regarding the expectations and requirements of participation in a research study or clinical procedure, is adapted to the cognitive capacities of that individual so as to assist in that individual's understanding, and is designed to record the assent of that individual.
definition editor: Yongqun He, Jonathan Vajda

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

study duration measurement
type: Class
subclass of: measurement datum
definition: A time measurement datum that measures the duration of a study.
definition editor: J. Neil Otte

participation duration
type: Class
subclass of: one-dimensional temporal region
definition: A temporal interval during which a human being participates in a process.
definition editor: J. Neil Otte

actual duration of study subject participation
type: Class
subclass of: temporal region
definition: Total length of time of subject's participation in a clinical study; from the time of enrollment to the completion of follow-up.
editor note: This duration is different with the 'planned duration of study subject participation'
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete credential letter
type: Class
subclass of: Obsolete Class
definition: A document that certifies that 1) a person may perform some action, or 2) which provides authentication for a claim, or 3) which confirms position or status.
editor note: 5/8/2014 Asiyah Yu Lin: May not included in the final ontology.
deprecated: true

obsolete follow-up visit
type: Class
subclass of: Obsolete Class
definition: The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done.
definition editor: Asiyah Yu Lin
definition source: NCIT:C16033
curator note: Elizabeth: Pay attention to definition "after study procedures and treatments have concluded." Does it fit our purposes?
term_mapping_to_NCIT: C16033
deprecated: true

minimal risk
type: Class
subclass of: risk
definition: A risk that is equal or lesser than those ordinarily encountered in daily life or during the performance of routine physical or psychological examinations or tests.
definition editor: Asiyah Yu Lin, Yongqun He
definition source: (45 CFR 46.102(i)). Available online from: http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html#46.102 Accessed 7/31/13.
curator note: Definition varies slightly for research on prisoners; see (45 CFR 46.303(d)).
curator note: This class is under group discussion as of 03/26/2019.

obsolete alcohol abuse treatment record
type: Class
subclass of: Obsolete Class
definition: A medical record that records the history of a subject's treatment for alcohol abuse.
definition editor: Asiyah Yu Lin, Yongqun He
deprecated: true

obsolete mental health care record
type: Class
subclass of: Obsolete Class
definition: A medical record that describes a patient's mental health care history.
definition editor: Asiyah Yu Lin
term_mapping_to_UMLS: C2114499
deprecated: true

explaining to participant candidate about the study participating information
type: Class
subclass of: planned process
definition: A planned process that involves explanation to a human subject candidate with relevant study information, including study purpose, protocol, and human subject benefits and risks, that indicated in an informed consent form.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

informed consent form for human urine biospecimen collection
type: Class
subclass of: informed consent form
definition: An informed consent form designed for use in human urine collection.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

research-related injury
type: Class
subclass of: injury
definition: A physical injury or illness that is a direct result of the treatment, or procedures required by the protocol, to which the subject would not have been exposed had they not participated in the study.
definition editor: Asiyah Yu Lin
definition source: 1) Citing Resnik, (2006), Mamotte N, Wassenaar D, Singh N (2013) define Research-related injury as “a physical, psychological, social, financial, or other injury, harm, or adverse event that a research participant experiences as a direct result of research participation or from use of the study product.” 2) Resnik, (2006)“A research-related injury is an injury that occurs to a subject as a result of research participation. Injuries may range from relatively minor harms (such as bruises or infected wounds) to major injuries (such as organ damage or temporary disability) to catastrophic injuries (such as permanent disability or death). An injury may require only acute or emergency care, or it may require continuing care. Injuries can be physical or psychological, or emotional.”p. 264

health information entity
type: Class
subclass of: information content entity
definition: An information content entity which is created or received by a health care provider, health plan, public health authority, employer, life insurer, school or university, or health care clearinghouse; and relates to the past, present, or future physical or mental health or condition of any individual, the provision of health care to an individual, or the past, present, or future payment for the provision of health care to an individual.
definition editor: Cooper Stansbury, Jonathan Vajda, J. Neil Otte
curator note: This is adapted from HIPAA.

obsolete information sharing process
type: Class
subclass of: Obsolete Class
definition: The process that shares the information under the informed consent context
definition editor: Asiyah Yu Lin
curator note: The definition needs to be improved.
deprecated: true

protected health information entity
type: Class
subclass of: health information entity
definition: A health information entity which is created, received, stored, or transmitted by covered entities and their business associates in relation to the provision of healthcare, healthcare operations and payment for healthcare services.
definition editor: Cooper Stansbury, J. Niel Otte, Jonathan Vadja
curator note: This is adapted from HIPAA.

informed consent form containing questionnaire
type: Class
subclass of: informed consent form
definition: An informed consent form that contains a questionnaire section.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

explaining study purpose to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: As a partial process of inform the candidate about the study participating information, the purpose of the study will be explained to make sure that the candidate is informed adequately from his/her perspective.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete legal name
type: Class
subclass of: Obsolete Class
definition: Legal name is the person name that identifies a person for legal, administrative and other official purposes. A person's first legal name generally is the name of the person that was given for the purpose of registration of the birth and which then appears on a birth certificate (see birth name), but may change subsequently.
definition editor: Asiyah Yu Lin
definition source: http://en.wikipedia.org/wiki/Legal_name
deprecated: true

study termination
type: Class
subclass of: process
definition: A process that terminates a study.
definition editor: Asiyah Yu Lin
curator note: Note from J. Neil Otte (7.24.18): This class is not to be confused with the terminal process boundary of a study process.

withdrawing participation in study
type: Class
subclass of: planned process
definition: A planned process in which an agent decides to discontinue further participation in a study.
definition editor: Asiyah Yu Lin, J. Neil Otte

act of canceling a permission
type: Class
subclass of: planned process
definition: A planned process that revokes a permission role inhering in some agent.
definition editor: J. Neil Otte

standard medical treatment
type: Class
subclass of: treatment
definition: A treatment currently in wide use and approved by a regulatory body or health authority, considered to be effective in the treatment of a specific disease or condition.
definition editor: Asiyah Yu Lin
definition source: CDISC

review board approval number
type: Class
subclass of: symbol
definition: A character string that is assigned by a review board upon approval of a regulatory document.
editor note: For the review board approval, different countries or continents may have different responsible entities for approving the study. For example, in USA, the board is called "Institutional Review Board" (IRB). In many countries in Europe, it is called Ethics committee.
editor note: This term definition is adapted from the definition of the NCIt term 'Review Board Approval Number Text'.
definition editor: Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He, Alla Karnovsky, Marcy Harris
term_mapping_to_UMLS: C2985863
term_mapping_to_NCIT: C93662

data administration function
type: Class
subclass of: function
definition: An organizational function that involves the areas of information systems and computer science; and that may be realized in planning, organizing, describing, and controlling data resources.
definition editor: Asiyah Yu Lin, J. Neil Otte
definition source: http://en.wikipedia.org/wiki/Data_administration

anonymized information content entity
type: Class
subclass of: information content entity
definition: An information content entity that has been processed to prevent the identification of the person with whom the data are associated, thereby enduring in a stasis of anonymization.
definition editor: Jonathan Vajda, Asiyah Yu Lin
comment: Anonymized data is applicable particularly for secondary use of health data.

obsolete anonymized genomic data
type: Class
subclass of: Obsolete Class
definition: An anonymized data item that is about a genomic sample.
editor note: Anonymized data and samples are initially single or double coded but the link between the subjects identifiers and the unique code(s) are subsequently deleted. Once the link has been deleted it is no longer possible to trace the data and samples back to the individual through the coding key(s). Anonymisation is intended to prevent subject re-identification. As anonymised samples and associated data are not traceable back to the subject it is not possible to undertake actions such as sample withdrawal, or the return of individual results. The use of anonymised data and samples does not allow for clinical monitoring, subject follow-up or the addition of new data. The deletion of the coding key(s) linking the data and samples to the subjects identifiers provides additional confidentiality and privacy protection over coded data and samples, as it prevents subject re-identification through the use of the coding key(s) (ICH).
definition editor: Asiyah Yu Lin, Yongqun He, J. Neil Otte
deprecated: true

obsolete anonymized genomic sample
type: Class
subclass of: Obsolete Class
definition: An anonymized information content entity about a genomic sample.
editor note: Anonymized data and samples are initially single or double coded but the link between the subjects identifiers and the unique code is subsequently deleted. Once the link has been deleted it is no longer possible to trace the data and samples back to the individual through the coding key. Anonymisation is intended to prevent subject re-identification. As anonymised samples and associated data are not traceable back to the subject it is not possible to undertake actions such as sample withdrawal, or the return of individual results. The use of anonymised data and samples does not allow for clinical monitoring, subject follow-up or the addition of new data. The deletion of the coding key linking the data and samples to the subjects identifiers provides additional confidentiality and privacy protection over coded data and samples, as it prevents subject re-identification through the use of the coding key (ICH).
deprecated: true

act of using study participant data
type: Class
subclass of: act of data use
definition: A planned process that involves using data which was an output of a human being's participation in a study and which is about that human being.
definition editor: J. Neil Otte, Elizabeth Umberfield

explaining study protocol to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: In order to make sure that the candidate is informed adequately from his or her perspective, the protocol of the study including the protocol of participating, for example, what kind of procedure the participant will be involved, how many scheduled visits will be explained.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

repository of documents
type: Class
subclass of: site
definition: A site where documents are preserved.
editor note: This term is extracted from Nick's comment on the ICBO paper draft version0.11_Yongqun He.
definition editor: Asiyah Yu Lin
see also: UMLS: C0003738

obsolete storage duration of signed informed consent form
type: Class
subclass of: Obsolete Class
editor note: This term is extracted from Nick's comment on the ICBO paper draft version0.11_Yongqun He.
definition editor: Asiyah Yu Lin
deprecated: true

archiving signed informed consent form
type: Class
subclass of: planned process
definition: A planned process that collect a signed informed consent form. During this process, the information is systematically kept in a repository.
editor note: We can put this axiom: inform... 's located in' some 'archive reposigtory of signed informed consent'
definition editor: Marcy Harris, Alla Karnovsky, Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He
alternative term: storage of signed informed consent form
curator note: This class is under group discussion as of 03/26/2019.

explaining benefits of participation to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: The potential benefit to the study subject that may arise from participating the study research is to be explained to candidate
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete US federal policy for the protection of human subjects
type: Class
subclass of: Obsolete Class
definition: A directive information entity that specifies US federal policy for the protection of human subjects.
definition editor: Elizabeth Eisenhauer, Marcy Harris, Alla Karnovsky, Yongqun He, Asiyah Yu Lin
alternative term: Common Rule
definition source: WEB: http://www.hhs.gov/ohrp/humansubjects/commonrule/
deprecated: true

act of storing signed informed consent form
type: Class
subclass of: act of storing
definition: An act of storing a complete informed consent form.
definition editor: Yongqun He, Elizabeth Eisenhauer, Alla Karnovsky, Marcy Harris, J. Neil Otte
comment: Note: there were previously some related classes that distinguished the format of the informed consent form (e.g. electronic vs. paper). These distinctions are collapsed here. If making this distinction is necessary, the outputs of an instance of this class may be distinguished in their formatting. For instance, storing in an electronic format would entail an instance of an act of storing signed informed consent form bearing an 'has output' relation to an instance of an informed consent form that is in an electronic format.

archiving signed electronic informed consent form
type: Class
subclass of: planned process
definition: A planned process of storage of signed informed consent form when the form is in digital format.
definition editor: Marcy Harris, Alla Karnovsky, Elizabeth Eisenhauer, Yongqun He
alternative term: storage of signed electronic informed consent form
curator note: This class is under group discussion as of 03/26/2019.

archiving signed scanned paper informed consent form
type: Class
subclass of: archiving signed informed consent form
definition: A process of storage of signed informed consent form when the form is in digital format.
definition editor: Marcy Harris, Alla Karnovsky, Elizabeth Eisenhauer, Yongqun He
alternative term: storage of signed scanned paper informed consent form
curator note: This class is under group discussion as of 03/26/2019.

storage duration of signed informed consent form
type: Class
subclass of: temporal region
definition: A temporal interval that represents a period of time during which a signed informed consent form is stored.
definition editor: Yongqun He, Elizabeth Eisenhauer, Asiyah Yu Lin, Alla Karnovsky, Marcy Harris
definition source: WEB: http://answers.hhs.gov/ohrp/questions/7223
curator note: This class is under group discussion as of 03/26/2019.

planned duration of study subject participation
type: Class
subclass of: plan specification
definition: A participation time that is the total length of time of subject's participation in a research study; from the time of enrollment to the completion of follow-up.
editor note: The term definition is adapted from NCIt definition of "Planned Duration of Study Subject Participation" (C70707) with modification. Compared to the NCIt definition, the ICO definition specifies research research study instead of a clinical study.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.
term tracker item: https://github.com/ICO-ontology/ICO/issues/35
term_mapping_to_UMLS: C2347527
term_mapping_to_NCIT: C70707

explaining risks of participation to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: The potential future harm that may arise from participating the study research is to be explained to candidate
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

informed consent form for human saliva sample collection
type: Class
subclass of: informed consent form
definition: An informed consent form for human sample collection that is specifically for human saliva sample collection.
definition editor: Alla Karnovsky, Frank Manion, Yongqun He, Elizabeth Eisenhauer, Marcy Harris, Asiyah Yu Lin
definition source: WEB: http://www.irb.umich.edu/policies/consent/
definition source: WEB: http://www.irb.umich.edu/policies/consent/samples/Sample_SalivaCollection.pdf
curator note: This class is under group discussion as of 03/26/2019.

institutional review board approval number
type: Class
subclass of: review board approval number
definition: A review board approval number that is assigned by an institutional review board.
definition editor: Asiyah Yu Lin, Elizabeth Eisenhauer, Yongqun He, Alla Karnovsky, Marcy Harris
alternative term: institutional review board approval number

explaining sample process and usage to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: In order to make sure that the candidate is informed adequately from his or her perspective, the process of collecting, storing or destroying the sample collected from the study subject is to be explained.
editor note: In the case of biobanking,collected tissue will be frozen and stored in a biorepository system. Other researchers will search and use the tissue for different purpose. The researchers may come from different organization and may need to access some of the personal information or may need to contact the study subject.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

explaining study derived data usage to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: In the case of promoting future data sharing, the usage of the data derived from a study is to be explained to the candidate.
editor note: For example, in the genomic data projects, the study subject's sequence data maybe used outside of the original organization. In this case, the study subject's privacy need to be protected.
definition editor: Asiyah Yu Lin, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

explaining record confidentiality to participant candidate
type: Class
subclass of: explaining to participant candidate in informed consent process
definition: In order to enable the candidate to make voluntary decision, the options for enhancing the protection of confidentiality for participants who have contributed personal information to a study is to be explained.
definition editor: Asiyah Yu Lin, Yongqun He
definition source: http://www.qualitative-research.net/index.php/fqs/article/view/1024/2207.#g42
curator note: This class is under group discussion as of 03/26/2019.

participant candidate making voluntary decision of acceptance
type: Class
subclass of: process
definition: A process in which a candidate makes a voluntary decision to join a study, following their consideration of adequate information presented to them regarding the study and their participation in it.
definition editor: Asiyah Yu Lin, Yongqun He
definition source: https://depts.washington.edu/bioethx/topics/consent.html
curator note: This class is under group discussion as of 03/26/2019.

obsolete assessment of participant candidate understanding
type: Class
subclass of: Obsolete Class
definition: In order for the consent valid, the candidate should be competent to understand what has been explained.
definition editor: Asiyah Yu Lin.
definition source: https://depts.washington.edu/bioethx/topics/consent.html
deprecated: true

informed consent form for vaccination
type: Class
subclass of: informed consent form
definition: An informed consent form that contains sections specific to procedures in vaccination.
definition editor: Yongqun He, Asiyah Yu Lin
alternative term: immunization consent form

obsolete Walgreens vaccine informed consent form'
type: Class
subclass of: Obsolete Class
definition: An informed consent form that is used for vaccination by Walgreens
definition editor: Yongqun He
alternative term: Walgreens Vaccine Administration Record Informed Concsent Form
deprecated: true

eligibility questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire whose purpose is to aid in identifying whether an agent is eligible to participate in a process.
definition editor: J. Neil Otte

question textual entity
type: Class
subclass of: textual entity
definition: A textual entity that is a sentence in the interrogative mood.
definition editor: J. Neil Otte

legally effective consenting
type: Class
subclass of: planned process
definition: A planned process that results in a legally effective consent status.
definition editor: Frank Manion, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete assent process
type: Class
subclass of: Obsolete Class
definition: A planned process of acknowledgement, or agreement, to participate in a procedure or study, where the participant is incapable of informed consent.
definition editor: Asiyah Yu Lin, Yongqun He, Frank Manion, Chris Stoeckert, Jihad Obeid, Jonathan Bona, Mathias Brochhausen, 2018 Informed Consent Workshop
alternative term: assent process
definition source: http://www.medtran.ru/eng/trials/protomechanics/ch3.htm
definition source: https://www.cancer.gov/about-cancer/treatment/clinical-trials/patient-safety/childrens-assent
definition source: https://www.hhs.gov/ohrp/regulations-and-policy/regulations/45-cfr-46/index.html#46.408
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777303/
comment: According to the Common Rule, the IRB shall determine that adequate provisions are made for soliciting the assent of the children, when in the judgment of the IRB the children are capable of providing assent.
comment: Specifically, "assent" is a term used to express willingness to participate in research by persons who are by definition too young to give informed consent but who are old enough to understand the proposed research in general, its expected risks and possible benefits, and the activities expected of them as subjects.
deprecated: true

legally effective consented participant role
type: Class
subclass of: role
definition: A role that inheres in a human being who participates in a consenting process and eventually becomes legally effectively consented.
definition editor: Frank Manion, Yongqun He, Mathias Bronchhausen, Chris Stoeckert, Jie Zheng, Jihad Obeid, Helena Ellis
curator note: This class is under group discussion as of 03/26/2019.

postmortem donation of biological specimen
type: Class
subclass of: planned process
definition: A planned process in which an agent's designated biological specimen is collected after the death of the agent.
definition editor: Yongqun He

eligibility of candidate participation
type: Class
subclass of: role
definition: A role that represents the eligibility of a candidate according to a study protocol.
definition editor: Frank Manion, Yongqun He, Mathias Brochhausen, William Duncan
curator note: This class is under group discussion as of 03/26/2019.

candidate eligible for study role
type: Class
subclass of: role
definition: A role inhering in a participant who meets all eligibility criteria defined within a study protocol.
definition source: NCI BBRB: Biorepositories and Biospecimen Research Branch

candidate ineligible for study role
type: Class
subclass of: role
definition: A role inhering in a participant who does not meet all eligibility criteria defined within the study protocol.
definition source: NCI BBRB: Biorepositories and Biospecimen Research Branch

act of contact for future research
type: Class
subclass of: planned process
definition: A planned process in which an agent contacts a participant of an informed consent process regarding opportunities related to future research.
definition editor: Jonathan Vajda with ICO Workgroup in Ann Arbor (2018)
definition editor: Yongqun He, Mathias Brochhausen, Jihad Obeid, Frank Manion
definition source: https://sbsirb.uchicago.edu/page/consent-form-templates-and-examples

eligibility screening process
type: Class
subclass of: planned process
definition: A planned process to screen the eligibility of a candidate for a study or procedure, verifying whether certain sufficient or necessary conditions for eligibility obtain.
definition editor: Frank Manion, Yongqun He

eligibility screening role
type: Class
subclass of: role
definition: A role that inheres in a person that, if realized, is realized in an eligibility screening process.
definition editor: Frank Manion, Yongqun He, J. Neil Otte

obsolete eligibility screening person
type: Class
subclass of: Obsolete Class
definition editor: Frank Manion, Yongqun He
deprecated: true

obsolete consenting to be contacted for tissue research
type: Class
subclass of: Obsolete Class
deprecated: true

explaining to participant candidate in informed consent process
type: Class
subclass of: planned process
definition: A planned process of communicating information about an informed consent process.
definition editor: Yongqun He, Cooper Stansbury

obsolete informed consent
type: Class
subclass of: Obsolete Class
definition: A planned process that a person agrees to participate in a research project, which is a part of an informed consent process.
definition: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777303/
definition editor: YH, 2018 Little Rock CTSOG ontology workshop
deprecated: true

adult consent process
type: Class
subclass of: informed consent process
definition: An informed consent process where the person who is being asked to consent is an adult.
definition editor: J. Neil Otte
definition source: https://oprs.usc.edu/files/2017/04/Informed-Consent-Booklet-4.4.13.pdf
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777303/

parental informed consent process
type: Class
subclass of: informed consent process
definition: An informed consent process in which a parent reaches a decision concerning whether or not to grant consent on a minor's behalf, when the minor is incapable of providing consent for themselves.
definition editor: J. Neil Otte
alternative term: parental permission
alternative term: parental permission consent
definition source: https://oprs.usc.edu/files/2017/04/Informed-Consent-Booklet-4.4.13.pdf
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777303/

act of declining to provide consent
type: Class
subclass of: planned process
definition: A planned process in which a person decides not to provide consent.
definition editor: J. Neil Otte

informed verbal consent
type: Class
subclass of: act of informed consenting
definition: An informed consent process in which the participant communicates consent orally rather than by filling out and signing a written form.
definition editor: Yongqun He, 2018 Little Rock CTSOG ontology workshop
definition source: https://oprs.usc.edu/files/2017/04/Informed-Consent-Booklet-4.4.13.pdf
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777303/

consenting in short form
type: Class
subclass of: informed consent process
definition: An informed consent process in which the participant is not able to read and write in the language of the informed consent form, but is aided in understanding the informed consent process by a translation into the agent's native language.
definition editor: J. Neil Otte
definition source: https://oprs.usc.edu/files/2017/04/Informed-Consent-Booklet-4.4.13.pdf
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777303/

biological sample collecting
type: Class
subclass of: planned process
definition: A planned process in which a biological sample from a subject is collected for testing.
definition editor: Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/books/NBK110047/

tissue sample collecting
type: Class
subclass of: biological sample collecting
definition: A biological sample collecting in which a tissue sample from a subject is collected for testing.
definition editor: Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/books/NBK110047/

blood sample collecting
type: Class
subclass of: biological sample collecting
definition: A biological sample collecting in which a blood sample from a subject is collected for testing.
definition editor: Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/books/NBK110047/

subject withdrawal with sample stored for unlimited time
type: Class
subclass of: planned process
definition: A planned process that represents a study participant withdrawing from the study and agreeing to have the participant sample stored for unlimited time.
definition editor: 2018 CTSOG informed consent ontology workshop in Little Rock (http://ncorwiki.buffalo.edu/index.php/Ontology_of_Informed_Consent:_An_Approach_to_Specimen_and_Data_Sharing)
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

subject withdrawal with sample stored for limited time
type: Class
subclass of: planned process
definition: A planned process that represents a study participant withdrawing from the study and agreeing to have the participant sample stored for a limited time period.
definition editor: 2018 CTSOG informed consent ontology workshop in Little Rock (http://ncorwiki.buffalo.edu/index.php/Ontology_of_Informed_Consent:_An_Approach_to_Specimen_and_Data_Sharing)
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

obsolete deontic role
type: Class
subclass of: Obsolete Class
curator note: Moved to d-acts
deprecated: true

obsolete permittee deontic role in genetic research
type: Class
subclass of: Obsolete Class
definition: A deontic role that if realized is realized by its bearer conducting or overseeing genetic research on the genome of a human donor.
comment: Note: this term wll be transferred to d-acts. - CTSOG ontology workshop 2018 Little Rock
deprecated: true

obsolete genetic research permission deontic declaration
type: Class
subclass of: Obsolete Class
definition: A deontic declaration that has output a permittee role that permits genetic research on a human donor as a specified outcome.
definition editor: Jonathan Vajda
comment: will add an equivalent class axiom 'has specified output' some 'permittee deontic role in genetic research'
deprecated: true

assenter role
type: Class
subclass of: role
definition: a role that inheres in a human subject who participates in an assending process.
definition editor: Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

filled questionnaire
type: Class
subclass of: questionnaire
definition: A questionnaire that is filled up with answers.
definition editor: Yongqun He, Asiyah Yu Lin
curator note: This class is under group discussion as of 03/26/2019.

filled multiple choice text entity
type: Class
subclass of: textual entity
definition: A textual entity that is the recorded response to a multiple choice question.
definition editor: J. Neil Otte

yes answer text entity
type: Class
subclass of: filled multiple choice text entity
definition: A filled multiple choice text entity that records a response indicating 'yes' to a multiple choice question.
definition editor: J. Neil Otte

no answer text entity
type: Class
subclass of: filled multiple choice text entity
definition: A filled multiple choice text entity that records a response indicating 'no' to a multiple choice question.
definition editor: J. Neil Otte

filling informed consent form
type: Class
subclass of: planned process
definition: A planned process that involves the filling of an informed consent form.
definition editor: Yongqun He, Asiyah Yu Lin
curator note: This class is under group discussion as of 03/26/2019.

filling questionnaire
type: Class
subclass of: planned process
definition: A planned process that involves the filling of a questionnaire form that includes a list of questions.
definition editor: Yongqun He, Asiyah Yu Lin
curator note: This class is under group discussion as of 03/26/2019.

obsolete permittee deontic role
type: Class
subclass of: Obsolete Class
definition: A deontic role that if realized is realized by its bearer conducting or overseeing genetic research on the genome of a human donor.
comment: Note: this term wll be transferred to d-acts. - CTSOG ontology workshop 2018 Little Rock
deprecated: true

consenting not to have financial benefit
type: Class
subclass of: act of informed consenting
definition: An informed consent for a subject agrees not to have financial benefit in the future.
definition editor: Christoph Brochhausen, Yongqun He

consenting to not to be informed about incidental finding
type: Class
subclass of: planned process
definition: A planned process for a subject agrees not to be informed about any incidental finding.
definition editor: Christoph Brochhausen, Yongqun He
curator note: This class is under group discussion as of 03/26/2019.

broad consent process
type: Class
subclass of: planned process
definition: A planned process for an unspecified range of future research subject to a few content or process restrictions.
definition editor: Frank Manion, Yongqun He, 2018 Little Rock CTSOG ontology workshop
definition source: https://www.hhs.gov/ohrp/sachrp-committee/recommendations/attachment-c-august-2-2017/index.html
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791589/
curator note: This class is under group discussion as of 03/26/2019.

obsolete process of providing broad consent for research with biological sample
type: Class
subclass of: Obsolete Class
definition: A broad consent that is for an unspecified range of future research subject to a few content or process restrictions with biological sample.
definition editor: Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791589/
deprecated: true

secondary use
type: Class
subclass of: planned process
definition: A planned process that involves a human biological specimen originally collected for the purpose of treatment or a different investigation.
definition editor: Frank Manion, Yongqun He, 2018 Little Rock CTSOG ontology workshop
definition source: https://www.hhs.gov/ohrp/sachrp-committee/recommendations/attachment-c-august-2-2017/index.html
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791589/
curator note: Note: not sure if the parent class should be 'investigation' or 'planned process.'
curator note: This definition is provisional, as 'secondary use' may apply to non-specimen entities. Adapted from the defintion found here: https://sunnybrook.ca/research/content/?page=sri-crs-reo-faq-secondaryusedata

obsolete consenting to the secondary use of EHR
type: Class
subclass of: Obsolete Class
definition source: https://www.ncbi.nlm.nih.gov/pubmed/15360890
deprecated: true

obsolete NEW_CLASSES
type: Class
subclass of: Obsolete Class
curator note: Note that some of these are defined classes.
deprecated: true

informed assent form for cognitively impaired
type: Class
subclass of: informed assent form
definition: An informed consent form that is adapted to the cognitive capacities of someone with significant mental impairment.
definition editor: Yongqun He, Jonathan Vajda

permission temporal region
type: Class
subclass of: temporal region
definition: A temporal region during which some act is permitted.
definition editor: Yongqun He, Jonathan Vajda
curator note: This class is under group discussion as of 03/26/2019.

legal representative role
type: Class
subclass of: role
definition: A deontic role, which may be realized in an Act of Consent, where the bearer of the legal representative role consents on behalf of a person who lacks the capability to provide consent.
definition editor: J. Neil Otte
curator note: It is a requirement of bearing a legal representative role in some jurisdiction(J) that one also bears a competency to consent in (J).
curator note: Mathias says this shouldn't mention 'act of consent'. I think the idea is that our definition is narrower than the class label indicates.
curator note: Note: Consent roles are created by Acts of Consent. It follows that one can’t be a consenter and bear a consenter role just because one participated in an informed consent process. Here, one would be a mere research candidate or human subject or...etc, who participated in an informed consent process. Assenter Role, likewise, is the output of an Act of Communicating Assent. Both these roles are backward looking--i.e. They are created by the processes of assent and consent and do not pre-date them. By contrast, ‘Legal Representative Role’ and ‘Permission Role’ are not, by definition, tied to Acts of Consenting and Acts of Assenting. Such roles are the output of other processes, including ‘Act of Permitting’ in the latter case, and perhaps ‘Act of Legal Representative Authorization’ in the former.

organization-specified contact role
type: Class
subclass of: contact person role
definition: A role borne by a human being who is part of a group of individuals and acts as a contact person for the group.
definition editor: Jonathan Vajda

contact directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes a human being who is to bear a contact role.
definition editor: Jonathan Vajda, Cooper Stansbury

description of participation benefit
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes potential benefit or estimates the likelihood of benefit.
definition editor: Jonathan Vajda, Cooper Stansbury
curator note: This is circulular. 'Benefit' and 'risk' definitions forthcoming.

obsolete description of allowed action types
type: Class
subclass of: Obsolete Class
definition: A document part that describes the action types to be permitted.
definition editor: Jonathan Vajda
deprecated: true

description of broad consent
type: Class
subclass of: descriptive information content entity
definition: A description of allowed action types that has in view a wide, unspecified range of action types, and is restricted only by a regulator body.
definition editor: Jonathan Vajda, Cooper Stansbury

act of filling out form
type: Class
subclass of: planned process
definition: A planned process of providing information according to prompts on a form.
definition editor: Jonathan Vajda

obsolete social act (placeholder)
type: Class
subclass of: Obsolete Class
definition: A process that is carried out by a conscious being or an aggregate of conscious beings, and is spontaneous, directed towards another conscious being or another aggregate of conscious beings, and that needs to be perceived.
curator note: This is a D-Act Term, included here as a placeholder untill D-acts is imported.
deprecated: true

act of permitting
type: Class
subclass of: deontic declaration
subclass of: Restriction
  on property: has specified output
  some values from: permission role
definition: A social act in which an agent bearing a deontic power role and realizes that role in the creation of a permission role.
definition editor: J. Neil Otte
curator note: Axiom: Every ‘Act of permitting’ has process part some (‘Speech Act’ or ‘Document Act’). Note: This class is very general, and doesn’t only apply to consent and healthcare contexts.
curator note: In contrast to the 'authentication' (see OMRSE), an act of permitting always involves a flow of power, in which one who grants permission has a power, and the agent to whom permission is granted gains access to a power that flows from that of the granter. By contrast, although it may be the case that a person who authenticates has power, this power is only the power to authenticate or verify, and this power does not flow to the authenticated document or identity.
curator note: Note: ‘Act of permitting’, ‘act of consenting’, and ‘act of communicating assent’ are all success terms, which is to say that no ‘act of permitting’ does not issue a permission, no ‘act of consenting’ does not issue a consent, and no ‘act of communicating assent’ does not issue an assent.

act of informed consenting
type: Class
equivalent class: Class
  intersection of: act of permitting
  intersection of: Restriction
    on property: part of
    some values from: informed consent process
subclass of: act of permitting
definition: An act of permitting that is a process part of some informed consent process.
definition editor: J. Neil Otte
curator note: Note: This class is very general, and doesn’t only apply to consent and healthcare contexts. There may be further subclasses of consenting for which there are also required process parts, such as a process of informing a patient of the risks associated with a medical procedure or research investigation. Also, 6/28: Mathias writes: This definition is probably incorrect. I assume we don't want to affirm that only within informed consent we do find acts of consenting.

act of communicating assent
type: Class
subclass of: social act
definition: An act of communicating one’s agreement.
definition editor: J. Neil Otte

permission role
type: Class
subclass of: deontic role
definition: A deontic role that inheres in an agent and which permits certain actions.
definition editor: J. Neil Otte
curator note: Important Note: When we use ‘consent’ to talk about the thing provided to an investigator then what we are referring to is a permission role, that was the output of an Act of Consent. This is all consent is, per this representation.
curator note: Note: This may become ‘permittee role’ in order to better distinguish it from the corresponding ‘permittor role’ (the person with the deontic power to grant permissions to others).
curator note: Note: Typically, in the context of consent, a permission role will inhere in a clinician or investigator as a result of an act of permitting, but possibly an act of authorizing. Authorizing is different from permitting, but this needs to be worked out. Perhaps one has provided permission, but the process and the documentation need to be authorized by some authority prior to a clinician acquiring a permission role. There is also the case Chris Stockert raised, where an organization authorizes some data or specimens to be used, despite no consent or assent having been provided.

obsolete consent power role
type: Class
subclass of: Obsolete Class
definition: A deontic power role that, if realized, may permit an Act of Consent and thereby create a permission role, or revoke or modify a previously provided permission role created by permitting an Act of Consent.
definition editor: J. Neil Otte
curator note: Note: A Consent Power Role inheres in all those who bear a legal right to consent. Such a role represents a de jure right that holds within some socio-legal jurisdiction. It follows that one may bear an instance of a consent power role within one jurisdiction but one may lack an instance of a consent power role within a second jurisdiction, given that one’s capability to consent may satisfy legal conditions in the former jurisdiction but not in the latter.
deprecated: true

capability to consent
type: Class
subclass of: disposition
subclass of: Restriction
  on property: characteristic of
  some values from: agent
definition: A cognitive capability inhering in some agent, which may be realized in an Act of Consent.
definition editor: J. Neil Otte
curator note: Note: Capability-talk is fraught and so attention to this particular, somewhat stipulative notion is necessary. First: Capabilities are BFO:Dispositions. Hence, we’re not talking about institutional power, which will be represented separately using deontic roles. This is compatible with institutional rules requiring a particular capability. Second: Like roles, capabilities can have other capabilities as parts. Thus, the capability to consent requires, as part, the capability to understand information, the capability to appreciate the consequences of one’s actions, and other capabilities related to a basic, agential capacity to be reasons-responsive. These capacities may be realized in other sub-parts of the informed consent process, and they may be identified in processes of cognitive assessment. Third: Capabilities may be assessed along a scale, with some having a greater capability to consent and some having a lesser ability to consent. The same capability at the same degree may pass muster in some jurisdictions but fail to pass in others. When it does succeed in passing some legal requirement, then the bearer of the capability has a Consent Power Role and their capability to consent now counts as a competency. Fourth: Capabilities are cognitive dispositions. As such, the class ‘capability to consent’ is not intended to be a catch-all for all the necessary conditions for legal consent. For instance, being under the age of 18 is not part of an instance of a capability to consent, but the capability to understand risks and benefits may be. Fifth: A capability that is so low on the scale as to not pass any tests is no longer a capability but a liability. The distinction between capabilities and liabilities may not be vague ontologically, but may be quite difficult to suss out epistemologically. More to the point: This is perhaps the most revisionist aspect of this reading of capabilities, for it requires that in some particular legal context, we might need to say tha…

competency to consent
type: Class
subclass of: capability to consent
definition: A capability to consent that is sufficiently robust as to pass the legal requirements of some jurisdiction.
definition editor: J. Neil Otte
curator note: Axiom: all l all c all t all m (competencytoconsent(m) & inheresin(m,x,t) -> (exists l exists c (legalpowerrole(l) & capabilitytoconsent(c) & (exists r exists o (hasorganizationalcontext(l,r,t) & hasorganizationalcontext(l,o,t) & r=o)) & inheresin(l,x,t) & inheresin(c,x,t)) -> (m=c))). %If one bears a competency to consent, then one bears a legal power role and a capability to consent in the same legal context at the same time and the competency to consent is identical to the capability to consent.
curator note: One may have the same capability to consent, but whether that capability to consent amounts to a competency might vary between jurisdictions that impose different requirements upon the bearer.

obsolete assenter role
type: Class
subclass of: Obsolete Class
definition: A role that is the output of an act of assent and which inheres in a human being, who, because they fail to satisfy certain criteria for consent, is thereby allowed the aid of a legal representative who aids them in an Act of Consent, and, in some contexts, may be realized in revoking or modifying the permission role that was output of the informed consent process of which the the Act of Assent was a process part.
definition editor: J. Neil Otte
deprecated: true

assenter
type: Class
equivalent class: Class
  intersection of: agent
  intersection of: Restriction
    on property: agent in
    some values from: act of communicating assent
subclass of: agent
definition: An agent who has communicated their assent.
definition editor: J. Neil Otte

consenter
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: consent power role
      intersection of: Restriction
        on property: realized in
        some values from: act of informed consenting
subclass of: Homo sapiens
definition: An agent who, at some time, was the bearer of a consent power role, which was, in fact, realized in an act of informed consenting, and who, as a result of this act of informed consenting, now bears a consenter role.
editor note: A consenter role may be realized, for example, in the withdraw of consent.
definition editor: J. Neil Otte

obsolete consenter role
type: Class
subclass of: Obsolete Class
definition: A deontic role that is output of some Act of Consent and, in some contexts, may be realized in revoking or modifying the permission role that was output of the same Act of Consent.
definition editor: J. Neil Otte
curator note: May be deleted. Consenter role just seems like permission role issued by an act of consenting.
deprecated: true

incomplete informed consent form
type: Class
subclass of: informed consent form
definition: A document act input document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and whose purpose is to assist in obtaining consent.
definition editor: J. Neil Otte
comment: Note: instances of 'incomplete informed consent form' include both blank informed consent forms that are waiting to be used in a process of informed consent, as well as those that have been left blank by a patient, whether on purpose or in error. Those that have been left blank on purpose have been used in a process of informed consent, where the patient must have reached a decision.

complete informed consent form indicating consent
type: Class
subclass of: informed consent form
definition: A document act input document that has, as part, an incomplete informed consent form, along with some additional parts, such as a signature, stamp, or initials, which serve as a record to an act of consent that had the incomplete informed consent form as a specified input.
definition editor: J. Neil Otte

deontic power role
type: Class
subclass of: deontic role
definition: A deontic role that, if realized, is realized in the creation, modification, or revoking of other deontic roles.
definition editor: J. Neil Otte

act of anonymizing
type: Class
subclass of: planned process
definition: A planned process that involves altering an information content entity that is associated with an individual, such that such association is lost or inaccessible.
definition editor: Jonathan Vajda

act of removing identifiable information
type: Class
subclass of: act of anonymizing
definition: An act of anonymization that alters an information content entity by removing information content which identifies that individual.
definition editor: Jonathan Vajda

agent
type: Class
equivalent class: Class
  union of: Homo sapiens
  union of: organization
subclass of: material entity
definition: A material entity (either a human being or an aggregate of humans such as an organization) which is active in a process or has the relevant capabilities of intentionality.
definition editor: Jonathan Vajda

act of informing
type: Class
subclass of: social act
definition: A social act in which information that is thought to be true, salient, or which is held to have a high degree of certainty is communicated to an agent that previously lacked that information.
definition editor: Cooper Stansbury, Jonathan Vajda, J. Neil Otte
curator note: If I communicate falsehoods, I do not inform--I mis-inform.

signature
type: Class
subclass of: information content entity
definition: An information content entity that is a handwritten depiction of a name.
definition editor: Jonathan Vajda, Cooper Stansbury, J. Neil Otte.

consent power role
type: Class
subclass of: deontic power role
definition: A deontic power role that may be realized in an act of consent that is a process part of an informed consent process.
definition editor: J. Neil Otte
curator note: a consent power role is a legal right that holds within a jurisdiction and is a necessary requirement to bear a competency to consent.

stasis of anonymization
type: Class
subclass of: stasis of generically dependent continuant
definition: A stasis of generically dependent continuant that has participant some information content entity which, during the stasis, is unable to be used to identify some agent which the information is about.
definition editor: Jonathan Vajda, Cooper Stansbury, J. Neil Otte
curator note: An information content entity that has previously undergone the process 'act of anonymization' participates in this stasis.
curator note: We expect to add a subclass axiom: 'preceded by' some 'Act of Anonymizing'

act of storing
type: Class
subclass of: planned process
definition: A planned process that involves placing a material entity in some location in order to maintain possession of it.
definition editor: J. Neil Otte

act of data sharing
type: Class
subclass of: planned process
definition: A planned process in which data possessed by one person or organization is shared with one or more other persons or organizations.
definition editor: J. Neil Otte

human subject-specified contact person role
type: Class
subclass of: contact person role
definition: A contact person role that is the output of either a human subject or patient assigning that person as their point of contact.
definition editor: J. Neil Otte
alternative term: emergency contact role
see also: organization-specified contact role

contact person role
type: Class
subclass of: role
definition: A role inhering in a person who is a designated contact for some other agent.
definition editor: J. Neil Otte
comment: The subclasses of 'contact person role' distinguish two types: a contact person who has been designated by an organization for others (primarily patients and human research subjects in clinical settings) to contact, and a contact person whom an agent has specified for an organization to contact in the event that the organization needs to contact the patient. Examples of the latter include 'emergency contact' persons, who are frequently specified in a form.

jurisdiction
type: Class
subclass of: site
definition: A site within which a deontic power may be realized, where that deontic power inheres in a formally created regulatory body.
definition editor: Cooper Stansbury
definition editor: J. Neil Otte
definition editor: Jonathan Vajda
curator note: 'Jurisdiction' is often defined in two senses: (1) a geopolitical context (BFO site), or (2) a power. We define jurisdiction as a BFO site, identifiable through shared context of other entities, like a country or state border, or the grounds of an institution. The term ‘deontic power role’ reflects the sense of ‘power’ sometimes used to describe jurisdiction.

obsolete regulatory body
type: Class
subclass of: Obsolete Class
definition: An organization that has a deontic power role prescribed by some regulatory document that occurs in a stasis of regulation.
definition editor: Cooper Stansbury
deprecated: true

regulatory document
type: Class
subclass of: document
definition: A document that either prescribes actions or prescribes the permissions, obligations, restrictions, or protections relating to public or legal policy.
definition editor: Cooper Stansbury
curator note: Rules, legal specifications, guidelines (both categorical and hypothetical), that exist together in one regulatory document. Regulations may contain a single, or multiple rules.
curator note: The clause ‘permissions, obligations, restrictions, or protections’ will be replaced with more general superclass, likely from d-acts, when that infrastructure becomes available. IOU Code.

human subject research regulatory document
type: Class
subclass of: regulatory document
example of usage: ‘HIPAA documents,’ ‘The Common Rule,’ an ‘Informed Consent Regulatory Document.’
definition: A regulatory document designed to prescribe research involving human subjects.
definition editor: Cooper Stansbury

informed consent regulatory document
type: Class
subclass of: regulatory document
definition: A regulatory document designed to prescribe an informed consent process or inputs in an informed consent process.
definition editor: Cooper Stansbury
expand assertion to: ‘Informed Consent Waivers,’ ‘Informed Consent Exemptions.’

informed consent rule
type: Class
subclass of: rule
example of usage: Do action (x).
definition: A rule in an informed consent regulatory document that prescribes either an informed consent process or deontic roles inhering in agents that participate in an informed consent process.
definition editor: Cooper Stansbury

conditional informed consent rule
type: Class
subclass of: rule
definition: A rule in an informed consent regulatory document that prescribes an informed consent process and has part trigger condition description.
definition editor: Cooper Stansbury
curator note: Those conditions that have important implications are enumerated in a specification of condition.
elucidation: The logical form of a conditional rule is as follows: if condition (y) obtains, then perform action (x).

broad consent rule
type: Class
subclass of: rule
definition: A rule in an informed consent regulatory document that prescribes deontic roles that may be realized in an unspecified range of activities, or which is subject to few restrictions.
definition editor: Cooper Stansbury

disclosure directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes information that must be revealed and prescribes to whom that information must be revealed.
definition editor: Cooper Stansbury

deontic power role directive
type: Class
subclass of: directive information entity
example of usage: A description of who can consent (but not the conditions required to be realizable).
definition: A directive information entity that prescribes a deontic power role or the process that realizes it.
definition editor: Cooper Stansbury

obsolete confidentiality directive
type: Class
subclass of: Obsolete Class
definition: A directive information entity that prescribes the limits of disclosure regarding an agent’s identity.
definition editor: Cooper Stansbury
curator note: May need ‘Conditional Confidentiality Directive' in the future.
deprecated: true

user input directive
type: Class
subclass of: directive information entity
example of usage: A ‘signature section,’ an ‘I understand’ clause, or a ‘checkbox.’
definition: A directive information entity that, when signed, stamped, or initialed realizes a deontic role as described by the document specifications, or specifications in another related document.
definition editor: Cooper Stansbury

consequent directive
type: Class
subclass of: directive information entity
definition: A directive information entity that enumerates the results if a trigger condition describing failure to comply with a rule is met.
definition editor: Cooper Stansbury, J. Neil Otte, Jonathan Vajda

permission directive
type: Class
subclass of: directive information entity
definition: A 'directive information entity' that prescribes an allowable action, where that action is otherwise impermissible.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) There is some ambiguity regarding process repition. This distinction may point to the central question of whether or not we permit 'universals' or . Take the following example: In the case of 'permission to destroy excess tissue' the instance of a 'process of destruction' is permitted only once. However, in the case of 'pemission to share data' this process may be performed multiple times.

obsolete conditional permission directive
type: Class
subclass of: Obsolete Class
definition: A conditional specification that prescirbes a permission, should some trigger condition obtain.
definition editor: Cooper Stansbury
elucidation: Permission to do (x), if condition (y).
deprecated: true

restriction directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes actions that are impermissible.
definition editor: Cooper Stansbury
elucidation: When particpating in an informed consent process (a), do not do action (y).

conditional restriction directive
type: Class
subclass of: conditional specification
definition: A conditional specification that prescirbes an impermissibility, should some trigger condition obtain.
definition editor: Cooper Stansbury and J. Neil Otte
elucidation: When particpating in an informed consent process (a), if conditon (x) do not do action (y).

obligation directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes an obligation that is realized a deontic role that is the output of a document act.
definition editor: Cooper Stansbury

conditional obligation directive
type: Class
subclass of: conditional specification
definition: A conditional specification that prescirbes an obligation, should some trigger condition obtain.
definition editor: Cooper Stansbury and J. Neil Otte

liability directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the agent that is liable if a trigger condition is met.
definition editor: Cooper Stansbury

description of medical procedure
type: Class
subclass of: descriptive information content entity
example of usage: The section of an informed consent document that describes a clinical procedure that the agent is consenting to.
definition: A descriptive information content entity that describes a medical procedure.
definition editor: Cooper Stansbury

trigger condition directive
type: Class
subclass of: directive information entity
definition: A directive information entity that describes some state of affairs such that, if that state of affairs holds, some other prescription follows.
definition editor: Cooper Stansbury
curator note: An antecedent.

description of voluntary participation
type: Class
subclass of: descriptive information content entity
definition editor: A descriptive information content entity that reports that participation in the procedures described elsewhere in the document are voluntary.
definition editor: Cooper Stansbury

witness role
type: Class
subclass of: role
definition: A role inhering in an agent as a result of that agent having observed some process.
definition editor: J. Neil Otte and Cooper Stansbury
elucidation: Typically, someone who bears a witness role has observed some history, such that one may attest to what has occurred.

withdrawal from participation directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes some process for withdraw from another planned process.
definition editor: Cooper Stansbury and J. Neil Otte

legal age
type: Class
subclass of: information content entity
definition: A temporal region identifier that designates the temporal region during which a living person is alive, and where the temporal region is such that the living person is qualified to exercise a deontic power within a legal jurisdiction.
definition editor: J. Neil Otte

act of approving
type: Class
subclass of: social act
definition: A social act in which formal or official endorsement of some entity is communicated.
definition editor: J. Neil Otte and Cooper Stansbury
comment: This 'act of approving' is distinct from the mental act of approving.

consent language directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the language that must be used in an informed consent process.
definition editor: Cooper Stansbury and J. Neil Otte

description of alternative
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes some process that may be elected.
definition editor: J. Neil Otte, Cooper Stansbury, Jonathan Vajda

description of coercion
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes expressions or implications of threat that may compel an agent to act out of fear against the agent's will.
definition editor: Cooper Stansbury and J. Neil Otte
curator note: It may be necessary to define processes of coercion in addition to descriptions of the process.
elucidation: An international review board (IRB) may require a research proposal to identify ways in which a participant may be under undue influence. For example, a prisoner may feel compelled, given their vulnerability, to provide more information or cooperation in a study than they would normally consent to, because of the benefits they might receive.

obsolete information about participant
type: Class
subclass of: Obsolete Class
curator note: "§46.102(f) Human subject means a living individual about whom an investigator (whether professional or student) conducting research obtains (1) Data through intervention or interaction with the individual, or 2) Identifiable private information. Intervention includes both physical procedures by which data are gathered (for example, venipuncture) and manipulations of the subject or the subject's environment that are performed for research purposes. Interaction includes communication or interpersonal contact between investigator and subject. Private information includes information about behavior that occurs in a context in which an individual can reasonably expect that no observation or recording is taking place, and information which has been provided for specific purposes by an individual and which the individual can reasonably expect will not be made public (for example, a medical record). Private information must be individually identifiable (i.e., the identity of the subject is or may readily be ascertained by the investigator or associated with the information) in order for obtaining the information to constitute research involving human subjects."
deprecated: true

cognitive impairment
type: Class
subclass of: disposition
definition: A disposition to abnormality realized in cognitive processes that are qualitatively below those of individuals belonging to some type, to which the bearer of the disposition also belongs.
definition editor: J. Neil Otte
definition source: HP_0100543
curator note: Adapted from http://purl.obolibrary.org/obo/HP_0100543
date: Imported and adapted 8.22.2018

economic vulnerability
type: Class
subclass of: vulnerability
definition: A vulnerability due to exposure to a depressed or impoverished economic environment.
definition editor: Cooper Stansbury, Jonathan Vajda

educational vulnerability
type: Class
subclass of: vulnerability
definition: A vulnerability due to exposure to a harsh learning environment.
definition editor: Cooper Stansbury, Jonathan Vajda

act of archiving informed consent
type: Class
subclass of: planned process
definition: A planned process of storing the document output of an 'act of consent' for future use.
definition editor: Cooper Stansbury and J. Neil Otte

contact method description
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes a method of some act of communicating.
definition editor: Cooper Stansbury, Jonathan Vajda

vulnerable population directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes some process in which vulnerable individuals participate.
definition editor: Cooper Stansbury and J. Neil Otte

confidentiality directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the nondisclosure of information.
definition editor: Cooper Stansbury and J. Neil Otte

act of communicating
type: Class
subclass of: social act
definition: A planned process in which some entity provides information to another entity.
definition editor: Cooper Stansbury and J. Neil Otte
definition source: adapted from "communicate." Merriam-Webster.com. 2011. https://www.merriam-webster.com (30 August 2018).
curator note: See ICO: 'act of informing.' This class is perhaps not needed.
comment: A note: 'entity' rather than 'agent' is used in this definition in order to allow that software can communicate with other software. However, it should be noted that this definition of communication excludes broader meanings, such as unintentional sharing of information.

obsolete benefit
type: Class
subclass of: Obsolete Class
deprecated: true

obsolete risk
type: Class
subclass of: Obsolete Class
deprecated: true

description of expected study participation duration
type: Class
subclass of: descriptive information content entity
definition editor: A descriptive information content entity that describes the expected duration of participation of some agent in an investigation.
definition editor: Cooper Stansbury

research method directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes some research process.
definition editor: Cooper Stansbury and J. Neil Otte

description of conditional compensation
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes the conditions under which compensation is due to some agent.
definition editor: J. Neil Otte and Cooper Stansbury

description of discomfort
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes an emotional state of mental or physical uneasiness.
definition editor: Cooper Stansbury and J. Neil Otte

description of collected biospecimens
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes biospecimens that have been collected.
definition editor: J. Neil Otte, Cooper Stansbury, Jonathan Vajda

description of collected information
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes information that may be collected or the processes of information collection.
definition editor: Cooper Stansbury

description of future biospecimen use
type: Class
subclass of: description of future use
definition: A descriptive information content entity that describes how biospecimens will be used.
definition editor: Cooper Stansbury, Jonathan Vajda

description of procedure for obtaining further information
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes some procedure for obtaining information only available at some future time.
definition editor: Cooper Stansbury and J. Neil Otte

contact method directive
type: Class
subclass of: directive information entity
example of usage: For instance, a patient may assert a preferred mode of communication for contact in the future. This may be given in terms of permitting a communication via email, phone call, etc. and it may mention the address or number to be used.
definition: A directive information entity that prescribes methods for contacting an agent.
definition editor: J. Neil Otte, Cooper Stansbury, Jonathan Vajda

description of breach of confidentiality
type: Class
subclass of: descriptive information content entity
definition editor: J. Neil Otte and Cooper Stansbury
curator note: A descriptive information content entity that describes some conditions that constitute unauthorized disclosure of information.
curator note: It is possible that classes like this will be useful in conjuction with descriptions of risk as in: 'description of risk of breach of confidentiality.'

description of legal responsibility
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes legal responsibility that an entity has due to some risk.
definition editor: Jonathan Vajda, Cooper Stansbury, J. Neil Otte
alternative term: description of liability

description of financial risk
type: Class
subclass of: descriptive information content entity
definition: A description of risk that describes the magnitude of potential financial loss.
definition editor: Cooper Stansbury and J. Neil Otte

description of reputational risk
type: Class
subclass of: descriptive information content entity
definition: A description of risk that describes the magnitude or probability of damage to the reputation of an agent in a social context.
definition editor: Cooper Stansbury and J. Neil Otte

vulnerable individual role
type: Class
subclass of: role
example of usage: E.g., "There are several definitions available for the term 'vulnerable population', the words simply imply the disadvantaged sub-segment of the community requiring utmost care, specific ancillary considerations and augmented protections in research. The vulnerable individuals’ freedom and capability to protect one-self from intended or inherent risks is variably abbreviated, from decreased freewill to inability to make informed choices." Preethi Shivayogi (2013). Vulnerable population and methods for their safeguard. Perspectives in clinical research, 4(1), 53-7.
definition: A role that inheres in an agent or group of agents that is the output of a process during which the agent or group of agents is designated as belonging to a vulnerable group.
definition editor: J. Neil Otte and Cooper Stansbury
curator note: Note: It is possible to belong to a vulnerable population and yet not bear a disposition of vulnerability. Typically, when a person is held to be a vulnerable individual, this is a designation that applies by fiat in virtue of their membership to some legally designated group, and not based on a clear investigation of their individual case. Hence, it seems prudent here to use roles for this purpose.

regulatory oversight role
type: Class
subclass of: role
definition: A role that inheres in a regulatory body that, if realized, is realized in some act of regulatory supervision.
definition editor: Cooper Stansbury

minor role
type: Class
subclass of: role
definition: A role inhering in a Homo sapiens that, if realized, is realized within the organizational context of a legal jurisdiction, when the bearer fails to meet the legal threshold for adulthood.
definition editor: Cooper Stansbury and J. Neil Otte
curator note: It is possible to create further defined classes here, such as 'abused minor role' that is a minor that participated in a process of abuse.

pregnant woman
type: Class
subclass of: object
definition: A woman who is pregnant.
curator note: Could reuse: http://purl.obolibrary.org/obo/ontoneo/ONTONEO_00000197

prisoner role
type: Class
subclass of: role
definition: A role inhering in a Homo sapiens that is realized in a process of incarceration.
definition editor: Cooper Stansbury, Jonathan Vajda
curator note: Note from Jonathan Vajda: Depending on the level of granluarity, we could have prisoner role, incarcerated role, etc. and these roles would differentiated by what kind of stasis of incarceration necessary.

waiver document
type: Class
subclass of: document
definition: A document designed for the purpose of assisting in an act of waiving, and which contains both some description of waiver and some waiver directive.
definition editor: Cooper Stansbury and J. Neil Otte

description of incentive
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes an entity that provides positive motivation for some material entity.
definition editor: Cooper Stansbury and J. Neil Otte
curator note: From NCI Thesaurus OBO Edition: Incentive: A benefit, consideration, or positive motivational influence, financial or otherwise, given to induce a specific action. [def-source: NCI]

study protocol
type: Class
subclass of: protocol
definition: A protocol that is formal plan of a research activity, including the objective, rationale, design, materials, and methods for the conduct of the activity.
definition editor: Cooper Stansbury and J. Neil Otte
curator note: This term was adapted from: http://purl.obolibrary.org/obo/NCIT_C70817

data sharing directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the information that is permitted to be shared or the processes for sharing that information.
definition editor: Cooper Stansbury

permission transfer directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the process of transferring a permission role from one bearer to another.
editor note: Note: Strictly speaking, of course, roles are not transferred; rather, the transfer of a permission involves the role of one agent ceasing to exist, and the role of a second agent coming into existence.
definition editor: Cooper Stansbury and J. Neil Otte

future use directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the processes that involve some entity as a participant.
definition editor: Cooper Stansbury and J. Neil Otte

description of consequences of voluntarily withdrawal
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes the negative impact or harm that may befall an agent who withdraws from an investigation.
definition editor: Cooper Stansbury, Jonathan Vajda

stasis of regulation
type: Class
subclass of: stasis of generically dependent continuant
definition: A stasis of generically dependent continuant that has participant some information content entity and during which that information content entity is recognized within that jurisdiction and directs governance within that jurisdiction.
definition editor: Cooper Stansbury

stasis of law
type: Class
subclass of: stasis of regulation
definition: A stasis of regulation that has participant some information content entity and during which that information content entity is recognized as a law within the jurisdiction in which the stasis of regulation is occurring.
definition editor: Cooper Stansbury, J. Neil Otte
curator note: The ‘stasis of law’ designates the spatial and temporal conditions that need to be met in order for a regulatory document to be a ‘law’ or a ‘policy.’ This is necessary because laws, or other regulations are overturned, made obsolete, ect..., but material entities concretizing them persist.
curator note: There are many definitions and conceptions of law, which can be elaborated in further work. There is a concern not to define law in such a way that we narrow the scope beyond an international context.

protection directive
type: Class
subclass of: trigger condition directive
definition: A trigger condition directive that prescribes conditions for which a individual bears a vulnerability role or disposition of vulnerability, or a population of such individuals.
definition editor: J. Neil Otte, Jonathan Vajda, Cooper Stansbury
curator note: See http://purl.unep.org/sdg/SDGIO_00000024 (Vulnerability): A disposition of an entity to undergo undesirable change in response to some exposure.

act of regulatory supervision
type: Class
subclass of: planned process
definition: A planned process in which a regulatory body directs or monitors another planned process.
definition editor: Cooper Stansbury and J. Neil Otte

act of abuse
type: Class
subclass of: process
definition: A process of mistreating an entity such that the mistreated entity is harmed.
definition editor: Cooper Stansbury, J. Neil Otte, and Jonathan Vajda
definition source: adapted from "abuse." Merriam-Webster.com. 2011. https://www.merriam-webster.com (30 August 2018).

act of disclosure
type: Class
subclass of: act of communicating
definition: An act of communicating in which information is shared, overriding or violating a judgment that the information should not be shared.
definition editor: J. Neil Otte and Cooper Stansbury
curator note: It is possible that there are meaningful defined classes here like: 'act of authorized disclosure' and 'act of unauthorized disclosure.'

description of research procedure
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes a research procedure.
definition editor: Cooper Stansbury

description of future data use
type: Class
subclass of: description of future use
definition: A descriptive information content entity that describes how data will be used.
definition editor: Cooper Stansbury, Jonathan Vajda

description of future use
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes future use of material or information.
definition editor: Cooper Stansbury

act of waiving
type: Class
subclass of: social act
definition: A social act of relinquishing a right, claim, or privilege.
definition editor: Cooper Stansbury, Jonathan Vajda
definition source: "waiver." Merriam-Webster.com. 2011. https://www.merriam-webster.com (30 August 2018).

waiver directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes an act of waiving.
definition editor: Cooper Stansbury

description of waiver
type: Class
subclass of: descriptive information content entity
definition: A descriptive information content entity that describes a directive information content entity that can be ignored.
definition editor: Cooper Stansbury
curator note: adapted from: http://purl.obolibrary.org/obo/NCIT_C113777

abused person role
type: Class
subclass of: role
definition: A role inhering in a Homo sapiens that, if realized, is realized in being a passive participant in some act of abuse process.
definition editor: Jonathan Vajda
elucidation: A passive participant in such a process would mean that the act of abuse has this entity as its target; i.e., the bearer of this role is entity that is mistreated.

directive about research of biospecimens
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes some investigation of biospecimens.
definition editor: J. Neil Otte

act of genetic testing
type: Class
subclass of: planned process
definition: A planned process that involves the investigation of some sequence of DNA.
definition editor: J. Neil Otte

genetic testing directive
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: prescribes
  some values from: act of genetic testing
definition: A directive information entity that prescribes some act of genetic testing.
definition editor: J. Neil Otte

excess material role
type: Class
subclass of: role
definition: A role inhering in some material entity that is realized in an act of artifact modification where the material entity is separated from another portion of material.
definition editor: J. Neil Otte, Elizabeth Umberfield

investigation objective specification
type: Class
subclass of: objective specification
definition: An objective specification whose intended process endpoint is an investigation.
definition editor: Cooper Stansbury

secondary use objective specification
type: Class
subclass of: objective specification
definition: An objective specification that prescribes the participation of an information content entity or a material entity in a process prescirbed by a future invesitgation objective specification.
editor note: "The use in research of information or human biological materials originally collected for a purpose other than the current research purpose."
definition editor: Cooper Stansbury
definition source: Adapted from: “Secondary Use of Data - FAQs - Research Ethics Office - Sunnybrook Research Institute.” [Online]. Available: https://sunnybrook.ca/research/content/?page=sri-crs-reo-faq-secondaryusedata. [Accessed: 07-Nov-2018].

role directive
type: Class
equivalent class: Restriction
  on property: prescribes
  some values from: role
subclass of: directive information entity
definition: A directive information entity that prescribes some role.
definition editor: Cooper Stansbury

patient role directive
type: Class
subclass of: role directive
definition: A role directive that prescribes the bearer of a patient role in a process.
definition editor: Cooper Stansbury

regulatory oversight role directive
type: Class
subclass of: role directive
definition: A role directive that prescirbes the bearer of a regulatory oversight role in a process.
definition editor: Cooper Stansbury

investigator role directive
type: Class
subclass of: role directive
definition: A role directive that prescribes the bearer of an investigator role in a process.
definition editor: Cooper Stansbury

legally authorized representative role directive
type: Class
subclass of: role directive
definition: A role directive that prescribes the bearer of a legally authorized representative role in process.
definition editor: Cooper Stansbury

consent directive
type: Class
subclass of: permission directive
definition: A 'permission directive' that prescribes some action that is made allowable by a consenting entity.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) We indend instances of 'consent directive' to be stated positively with repect to the act of permitting. A 'consent directive' may only allow for different actions, not forbid them. However, since 'consent directives' may simultaneously create new duties or obligations, we define 'designated consent condition' in order to help manage these nested deontic statements. (2) Another, less formal definition: 'A statement that guides action that is made allowable by a consenting entity, where that action is otherwise impermissible.' (3) The definition from HL7: "The legal record of a healthcare consumer's agreement with a party responsible for enforcing the consumer’s choices, which permits or denies identified actors or roles to perform actions affecting the consumer within a given context for specific purposes and periods of time." https://www.hl7.org/fhir/consent.html

assent directive
type: Class
subclass of: permission directive
definition: A 'permission directive' that prescribes some action that is made allowable by an assenting entity.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) We indend instances of 'assent directive' to be stated positively with repect to the act of permitting. A 'assent directive' may only allow for different actions, not forbid them. However, since 'assent directives' may simultaneously create new duties or obligations, we define 'designated consent condition' in order to help manage these nested deontic statements.

designated action
type: Class
subclass of: Designative Information Content Entity
definition: A 'Directive Information Content Entity' that designates a process as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) It is critical that these classes not be mistaken for processes themselves. If you intend to build logical axioms within the BFO framework it will be necessary to create realtions between instances of 'designated actions' and 'processes.' We leave this mapping undone in order to accomodate various non-BFO process value sets. (2) We believe it is important to separate 'processes' from their inputs, outputs, or participants in action designatation. For example: instead of a 'designated process of blood extraction' we would advocate for creation of a designated action such as 'designated process of extraction' so that this class may also be used with different objects, like teeth. This is of course, application dependent. This is only a guide. (3) It is our intent that all instances of 'designated actions' that are related to instances of 'permission directive' be processes or events in which deontic roles of some kind may be realized. Stated another way, a 'designated action' should be an action that is not allowable unless a process makes it so: for example, a 'process of informed consent' with a subprocess 'act of permitting.'

designated actor
type: Class
subclass of: Designative Information Content Entity
definition: A 'Designative Information Content Entity' that designates an entity which can bear deontic roles.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) In the general sense, 'designated actors' should designate entities which perform, or participate in an action. While the notion of 'agency' is important for some entiites, at some times, involved in processes of informed consent, we do not define actors in terms of their agency. (2) Within the greater BFO, D-acts, and ICO frameworks, we believe that a 'designated actor' has some capability to bear deontic roles.

designated object
type: Class
subclass of: Designative Information Content Entity
definition: A 'Designative Information Content Entity' that designates the object of a 'designated action'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) In English, this is typically the 'object' of the clause where the 'designated action' is the verb. We may also refer to this as the 'designated target' of the action. However, we choose 'object' to more clearly separate the objects of the actions from the ends.

permission condition directive
type: Class
subclass of: directive information entity
definition: A 'directive information entity' that directs the conditions of 'allowability' for a 'consent directive'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) A 'designated consent condition' defines or delimits the scope, boundaries, requirements, attributes, antecendents, or limitations the 'designated action' which may be permitted. As such, it is specifically tied to permissions to avoid complex nested impertives as much as possible. The central question to ask is: 'what does permission to undertake this action depend on?' (2) Our intent is to focus on conditionals related to 'obtaining permission' rather than all possible conditionals.

permission purpose directive
type: Class
subclass of: permission restriction directive
definition: A 'permission condition directive' that directs the purpose for a 'permission directive'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: purpose: https://www.merriam-webster.com/dictionary/purpose (1) to propose as an aim to oneself 'means to an end': https://www.merriam-webster.com/dictionary/a%20means%20to%20an%20end (1) something done only to produce a desired result
comment: (1) We refer to 'designated purpose' as the specific end, outcome, or target of some designated action. We note that this necessarily involves the notion of 'intentionality.' Because this may be regarded as problematic in a realist ontology, please tread with caution.

designated process of access
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of access as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: access: https://www.merriam-webster.com/dictionary/access (1) to get at (2) to gain access to (3) to be able to use, enter, or get near (something) (4) to open or load (a computer file, an Internet site, etc.) (5) permission, liberty, or ability to enter, approach, or pass to and from a place or to approach or communicate with a person or thing (6) freedom or ability to obtain or make use of something
comment: (1) Access is a complex issue. We intend this class to cover instances whereby an entity may gain the ability to act upon an object whereby they previously were not able to do so. Examples may include: accessing PHI in a database, linking sensitive information to a biospecimen repository, ect.

designated process of analysis
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of analysis as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: analyze: https://www.merriam-webster.com/dictionary/collect (1) to study or determine the nature and relationship of the parts of (something) by analysis

designated procedure
type: Class
subclass of: designated action
definition: A 'designated action' that designates a procedure as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) It is our intent for this term to serve as a blanket class for all types of clinical procedures. If an application demands specificity of procedures, for example administration of anesthetic, this would be a good parent class for such a list or subtree of procedures.

designated process of collection
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of collection as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: collect: https://www.merriam-webster.com/dictionary/collect (1) to bring together into one body or place (2) to gather or exact from a number of persons or sources (3) to gain or regain control of
comment: (1) It is our intent that this class includes instances of collection of material and of information. We note that the actual processes of 'retention' (read: 'storage') and 'collection' may be ambigously differentiated. (2) We intend this class to primarily cover de novo collection.

designated process of destruction
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of destruction as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: destroy: https://www.merriam-webster.com/dictionary/destroy (1) to put out of existence

designated process of disclosure
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of disclosure as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: disclose: https://www.merriam-webster.com/dictionary/disclose (1) to make known or public (2) to expose to view

designated process of duplication
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of duplication as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: duplicate: https://www.merriam-webster.com/dictionary/duplicate (1) to make double or twofold (2) to make a copy of
comment: (1) We intend this designation to include processes of 'copying.'

designated process of unspecified use
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process unspecified use as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: 'use' (1) to put into action or service (2) to carry out a purpose or action by means of
Merriam-Webster Definition: unspecified: https://www.merriam-webster.com/dictionary/unspecified (1) not named or stated explicitly
comment: (1) this is a 'catch-all' bucket to define those 'designated action'(s) that are not explicit. (2) does this require a 'designated purpose' specification? (this is boarderline rule enforcement that may be appropriate at implmentation, but not here).

designated process of modification
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of modifcation as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: modify: https://www.merriam-webster.com/dictionary/modify (1) to make basic or fundamental changes in often to give a new orientation to or to serve a new end

designated process of contact
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of contact permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This includes instances of recontact.

designated process of retention
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of retention as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: retain: https://www.merriam-webster.com/dictionary/retain (1) to keep in possession or use (2) to keep in one's pay or service (3) to hold secure or intact
comment: (1) these may often be accompanied by a 'designated temporal conditon'. (2) if these are do not follow (1), they may be more approproately labeled 'stases' instead of 'process.' (3) we believe this includes storage, should it be re-labeled 'storage?'

designated process of sharing
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of sharing permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: share: https://www.merriam-webster.com/dictionary/share (1) to partake of, use, experience, occupy, or enjoy with others
comment: (1) this, along with 'transfer' need to be properly fleshed out. Perhaps the difference is 'ownership.' When you share, you may retain the right to ownership, but when you transfer, you yield this right.... (2) does sharing including publishing PHI? De-anonymizing? (3) what about 'release?'

designated process of study
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of study as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) require link to a 'Descriptive Information Content Entity' like: 'STUDY DETAILS?' (2) STUDY PRTICIPATION

designated process of surveillance
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of surveillance.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: surveil: https://www.merriam-webster.com/dictionary/surveil (1) to subject to surveillance
comment: (1) our usage more closely resembles the use in NCIT.

designated process of transfer
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of transferral of ownership permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: transfer: https://www.merriam-webster.com/dictionary/transfer (1) to convey from one person, place, or situation to another (2) to make over the possession or control of (3) to move to a different place, region, or situation
comment: (1) is collection a tranfer of ownership?

designated research purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a research process as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This is a pointer to ADAM Matrix. (2) covers future

designated biomedical research purpose
type: Class
subclass of: designated research purpose
definition: A 'designated research purpose' that designates a biomedical research process as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated genetic research purpose
type: Class
subclass of: designated biomedical research purpose
definition: A 'designated research purpose' that designates a process of genetic research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated administrative purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a process relating to the management of an organization as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
Merriam-Webster Definition: administrative: https://www.merriam-webster.com/dictionary/administrative (1) relating to the management of a company, school, or other organization administrative tasks/duties/responsibilities
comment: (1) actions undertaken support system processing

designated diagnostic purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a process of diagnosis as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) related to, but perhaps not limited to the following classes in OGMS: (2) diagnosis (http://purl.obolibrary.org/obo/OGMS_0000073) (3) diagnostic process (http://purl.obolibrary.org/obo/OGMS_0000104)

designated educational purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates an educational process as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated evaluation purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a process of evaluation as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated commercial purpose
type: Class
subclass of: permission purpose directive
disjoint with: designated non-commercial purpose
definition: A 'permission purpose directive' that designates a for-profit activity as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated healthcare operation purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a healthcare operation process as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) quality and safety purposes

designated non-commercial purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a nonprofit activity as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated therapeutic purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a process related to healing a disease as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated unspecified purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates an unspecified process as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

permission precondition
type: Class
subclass of: permission condition directive
definition: A 'permission condition directive' which states a preceding event or condition.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) 'antecedent' (2) may need to specific 'post-cendents' also.

permission restriction directive
type: Class
subclass of: permission condition directive
definition: A 'permission requirement directive' that directs a 'permissable' limit of a 'consent directive'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) Restrictions narrow the scope of the 'designated action'. They operate on the 'allowability' conditionally. (2) "Allowable IF NOT <'designated restriction'>" (3) Alternatively: 'A LIMIT ON THE SCOPE OF THE ACTION' (4) up until the point of. (5) RESTRAINNING

permitted actor restriction directive
type: Class
subclass of: permission restriction directive
definition: A 'permission restriction directive' that designates an actor.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

jurisdiction restriction directive
type: Class
subclass of: permission restriction directive
definition: A 'permission restriction directive' that defines the spatial boundaries of a 'designated action'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) 'Jurisdiction' is often defined in two senses: (1) a geopolitical context (BFO site), or (2) a power. We define jurisdiction as a BFO site, identifiable through shared context of other entities, like a country or state border. The term ‘deontic power role’ reflects the sense of ‘power’ sometimes used to describe jurisdiction.

temporal restriction directive
type: Class
subclass of: permission restriction directive
definition: A 'permission restriction directive' that designates the temporal boundaries of the 'designated action'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

permission requirement directive
type: Class
subclass of: permission condition directive
definition: A 'permission condition directive' that states an additional requirement.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) NOTE: this is an imperitive - it is not strictly part of a permission but is inextricably tied to it. (2) these are obligations that are dependent on a permission (conditioned on a permission) (3) MUST BE FULLFILLED (4) allowability is necessarily dependent on this being fulfilled

permission sub-directive
type: Class
subclass of: permission condition directive
definition: A 'permission condition directive' that directs another 'consent directive' as a requirement of a primary 'consent directive'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This permission is dependent on another permission (2) a good example of this are data use agreements that must be signed in addition to an informed consent form to allow for PHI data sharingor disclosure.

possibility of withdraw directive
type: Class
subclass of: permission requirement directive
definition: A 'permission requirement directive' that directs the possibility of withdraw.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) typically from 'study participation.'

designated data
type: Class
subclass of: designated object
definition: A 'designated object' that designates data or information.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This is really saying that this is information that designates other information content entities (in BFO-speak).
comment: See: http://purl.obolibrary.org/obo/IAO_0000030

designated waveform data
type: Class
subclass of: designated data
definition: A 'designated data' that designates waveform data.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated genetic data
type: Class
subclass of: designated data
definition: A 'designated data' that designates genetic data.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated health information
type: Class
subclass of: designated data
definition: A 'designated data' that designates data about health.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated identifiable information
type: Class
subclass of: designated data
definition: A 'designated data' that designates information that may identify an entity.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) How broad is this notion of 'entity' here? (2) NOTE: this not nested under 'designated health information' because information does not need to be health information to be identifiable. (3) HIPAA Identifiers (4) Includes fully and partially identifiable information.

designated image data
type: Class
subclass of: designated data
definition: A 'designated data' that designates image data.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated video data
type: Class
subclass of: designated data
definition: A 'designated data' that designates video data.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated human object
type: Class
subclass of: designated object
definition: A 'designated object' that designates a person, or part of a person, as the target of a 'designated action.'
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) for when the permitting party is the target of the 'designated action' (2) you may operate on my leg (3) this includes 'study participant' as the target of an action. May also include patient.

designated biospecimen
type: Class
subclass of: designated object
definition: A 'designated object' that designates a biospecimen.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) this should be mapped to robust specimen heirarchies such as: http://purl.obolibrary.org/obo/OBI_0100051
comment: A 'designated object' that designates a specimen.

designated residual tissue
type: Class
subclass of: designated biospecimen
definition: A 'designated biospecimen' that designates a portion of excess tissue.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated unspecified object
type: Class
subclass of: designated object
definition: A 'designated object' that designates an unspecified object.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated permitted actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an actor that may bear a permission role that may be realized in the process prescribed by the process designated by the 'designated action.'
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This designation points towards deontic roles and social processes. (2) This can be read as: 'the actor TO BE permitted.' It is not intended to create a permission the same way the creation of an ICO:permission role might. However, we leave this somewhat open to implementation interpretation.

designated affiliated actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an actor with an affilitation to an organization or institution.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) actor with a designated affiliation to an organization/institution. (2) intended for single individuals rather than groups, but as a way to relate groups and actors performing on the group's behalf.

designated corporation
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates a corporation.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated institution
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an institution.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) established organization (2) an entity that has independent financial, legal, interests or identity.

designated principal investigator
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates a principal investigator.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated information system actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an information system.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated organization
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) where does surgical team fit in? (2) how do we define aggregates of people? (3) possible mapping to (OBI: organization) http://purl.obolibrary.org/obo/OBI_0000245

designated educational organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that desginates an educational organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated biobank organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a biobank organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated for-profit organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a for-profit organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated funding organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a funding organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated government organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a government organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated healthcare organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a healthcare organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated regulatory organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a regulatory organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated media organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a media organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated non-profit organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designated a non-profit organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated public health organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates a public health organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) groups that may have the ability to override specific norms?

designated research organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that desginates a research organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated team
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates a team.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) this is useful in defining things like 'research team' or 'clinical team.'

designated unspecified organization
type: Class
subclass of: designated organization
definition: A 'designated organization' that designates an unspecified organization.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated permitting actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an actor that may permit some 'designated action'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This designation points towards deontic roles and social processes.

designated assenting actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates the entity that is permitting some 'designated action'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) not to be confused with 'designated consenting actor'. (2) this definition is currently the same as the definition for 'designated consenting actor'. We need to remedy this without appealing to U.S. specific legislative definitions.

designated consenting actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates the actor that is permitting some 'designated action'.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) Not to be confused with 'designed assenting actor' (2) By 'permitting' we mean 'making the otherwise impermissable action permissable' or 'making allowable.'

designated authorized representative
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an authorized representative.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) legally authorized representative (LAR): has the ability to act on behalf of another person (under the rule of law). (2) not sure if this should be under the 'designated permitting actor'. (3) surrogates are included here.

designated unspecified actor
type: Class
subclass of: designated actor
definition: A 'designated actor' that designates an unspecified actor.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated health services research purpose
type: Class
subclass of: designated research purpose
definition: A 'designated research purpose' that designates a health services research process as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated methods development purpose
type: Class
subclass of: designated research purpose
definition: A 'designated research purpose' that designates a process of methods development research as it's end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated control material research purpose
type: Class
subclass of: designated research purpose
definition: A 'designated research purpose' that designates reference control material research processes as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated populations research purpose
type: Class
subclass of: designated research purpose
definition: A 'designated research purpose' that designates a process of population research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated ancestry research purpose
type: Class
subclass of: designated research purpose
definition: A 'designated research purpose' that designates ancestry research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated drug research purpose
type: Class
subclass of: designated biomedical research purpose
definition: A 'designated biomedical research purpose' that designates a process of drug research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated disease research purpose
type: Class
subclass of: designated biomedical research purpose
definition: A 'designated biomedical research purpose' that designates a process of disease specific research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated age category research purpose
type: Class
subclass of: designated biomedical research purpose
definition: A 'designated biomedical research purpose' that designates a process of age category research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated gender research purpose
type: Class
subclass of: designated biomedical research purpose
definition: A 'designated biomedical research purpose' that designates a process of gender category research as its end.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated process of administration
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process of administration as permissable.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This class is intended for actions such as 'drug administration.'

designated pharmaceutical object
type: Class
subclass of: designated object
definition: A 'designated object' that designates a pharmaceutical object
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated recruitment purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a process of recruitment.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris

designated return of results purpose
type: Class
subclass of: permission purpose directive
definition: A 'permission purpose directive' that designates a return of results.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This is intended to cover communication from a healthcare organization to a patient or study participant regarding their health.

sensitive information protection directive
type: Class
subclass of: permission requirement directive
definition: A 'permission requirement directive' that directs sensitive infotmation proctection.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) This definition is left purposefully broad to cover a wide range of use cases including processes or methods.

designated process of treatment
type: Class
subclass of: designated action
definition: A 'designated action' that designates a process fo treament.
definition editor: Cooper Stansbury, Elizabeth Umberfield, Kathleen Ford, Marcy Harris
comment: (1) consent to treat

act of data use
type: Class
subclass of: planned process
definition: A planned process in which data is put to some use by an entity.
definition editor: Cooper Stansbury, Elizabeth Umberfield

patient
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: bearer of
    some values from: patient role
subclass of: Homo sapiens
definition: An agent who bears a patient role.
definition editor: J. Neil Otte

act of selling
type: Class
subclass of: planned process
definition: A planned process in which goods or services are exachanged for money.
definition editor: Elizabeth Umberfield, Cooper Stansbury
definition source: https://www.merriam-webster.com/dictionary/sell
curator note: From definition of 'sell' from Merriam-Webster: To give up (property) to another for something of value (such as money).'

covered entity role
type: Class
subclass of: role
definition: A role based on the Health Insurance Portability and Accountability Act that inheres in individuals, organizations, and agencies that are also health care providers, health plans, or health care clearinghouse.
definition editor: Elizabeth Umberfield, Cooper Stansbury
curator note: Adapted from HIPAA.

data recipient role
type: Class
subclass of: role
definition: A role which is realized in processes of data disclosure.
definition editor: Elizabeth Umberfield, Cooper Stansbury
curator note: Definition from adapted from GDPR Article 4(9): A natural or legal person, public authority, agency or another body, to which the data are disclosed.

limited data set
type: Class
subclass of: protected health information entity
definition: Protected health information that excludes HIPAA-specified identifiers of the individual or of relatives, employers, or household members of the individual.
definition editor: Elizabeth Umberfield, Cooper Stansbury
curator note: Definition adapted from HIPAA.

owner role directive
type: Class
subclass of: directive information entity
definition: A directive information entity that prescribes the owner role.
definition editor: Elizabeth Umberfield, Cooper Stansbury

ownership statis
type: Class
subclass of: stasis
definition: A stasis in which an entity bears an ownership role.
definition editor: Elizabeth Umberfield, Cooper Stansbury

residual clinical biospecimen
type: Class
subclass of: material entity
definition: A material entity, collected during some health care process, that bears both a specimen role and an excess material role following some act of artifact modification.
definition editor: Elizabeth Umberfield, Cooper Stansbury

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

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

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

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

Eukaryota
type: Class
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

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

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

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

Metazoa
type: Class
subclass of: Opisthokonta
editor preferred label: Metazoa
alternative term: metazoans
alternative term: multicellular animals
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

Bilateria
type: Class
subclass of: Metazoa
editor preferred label: Bilateria
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

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

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

Homo sapiens
type: Class
subclass of: agent
subclass of: Euarchontoglires
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
imported from: ncbitaxon.owl
imported from: Ontology for Biomedical Investigations

Institutional Review Board Approval
type: Class
subclass of: document
definition: A document containing the determination of the Institutional Review Board (IRB) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the IRB and other institutional and federal requirements. The regulations require that an IRB conduct continuing review of research at intervals appropriate to the degree of risk, but not less than once a year.
imported from: ncit.owl
code: C70800
Semantic_Type: Regulation or Law
Preferred_Name: Institutional Review Board Approval
UMLS_CUI: C2346499
Contributing_Source: CDISC-GLOSS
Contributing_Source: CareLex
ALT_DEFINITION: Study Site specific document containing the determination of the Institutional Review Board (IRB) or Independent Ethics Committee (IEC) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the IRB and other institutional and federal requirements. [NCI]
ALT_DEFINITION: The affirmative decision of the IRB that the clinical trial has been reviewed and may be conducted at the institution site within the constraints set forth by the IRB, the institution, good clinical practice (GCP), and the applicable regulatory requirements. [ICH E6]
Legacy Concept Name: Institutional_Review_Board_Approval
has exact synonym: IRB Approval
has exact synonym: IRB-IEC Approv
has exact synonym: IRB-IEC Approval
has exact synonym: IRB/IEC Submission Approval
has exact synonym: Institutional Review Board Approval
has exact synonym: Institutional Review Board Independent Ethics Committee Approval
has exact synonym: approval (in relation to Institutional Review Boards)
in subset: NCIT C114548
in subset: NCIT C61410
in subset: NCIT C67497

Incarceration
type: Class
subclass of: process
definition: The state of being confined to jail or prison.
imported from: ncit.owl
code: C85521
Semantic_Type: Activity
Preferred_Name: Incarceration
UMLS_CUI: C0205255
Contributing_Source: CDISC
ALT_DEFINITION: The state of being confined to jail or prison.
has exact synonym: INCARCERATION
has exact synonym: Incarceration
in subset: NCIT C102587
in subset: NCIT C61410
in subset: NCIT C66830

adverse event
type: Class
subclass of: bodily process
definition: a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
editor note: Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
editor note: YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
editor note: YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
editor note: YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
editor note: YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
editor note: YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
editor note: YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
definition editor: Yongqun He
alternative term: AE
alternative term: adverse reaction
definition source: WEB: http://en.wikipedia.org/wiki/Adverse_event
definition source: WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
imported from: oae.owl
comment: The OAE official website is: http://www.oae-ontology.org/.

blood specimen on blood spot card
type: Class
subclass of: blood specimen
definition: A blood specimen that is located on a blood spot card.
definition editor: Person: Jie Zheng, Chris Stoeckert
definition source: Penn Group
imported from: obib.owl
comment: A specimen that located in a blood spot card via blood spotting process.

biobank organization
type: Class
subclass of: organization
definition: An organization bearing legal personality that owns or adminstrates a biobank.
definition editor: Mathias Brochhausen
alternative term: biobank juristic person
imported from: obib.owl

department
type: Class
subclass of: organization
definition: An organization with a specific responsibility that is a part of a larger organization with a specific responsibility.
definition source: http://en.wikipedia.org/wiki/Department
imported from: obib.owl

medical record
type: Class
subclass of: document
definition: A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting.
definition editor: Martin Fransson
imported from: obib.owl
comment: It is a chronological written account of examination, treatment, medical history or complaints.
comment: It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: Ontology for Biomedical Investigations

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

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

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

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has specified output
      some values from: study design
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
definition editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: Ontology for Biomedical Investigations
ISA alternative term: study

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
definition editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: Ontology for Biomedical Investigations

reagent role
type: Class
subclass of: reactant role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
definition editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: Ontology for Biomedical Investigations
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

patient role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
editor preferred label: patient role
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has curation status: metadata complete
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
editor note: See also OMRSE:00000011 'patient role'
definition editor: GROUP:Role Branch
alternative term: patient
definition source: OBI, CDISC
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
imported from: Ontology for Biomedical Investigations

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

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
editor preferred label: study subject role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: ready for release
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: Ontology for Biomedical Investigations

responsible party role
type: Class
subclass of: investigation agent role
editor preferred label: responsible party role
example of usage: he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
has curation status: metadata complete
definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
definition editor: Person: Jennifer Fostel
alternative term: responsible party
definition source: OBI
imported from: Ontology for Biomedical Investigations

principal investigator role
type: Class
subclass of: responsible party role
editor preferred label: principal investigator role
has curation status: metadata incomplete
definition: a responsible party role played by a person responsible for the overall conduct of a study
definition editor: Person: Jennifer Fostel
alternative term: principal investigator
curator note: CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
imported from: Ontology for Biomedical Investigations

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: ready for release
definition: A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen.
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
definition editor: GROUP: Role Branch
definition source: OBI
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: Ontology for Biomedical Investigations

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

population
type: Class
subclass of: material entity
editor preferred label: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: pending final vetting
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
definition editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process
imported from: Ontology for Biomedical Investigations

investigation agent role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: Restriction
      on property: bearer of
      some values from: Restriction
        on property: concretizes
        some values from: Restriction
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: investigation
editor preferred label: investigation agent role
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: ready for release
definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
definition editor: GROUP: Role Branch
alternative term: investigator
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: Ontology for Biomedical Investigations
ISA alternative term: study person role
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)

organization
type: Class
subclass of: agent
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
definition: An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: Ontology for Biomedical Investigations

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

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: ready for release
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: Ontology for Biomedical Investigations
ISA alternative term: study protocol

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

material to be added role
type: Class
subclass of: role
editor preferred label: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: metadata complete
definition: A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target).
definition editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch
imported from: Ontology for Biomedical Investigations

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: data item
subclass of: Restriction
  on property: has specified output
  some values from: conclusion based on data
editor preferred label: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: ready for release
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters
imported from: Ontology for Biomedical Investigations

planning
type: Class
subclass of: process
editor preferred label: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: ready for release
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
definition editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch
imported from: Ontology for Biomedical Investigations

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

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

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

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

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

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

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

regulatory agency
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: has role
    some values from: regulator role
subclass of: organization
editor preferred label: regulatory agency
example of usage: The US Environmental Protection Agency
has curation status: ready for release
definition: A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: en.wikipedia.org/wiki/Regulator
imported from: Ontology for Biomedical Investigations

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has specified output
    some values from: measurement datum
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: ready for release
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Frank Gibson
imported from: Ontology for Biomedical Investigations

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

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
editor preferred label: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: ready for release
definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: Ontology for Biomedical Investigations

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

urine specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: urine
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: urine specimen
has curation status: metadata complete
definition: a portion of urine collected from an organism
editor note: 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
editor note: This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
editor note: are we happy calling collection of urine a material separation?
imported from: Ontology for Biomedical Investigations

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

blood specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: blood
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: blood specimen
example of usage: blood drawn from a human for glucose assay
has curation status: ready for release
definition: a material entity derived from a portion of blood collected from an organism
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: Ontology for Biomedical Investigations

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: specimen
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site
has curation status: ready for release
definition: A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed.
editor note: Definition updated following discussion on 2024-10-07 OBI dev call.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
definition editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
imported from: Ontology for Biomedical Investigations

sample from organism
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
editor preferred label: sample from organism
has curation status: example to be eventually removed
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
imported from: Ontology for Biomedical Investigations

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

whole organism preparation
type: Class
subclass of: specimen
subclass of: Restriction
  on property: derives from
  some values from: organism
editor preferred label: whole organism preparation
example of usage: putting a mouse in the blender. Not: putting a mouse on a scale
has curation status: metadata incomplete
definition: A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
editor note: does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
imported from: Ontology for Biomedical Investigations

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: metadata complete
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: Ontology for Biomedical Investigations

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed.
editor note: OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: Ontology for Biomedical Investigations

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

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: pending final vetting
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: Ontology for Biomedical Investigations

material sample
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
editor preferred label: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
definition editor: OBI: workshop
alternative term: sample
alternative term: sample population
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: Ontology for Biomedical Investigations

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

informed consent process
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has specified input
  some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role
editor preferred label: informed consent process
has curation status: ready for release
definition: A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate.
editor note: 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
definition editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
imported from: Ontology for Biomedical Investigations

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

high molecular weight DNA extract
type: Class
subclass of: DNA extract
editor preferred label: high molecular weight DNA extract
example of usage: Extraction of chromosomal DNA from mammalian cells by first isolating nucei
has curation status: metadata complete
definition: The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
definition editor: PERSON:Chris Stoeckert
definition source: OBI
imported from: Ontology for Biomedical Investigations

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

polyA RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: polyA RNA extraction
has curation status: metadata complete
definition: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

organellar RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: organellar RNA extraction
has curation status: metadata complete
definition: A RNA extraction process in which the desired output material is RNA in the organelle(s).
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

total RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: total RNA extraction
has curation status: metadata complete
definition: A RNA extraction process in which total cellular and organelle RNA are extracted.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

cytoplasmic RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: cytoplasmic RNA extraction
has curation status: metadata complete
definition: A RNA extraction process in which the desired output material is RNA in the cytoplasm.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

nuclear RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is specified output of
  some values from: nuclear RNA extraction
editor preferred label: nuclear RNA extract
example of usage: Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
has curation status: metadata complete
definition: A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

polyA RNA extract
type: Class
subclass of: RNA extract
subclass of: Restriction
  on property: is specified output of
  some values from: polyA RNA extraction
editor preferred label: polyA RNA extract
example of usage: Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
has curation status: metadata complete
definition: A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

pre-mortem specimen
type: Class
equivalent class: Class
  intersection of: specimen with pre- or post-mortem status
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen with pre- or post-mortem status
editor preferred label: pre-mortem specimen
example of usage: material obtained through a liver biopsy from a human patient
has curation status: metadata complete
definition: a specimen that was taken from a live organism
definition editor: Bjoern Peters
definition source: MO_705 premortem
imported from: Ontology for Biomedical Investigations

cytoplasmic RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: cytoplasmic RNA extraction
subclass of: RNA extract
editor preferred label: cytoplasmic RNA extract
example of usage: Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
has curation status: metadata complete
definition: A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
definition editor: PERSON:Chris Stoeckert
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

RNA extract
type: Class
equivalent class: Class
  intersection of: nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: RNA extraction
  intersection of: Restriction
    on property: has grain
    some values from: ribonucleic acid
subclass of: nucleic acid extract
editor preferred label: RNA extract
has curation status: metadata complete
definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: Group: UPenn Group
imported from: Ontology for Biomedical Investigations

nuclear RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: nuclear RNA extraction
has curation status: metadata complete
definition: A RNA extraction process in which the desired output material is RNA in the nucleus.
definition editor: Person: Chris Stoeckert
definition editor: Person: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

total RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: total RNA extraction
subclass of: RNA extract
editor preferred label: total RNA extract
example of usage: Extraction of total RNA from cells with Qiagen mini RNeasy kit
has curation status: metadata complete
definition: A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

organellar RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: organellar RNA extraction
subclass of: RNA extract
editor preferred label: organellar RNA extract
example of usage: Extraction of organellar RNA from plant cells using organellar RNA binding protein.
has curation status: metadata complete
definition: A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

post mortem specimen
type: Class
equivalent class: Class
  intersection of: specimen with pre- or post-mortem status
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen with pre- or post-mortem status
editor preferred label: post mortem specimen
example of usage: the spleen taken from a dead mouse
has curation status: metadata complete
definition: a specimen that was taken from a dead organism
definition editor: Bjoern Peters
definition source: MO_416 postmortem
imported from: Ontology for Biomedical Investigations

labeled DNA extract
type: Class
equivalent class: Class
  intersection of: labeled nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has specified input
        some values from: DNA extract
  intersection of: Restriction
    on property: has grain
    some values from: deoxyribonucleic acid
subclass of: labeled nucleic acid extract
editor preferred label: labeled DNA extract
has curation status: metadata complete
definition: a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
editor note: Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
definition editor: Group: OBI group
definition source: Group: OBI group
imported from: Ontology for Biomedical Investigations

cloacal specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: cloaca
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: cell specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete
definition: A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
imported from: Ontology for Biomedical Investigations

nasopharyngeal aspirate specimen
type: Class
subclass of: nasopharynx specimen
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: nasopharynx
subclass of: Restriction
  on property: is specified output of
  some values from: aspiration specimen collection
editor preferred label: nasopharyngeal aspirate specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete
definition: A specimen which derives from nasopharyngeal mucosa after aspiration.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
imported from: Ontology for Biomedical Investigations

freezing storage
type: Class
subclass of: storage
subclass of: Class
  intersection of: Restriction
    on property: has specified input
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: frozen
  intersection of: Restriction
    on property: has specified output
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has quality
        some values from: frozen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: freezing storage
example of usage: a fozen pellet used for later assay
has curation status: metadata complete
definition: A storage process in temperature that maintenance the frozen status of the stored entities.
editor note: 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen.
definition editor: Person: Alan Ruttenberg, Mathias Brochhausen
definition source: MO_481 frozen_storage
definition source: OBI
imported from: Ontology for Biomedical Investigations

nasal swab specimen
type: Class
equivalent class: Class
  intersection of: upper respiratory tract specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: nasal cavity mucosa
subclass of: swab specimen
subclass of: upper respiratory tract specimen
editor preferred label: nasal swab specimen
example of usage: type of sample used in the PCIRN influenza network
has curation status: metadata complete
definition: A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
imported from: Ontology for Biomedical Investigations

labeled RNA extract
type: Class
equivalent class: Class
  intersection of: labeled nucleic acid extract
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has specified input
        some values from: RNA extract
  intersection of: Restriction
    on property: has grain
    some values from: ribonucleic acid
subclass of: labeled nucleic acid extract
editor preferred label: labeled RNA extract
has curation status: metadata complete
definition: a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
editor note: Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call
definition editor: Group: OBI group
definition source: Group: OBI group
imported from: Ontology for Biomedical Investigations

frozen specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: freezing storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred label: frozen specimen
example of usage: Frozen blood plasma
has curation status: metadata incomplete
definition: A specimen that has been frozen in order to store it.
definition editor: Person:Alan Ruttenberg
definition source: MO_610 frozen_sample
imported from: Ontology for Biomedical Investigations

labeled specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is specified output of
    some values from: addition of molecular label
subclass of: processed specimen
subclass of: molecular-labeled material
editor preferred label: labeled specimen
has curation status: metadata incomplete
definition: A specimen that has been modified in order to be able to detect it in future experiments
editor note: added during call 3/1/2010
definition editor: OBI group
imported from: Ontology for Biomedical Investigations

lyophilization storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: lyophilization storage
has curation status: metadata incomplete
definition: a storage process with input material entity and output freeze dried material for long time storage
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
imported from: Ontology for Biomedical Investigations
comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed

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

paraffin specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: paraffin storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred label: paraffin specimen
example of usage: liver tissue embedded in paraffin
has curation status: metadata incomplete
definition: a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: MO_990 paraffin_sample
imported from: Ontology for Biomedical Investigations

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

lyophilized specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: lyophilization storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred label: lyophilized specimen
example of usage: freezing dried DNA
has curation status: metadata incomplete
definition: a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: MO_589 freeze_dried_sample
imported from: Ontology for Biomedical Investigations

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: Ontology for Biomedical Investigations

fresh specimen
type: Class
subclass of: specimen with known storage state
editor preferred label: fresh specimen
example of usage: a liver freshly removed from a rat
has curation status: metadata incomplete
definition: a specimen that is output of a specimen creation process used for an investigation without storage.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: MO_730 fresh_sample
imported from: Ontology for Biomedical Investigations

paraffin storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: organism
    union of: material anatomical entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: paraffin storage
has curation status: metadata complete
definition: a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations
comment: need to specify paraffin or wax is one of specified input of the process

agar stab specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: agar stab storage
      intersection of: Restriction
        on property: has specified input
        some values from: Restriction
subclass of: specimen with known storage state
editor preferred label: agar stab specimen
has curation status: metadata incomplete
definition: a specimen that is output of a process that cell culture inoculated into agar for long term storage.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: MO_971 agar_stab
imported from: Ontology for Biomedical Investigations

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

agar stab storage
type: Class
subclass of: storage
subclass of: Restriction
  on property: has specified input
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: agar stab storage
has curation status: metadata complete
definition: a storage process with input cell culture and agar and output agar stab for long time storage
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations
comment: need to specify that agar is one of input for this process

nucleic acid extract
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: nucleic acid extraction
subclass of: processed specimen
editor preferred label: nucleic acid extract
has curation status: metadata complete
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
definition editor: Person: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

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

labeled nucleic acid extract
type: Class
equivalent class: Class
  intersection of: labeled specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has specified input
        some values from: nucleic acid extract
  intersection of: Restriction
    on property: has grain
    some values from: nucleic acid
subclass of: labeled specimen
editor preferred label: labeled nucleic acid extract
has curation status: metadata complete
definition: a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
definition editor: Person: Jie Zheng
alternative term: labeled extract
definition source: MO_221 labeledExtract
imported from: Ontology for Biomedical Investigations

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

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

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

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

cell specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: has part
    some values from: cell
subclass of: specimen from organism
editor preferred label: cell specimen
has curation status: metadata incomplete
definition: A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture.
editor note: Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828
definition editor: PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl
definition source: MO_612 cell
imported from: Ontology for Biomedical Investigations

specimen with known storage state
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Class
    union of: fresh specimen
    union of: Class
      intersection of: specimen
      intersection of: Restriction
        on property: is specified output of
        some values from: storage
subclass of: specimen
editor preferred label: specimen with known storage state
has curation status: metadata incomplete
definition: A specimen for which it is known whether it has been subjected to storage of a specified type.
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_95 BiosourceType
imported from: Ontology for Biomedical Investigations

specimen from organism
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen
editor preferred label: specimen from organism
has curation status: ready for release
definition: A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
alternative term: tissue specimen
definition source: MO_954 organism_part
imported from: Ontology for Biomedical Investigations

specimen with pre- or post-mortem status
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: Class
subclass of: specimen from organism
editor preferred label: specimen with pre- or post-mortem status
has curation status: metadata complete
definition: A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
editor note: organizational term, used in description of specimen that is created from known pre- or post-mortem status
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: MO_84 OrganismStatus
imported from: Ontology for Biomedical Investigations

investigation title
type: Class
subclass of: comment on investigation
subclass of: Restriction
  on property: denotes
  some values from: investigation
editor preferred label: investigation title
has curation status: metadata complete
definition: A textual entity that denotes an investigation.
definition editor: Person:Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: Ontology for Biomedical Investigations
ISA alternative term: study title
NIAID GSCID-BRC alternative term: project title
Source: NIAID GSCID-BRC

reagent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: reagent role
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: material processing
editor preferred label: reagent
has curation status: metadata complete
definition: A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
editor note: 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device.
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: Ontology for Biomedical Investigations
comment: (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some…

comment on investigation
type: Class
equivalent class: Class
  intersection of: textual entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: investigation
      union of: Restriction
        on property: part of
        some values from: investigation
      union of: Restriction
        on property: participates in
        some values from: investigation
subclass of: textual entity
editor preferred label: comment on investigation
has curation status: metadata complete
definition: A textual entity that is about any of the aspects of an investigation worth noting
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: Ontology for Biomedical Investigations
NIAID GSCID-BRC alternative term: Comments
Source: NIAID GSCID-BRC

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is specified output of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has curation status: ready for release
definition: An information content entity that is inferred from data.
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
definition editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group
imported from: Ontology for Biomedical Investigations

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: metadata complete
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
definition editor: PERSON: Matthew Brush
imported from: Ontology for Biomedical Investigations

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
definition editor: PERSON:Bjoern Peters
imported from: Ontology for Biomedical Investigations

molecular-labeled material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is specified output of
    some values from: addition of molecular label
subclass of: processed material
editor preferred label: molecular-labeled material
has curation status: pending final vetting
definition: a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
definition editor: PERSON:Matthew Brush
definition source: OBI developer call, 3-12-12
imported from: Ontology for Biomedical Investigations

grant agency
type: Class
subclass of: organization
editor preferred label: grant agency
has curation status: metadata complete
definition: An organization that provides funding support for projects such as investigations.
definition editor: PERSON: Jie Zheng, Chris Stoeckert
alternative term: funding organization
definition source: NIAID GSCID-BRC metadata working group
imported from: Ontology for Biomedical Investigations
Source: NIAID GSCID-BRC
see also: 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization

IHC slide staining
type: Class
subclass of: staining
subclass of: Class
  intersection of: staining
  intersection of: Restriction
    on property: has specified input
    some values from: fixed tissue slide specimen
editor preferred label: IHC slide staining
has curation status: pending final vetting
definition: A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues.
definition editor: Chris Stoeckert, Ned Haubein
definition source: http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf
imported from: Ontology for Biomedical Investigations

H&E slide staining
type: Class
subclass of: staining
subclass of: Class
  intersection of: staining
  intersection of: Restriction
    on property: has specified input
    some values from: fixed tissue slide specimen
editor preferred label: H&E slide staining
has curation status: pending final vetting
definition: A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink.
definition editor: Chris Stoeckert, Ned Haubein
definition source: http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/
imported from: Ontology for Biomedical Investigations

H&E-stained fixed tissue slide specimen
type: Class
equivalent class: Class
  intersection of: fixed tissue slide specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: H&E slide staining
subclass of: fixed tissue slide specimen
editor preferred label: H&E-stained fixed tissue slide specimen
has curation status: pending final vetting
definition: A fixed tissue slide specimen that is the output of H&E slide staining.
definition editor: Chris Stoeckert, Ned Haubein
definition source: OBIB, OBI
imported from: Ontology for Biomedical Investigations

IHC-stained fixed tissue slide specimen
type: Class
equivalent class: Class
  intersection of: fixed tissue slide specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: IHC slide staining
subclass of: fixed tissue slide specimen
editor preferred label: IHC-stained fixed tissue slide specimen
has curation status: pending final vetting
definition: A fixed tissue slide specimen that is the output of immunohistochemistry slide staining.
definition editor: Chris Stoeckert, Ned Haubein
definition source: OBIB, OBI
imported from: Ontology for Biomedical Investigations

single cell specimen
type: Class
subclass of: cell specimen
editor preferred label: single cell specimen
has curation status: metadata complete
definition: A cell specimen that contains only one cell.
editor note: Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/
definition editor: PERSON: Jie Zheng, Alexander Diehl
definition source: PERSON: Jie Zheng, Alexander Diehl
imported from: Ontology for Biomedical Investigations

age of majority inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: age of majority inclusion criterion
has curation status: metadata complete
definition: An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

chemotherapy treatment exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: chemotherapy treatment exclusion criterion
has curation status: metadata complete
definition: An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

radiation treatment exclusion criteria
type: Class
subclass of: exclusion criterion
editor preferred label: radiation treatment exclusion criteria
has curation status: metadata complete
definition: An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

chemotherapy treatment within the recent past exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: chemotherapy treatment within the recent past exclusion criterion
example of usage: An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years.
has curation status: metadata complete
definition: An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

radiation treatment within the recent past exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: radiation treatment within the recent past exclusion criterion
example of usage: An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years.
has curation status: metadata complete
definition: An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

BMI range inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: BMI range inclusion criterion
example of usage: An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
has curation status: metadata complete
definition: An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

blood transfusion exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: blood transfusion exclusion criterion
example of usage: An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death.
has curation status: metadata complete
definition: An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

history of metastatic cancer exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: history of metastatic cancer exclusion criterion
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

intravenous drug use exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: intravenous drug use exclusion criterion
example of usage: Donor eligibility based on history of intravenous drug abuse in the last 5 years.
has curation status: metadata complete
definition: An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

history of sex with someone with a history of blood borne infection exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: history of sex with someone with a history of blood borne infection exclusion criterion
example of usage: Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years.
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

history of sex with someone with a history of intravenous drugs exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: history of sex with someone with a history of intravenous drugs exclusion criterion
example of usage: Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years.
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

HIV exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: HIV exclusion criterion
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

exposure to blood borne infectious disease exclusion criterion
type: Class
subclass of: exclusion criterion
editor preferred label: exposure to blood borne infectious disease exclusion criterion
example of usage: Donor eligibility based on whether the donor has been exposed to HIV/AIDS.
has curation status: metadata complete
definition: An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process.
definition editor: Chris Stoeckert, Helena Ellis
definition source: NCI BBRB, OBIB
ontology term requester: NCI BBRB
imported from: Ontology for Biomedical Investigations

health status inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: health status inclusion criterion
example of usage: ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: Ontology for Biomedical Investigations

clinically relevant lifestyle inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: clinically relevant lifestyle inclusion criterion
example of usage: 'smoking behavior’
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: Ontology for Biomedical Investigations

clinically relevant exposure inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: clinically relevant exposure inclusion criterion
example of usage: 'exposure to cigarette smoke’, ‘exposure to lead through drinking water'
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: Ontology for Biomedical Investigations

gravidity inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: gravidity inclusion criterion
example of usage: 'pregnant’, ‘not pregnant'
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
ontology term requester: MIABIS2.0
imported from: Ontology for Biomedical Investigations

defined population inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: defined population inclusion criterion
example of usage: inclusion based on age, sex, and living region (rural area or specified city).
has curation status: metadata complete
definition: An inclusion criterion that is based on fitting within the defined characteristics of a population based study design.
definition editor: Chris Stoeckert, Mathias Brochhausen
definition source: MIABIS 2.0
term tracker item: https://github.com/obi-ontology/obi/issues/920
ontology term requester: MIABIS 2.0
imported from: Ontology for Biomedical Investigations

amniotic fluid specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: amniotic fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: amniotic fluid specimen
has curation status: ready for release
definition: A specimen that is derived from amniotic fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

bile specimen
type: Class
equivalent class: Class
  intersection of: digestive system fluid or secretion specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: bile
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive system fluid or secretion specimen
editor preferred label: bile specimen
has curation status: ready for release
definition: A specimen that is derived from bile.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

cerebrospinal fluid specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: cerebrospinal fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: cerebrospinal fluid specimen
has curation status: ready for release
definition: A specimen that is derived from cerbrospinal fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

feces specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: feces
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: feces specimen
has curation status: ready for release
definition: A specimen that is derived from feces.
definition editor: Chris Stoeckert
alternative term: stool specimen
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

digestive system fluid or secretion specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: digestive system secreted substance
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: digestive system fluid or secretion specimen
has curation status: ready for release
definition: A specimen that is derived from digestive system fluid or secretion.
definition editor: Chris Stoeckert
alternative term: gastric fluid specimen
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

milk specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: milk
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: milk specimen
has curation status: ready for release
definition: A specimen that is derived from milk.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

pericardial fluid specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: pericardial fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: pericardial fluid specimen
has curation status: ready for release
definition: A specimen that is derived from pericardial fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

saliva specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: saliva
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: saliva specimen
has curation status: ready for release
definition: A specimen that is derived from saliva.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

sputum specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: sputum
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: sputum specimen
has curation status: ready for release
definition: A specimen that is derived from sputum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

sweat specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: sweat
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: sweat specimen
has curation status: ready for release
definition: A specimen that is derived from sweat.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

synovial fluid specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: synovial fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: synovial fluid specimen
has curation status: ready for release
definition: A specimen that is derived from synovial fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

vitreous humor specimen
type: Class
equivalent class: Class
  intersection of: eye specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: eye specimen
editor preferred label: vitreous humor specimen
has curation status: ready for release
definition: A specimen that is derived from vireous humor.
definition editor: Chris Stoeckert
alternative term: vitreous fluid specimen
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

bone marrow specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: bone marrow
  intersection of: Restriction
    on property: is specified output of
    some values from: bone marrow biopsy
subclass of: specimen from organism
editor preferred label: bone marrow specimen
has curation status: ready for release
definition: A specimen that is derived from bone marrow.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

placenta specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: placenta specimen
has curation status: ready for release
definition: A specimen that is derived from placenta.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

peritoneal fluid specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: peritoneal fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: peritoneal fluid specimen
has curation status: ready for release
definition: A specimen that is derived from peritoneal fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

pleural fluid specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: pleural fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: pleural fluid specimen
has curation status: ready for release
definition: A specimen that is derived from pleural fluid.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, Penn Medicine Biobank
imported from: Ontology for Biomedical Investigations

brain specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: brain specimen
has curation status: ready for release
definition: A specimen that is derived from brain.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

hair specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: strand of hair
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: hair specimen
has curation status: ready for release
definition: A specimen that is derived from hair.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

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

skeletal muscle tissue specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: skeletal muscle tissue
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: skeletal muscle tissue specimen
has curation status: ready for release
definition: A specimen that is derived from skeletal muscle.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

heart specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: heart specimen
has curation status: ready for release
definition: A specimen that is derived from heart.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

renal medulla specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: renal medulla specimen
has curation status: ready for release
definition: A specimen that is derived from renal medulla.
definition editor: Chris Stoeckert
alternative term: kidney medulla specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

adrenal gland specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: adrenal gland specimen
has curation status: ready for release
definition: A specimen that is derived from adrenal gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

breast specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: breast specimen
has curation status: ready for release
definition: A specimen that is derived from breast.
definition editor: Chris Stoeckert
alternative term: mammary tissue specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

urinary bladder specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: urinary bladder specimen
has curation status: ready for release
definition: A specimen that is derived from urinary bladder.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

tibial artery specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: tibial artery specimen
has curation status: ready for release
definition: A specimen that is derived from tibial artery.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

skin of body specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: skin of body specimen
has curation status: ready for release
definition: A specimen that is derived from skin.
definition editor: Chris Stoeckert
alternative term: skin specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

pancreas specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: pancreas specimen
has curation status: ready for release
definition: A specimen that is derived from pancreas.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

stomach specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: stomach specimen
has curation status: ready for release
definition: A specimen that is derived from stomach.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

pituitary gland specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: pituitary gland specimen
has curation status: ready for release
definition: A specimen that is derived from pituitary gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

adipose tissue specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: adipose tissue
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: adipose tissue specimen
has curation status: ready for release
definition: A specimen that is derived from adipose tissue.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

cortex of kidney specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: cortex of kidney specimen
has curation status: ready for release
definition: A specimen that is derived from cortex of kidney.
definition editor: Chris Stoeckert
alternative term: kidney cortex specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

esophagus mucosa specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: esophagus mucosa specimen
has curation status: ready for release
definition: A specimen that is derived from esophagus mucosa.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

colon specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: colon specimen
has curation status: ready for release
definition: A specimen that is derived from colon.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

lung specimen
type: Class
equivalent class: Class
  intersection of: lower respiratory tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: lower respiratory tract specimen
editor preferred label: lung specimen
has curation status: ready for release
definition: A specimen that is derived from lung.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

esophagus muscularis mucosa specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: esophagus muscularis mucosa specimen
has curation status: ready for release
definition: A specimen that is derived from esophagus muscularis mucosa.
definition editor: Chris Stoeckert
alternative term: esophagus muscularis specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

cerebral cortex specimen
type: Class
equivalent class: Class
  intersection of: brain specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: brain specimen
editor preferred label: cerebral cortex specimen
has curation status: ready for release
definition: A specimen that is derived from cerebral cortex.
definition editor: Chris Stoeckert
alternative term: brain cortex specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

thyroid gland specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: thyroid gland specimen
has curation status: ready for release
definition: A specimen that is derived from thyroid gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

cerebellum specimen
type: Class
equivalent class: Class
  intersection of: brain specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: brain specimen
editor preferred label: cerebellum specimen
has curation status: ready for release
definition: A specimen that is derived from cerebellum.
definition editor: Chris Stoeckert
alternative term: brain cerebellum specimen
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

tibial nerve specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: tibial nerve specimen
has curation status: ready for release
definition: A specimen that is derived from tibial nerve.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

coronary artery specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: coronary artery specimen
has curation status: ready for release
definition: A specimen that is derived from coronary artery.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

spleen specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: spleen specimen
has curation status: ready for release
definition: A specimen that is derived from spleen.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

aorta specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: aorta specimen
has curation status: ready for release
definition: A specimen that is derived from aorta.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

atrial appendage specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: atrial appendage specimen
has curation status: ready for release
definition: A specimen that is derived from the atrium auricular region.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

esophagogastric junction specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: esophagogastric junction specimen
has curation status: ready for release
definition: A specimen that is derived from the esophagogastric junction.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

ileum specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: ileum specimen
has curation status: ready for release
definition: A specimen that is derived from ileum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

liver specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: liver specimen
has curation status: ready for release
definition: A specimen that is derived from liver.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

minor salivary gland specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: minor salivary gland specimen
has curation status: ready for release
definition: A specimen that is derived from minor salivary gland.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

omentum specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: omentum specimen
has curation status: ready for release
definition: A specimen that is derived from omentum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

ovary specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: ovary specimen
has curation status: ready for release
definition: A specimen that is derived from female gonad.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

sigmoid colon specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: digestive tract specimen
editor preferred label: sigmoid colon specimen
has curation status: ready for release
definition: A specimen that is derived from sigmoid colon.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

suprapubic skin specimen
type: Class
equivalent class: Class
  intersection of: skin of body specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: skin of body specimen
editor preferred label: suprapubic skin specimen
has curation status: ready for release
definition: A specimen that is derived from suprapubic skin.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

testis specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: testis specimen
has curation status: ready for release
definition: A specimen that is derived from testis.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

uterus specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: uterus specimen
has curation status: ready for release
definition: A specimen that is derived from uterus.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

vagina specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: vagina specimen
has curation status: ready for release
definition: A specimen that is derived from vagina.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, NCI BBRB
imported from: Ontology for Biomedical Investigations

age group inclusion criterion
type: Class
subclass of: inclusion criterion
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: minimum age value specification
  intersection of: Restriction
    on property: has part
    some values from: maximum age value specification
editor preferred label: age group inclusion criterion
example of usage: "18-33 years old"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
term tracker item: https://github.com/obi-ontology/obi/issues/839
imported from: Ontology for Biomedical Investigations

minimum age value specification
type: Class
subclass of: value specification
editor preferred label: minimum age value specification
has curation status: metadata incomplete
definition: A value specifcation that specifies the youngest age when specifying an age range.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

maximum age value specification
type: Class
subclass of: value specification
editor preferred label: maximum age value specification
has curation status: metadata incomplete
definition: A value specifcation that specifies the oldest age when specifying an age range.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

use of medication inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: use of medication inclusion criterion
example of usage: "received at least 2 days of vancomycin"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
term tracker item: https://github.com/obi-ontology/obi/issues/840
imported from: Ontology for Biomedical Investigations

hospital patient inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: hospital patient inclusion criterion
example of usage: "included hospital patients"
has curation status: metadata incomplete
definition: An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

family status inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: family status inclusion criterion
example of usage: "included married and unmarried patients", "included divorced individuals"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

sex inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: sex inclusion criterion
example of usage: "included males and females", "included male patients"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

country of residence inclusion criteria
type: Class
subclass of: inclusion criterion
editor preferred label: country of residence inclusion criteria
example of usage: "include US residents"
has curation status: metadata incomplete
definition: An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

ethnicity inclusion criterion
type: Class
subclass of: inclusion criterion
editor preferred label: ethnicity inclusion criterion
example of usage: "include only Hispanic individuals"
has curation status: metadata incomplete
definition: An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
imported from: Ontology for Biomedical Investigations

polyA depleted RNA extract
type: Class
equivalent class: Class
  intersection of: RNA extract
  intersection of: Restriction
    on property: is specified output of
    some values from: RNA extraction with polyA depletion
subclass of: RNA extract
editor preferred label: polyA depleted RNA extract
has curation status: metadata complete
definition: A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified.
definition editor: Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations

RNA extraction with polyA depletion
type: Class
subclass of: RNA extraction
editor preferred label: RNA extraction with polyA depletion
has curation status: metadata complete
definition: A RNA extraction process in which only RNAs lacking a polyA tail are retained
definition editor: Mark A. Miller, based on OBI_0000848
definition source: UPenn Group
imported from: Ontology for Biomedical Investigations
date: 2018-05-11T15:01:14Z

swab specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
subclass of: specimen
editor preferred label: swab specimen
has curation status: ready for release
definition: A specimen that is stored on a swab as the output of a collecting specimen with swab process.
definition editor: Chris Stoeckert
definition source: OBIB/OBI
term tracker item: https://github.com/obi-ontology/obi/issues/910
ontology term requester: OBIB
imported from: Ontology for Biomedical Investigations

collecting specimen with swab
type: Class
subclass of: specimen collection process
editor preferred label: collecting specimen with swab
has curation status: ready for release
definition: A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick).
definition editor: Chris Stoeckert
definition source: OBIB
term tracker item: https://github.com/obi-ontology/obi/issues/910
ontology term requester: OBIB
imported from: Ontology for Biomedical Investigations

areolar swab specimen
type: Class
equivalent class: Class
  intersection of: breast swab specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: areola
subclass of: breast swab specimen
editor preferred label: areolar swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of an areola of a breast.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

breast swab specimen
type: Class
equivalent class: Class
  intersection of: breast specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: breast
subclass of: breast specimen
subclass of: swab specimen
editor preferred label: breast swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a breast.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

cheek swab specimen
type: Class
equivalent class: Class
  intersection of: oral swab specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: cheek
subclass of: oral swab specimen
editor preferred label: cheek swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

nasopharyngeal swab specimen
type: Class
equivalent class: Class
  intersection of: nasopharynx specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: nasopharynx
subclass of: swab specimen
subclass of: nasopharynx specimen
editor preferred label: nasopharyngeal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a nasopharynx.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

oral swab specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: mouth
subclass of: specimen from organism
subclass of: swab specimen
editor preferred label: oral swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the inside surface of a mouth.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

oropharyngeal swab specimen
type: Class
equivalent class: Class
  intersection of: upper respiratory tract specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: oropharynx
subclass of: swab specimen
subclass of: upper respiratory tract specimen
editor preferred label: oropharyngeal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a oropharynx.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

rectal swab specimen
type: Class
equivalent class: Class
  intersection of: digestive tract specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: rectum
subclass of: swab specimen
subclass of: digestive tract specimen
editor preferred label: rectal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a rectum.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

tongue swab specimen
type: Class
equivalent class: Class
  intersection of: oral swab specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: tongue
subclass of: oral swab specimen
editor preferred label: tongue swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a tongue.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

vagina swab specimen
type: Class
equivalent class: Class
  intersection of: vagina specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: vagina
subclass of: vagina specimen
subclass of: swab specimen
editor preferred label: vagina swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a vagina.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

fecal swab specimen
type: Class
equivalent class: Class
  intersection of: feces specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: feces
subclass of: feces specimen
subclass of: swab specimen
editor preferred label: fecal swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of a feces.
definition editor: Chris Stoeckert
alternative term: stool swab specimen
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

environmental swab specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: environmental material
subclass of: swab specimen
editor preferred label: environmental swab specimen
has curation status: ready for release
definition: A specimen that is collected with a swab from the surface of an environmenal material.
definition editor: Chris Stoeckert
definition source: Chris Stoeckert, OBIB
imported from: Ontology for Biomedical Investigations

ribosomal RNA-depleted RNA extract
type: Class
subclass of: RNA extract
editor preferred label: ribosomal RNA-depleted RNA extract
example of usage: Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation.
has curation status: pending final vetting
definition: An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species).
definition editor: Dan Berrios
definition source: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1
imported from: Ontology for Biomedical Investigations

individual organism specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: has component
    qualified cardinality: 1
    on class: organism
subclass of: specimen
editor preferred label: individual organism specimen
has curation status: metadata complete
definition: A specimen composed of an individual organism to be studied in an investigation.
definition editor: Person: Jie Zheng
definition source: EFO_0000542 individual
term tracker item: https://github.com/obi-ontology/obi/issues/1092
imported from: Ontology for Biomedical Investigations

biopsy
type: Class
subclass of: collecting specimen from organism
subclass of: Restriction
  on property: has specified input
  some values from: device
subclass of: Restriction
  on property: has specified input
  some values from: material anatomical entity
subclass of: Restriction
  on property: has specified output
  some values from: pre-mortem specimen
editor preferred label: biopsy
example of usage: Biopsy of a potentially cancerous mole.
has curation status: ready for release
definition: A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
definition editor: Damion Dooley
definition editor: Nicole Vasilevsky
definition source: https://en.wikipedia.org/wiki/Biopsy
imported from: Ontology for Biomedical Investigations

bone marrow biopsy
type: Class
subclass of: biopsy
subclass of: Restriction
  on property: has specified input
  some values from: bone marrow
editor preferred label: bone marrow biopsy
example of usage: A bone marrow biopsy removes bone with the marrow inside to look at under a microscope
has curation status: ready for release
definition: A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected.
definition editor: Nicole Vasilevsky
definition source: http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy
imported from: Ontology for Biomedical Investigations

arthropod meal of blood specimen
type: Class
subclass of: blood specimen
subclass of: Restriction
  on property: is specified output of
  some values from: collecting specimen from organism
editor preferred label: arthropod meal of blood specimen
example of usage: A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito.
has curation status: metadata complete
definition: A specimen of the blood ingested by an arthropod.
editor note: The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
alternative term: blood meal
definition source: VEuPathDB
term tracker item: https://github.com/obi-ontology/obi/issues/1117
ontology term requester: VEuPathDB
imported from: Ontology for Biomedical Investigations

molecular label role
type: Class
subclass of: reagent role
editor preferred label: molecular label role
has curation status: metadata complete
definition: A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
editor note: MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743.
definition editor: Group: OBI
alternative term: molecular tracer role
definition source: OBI developer call, 3-12-12
term tracker item: https://github.com/obi-ontology/obi/issues/1135
imported from: Ontology for Biomedical Investigations

molecular label
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has role
    some values from: molecular label role
subclass of: molecular entity
subclass of: reagent
editor preferred label: molecular label
has curation status: metadata complete
definition: A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
editor note: JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744.
definition editor: Group: OBI
alternative term: molecular tracer
definition source: OBI developer call, 3-12-12
term tracker item: https://github.com/obi-ontology/obi/issues/1135
imported from: Ontology for Biomedical Investigations

induced sputum specimen
type: Class
subclass of: sputum specimen
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: sputum
subclass of: Restriction
  on property: is specified output of
  some values from: collecting specimen from organism
editor preferred label: induced sputum specimen
has curation status: metadata complete
definition: A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution.
definition editor: John Judkins
definition source: PMC3297553
imported from: Ontology for Biomedical Investigations

platelet-poor plasma specimen
type: Class
subclass of: blood plasma specimen
editor preferred label: platelet-poor plasma specimen
has curation status: metadata incomplete
definition: A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter.
definition editor: PERSON: Matthew Diller
imported from: Ontology for Biomedical Investigations

tracheal aspirate specimen
type: Class
equivalent class: Class
  intersection of: lower respiratory tract specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: aspiration specimen collection
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: trachea
subclass of: lower respiratory tract aspirate specimen
editor preferred label: tracheal aspirate specimen
has curation status: metadata complete
definition: A specimen that is collected with a suctioning tube from the trachea.
definition editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
alternative term: tracheal wash specimen
definition source: PMID:25338241
imported from: Ontology for Biomedical Investigations

mid-turbinate nasal swab specimen
type: Class
equivalent class: Class
  intersection of: nasal swab specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: middle nasal concha
subclass of: nasal swab specimen
editor preferred label: mid-turbinate nasal swab specimen
has curation status: metadata complete
definition: A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity.
definition editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
definition source: https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633
imported from: Ontology for Biomedical Investigations

nasal aspirate specimen
type: Class
equivalent class: Class
  intersection of: upper respiratory tract specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: aspiration specimen collection
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: nasal cavity mucosa
subclass of: upper respiratory tract specimen
editor preferred label: nasal aspirate specimen
has curation status: metadata complete
definition: A specimen that is collected with a suctioning tube from the nasal cavity.
definition editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
alternative term: nasal wash specimen
alternative term: nasopharyngeal aspirate
definition source: Asiyah Yu Lin ORCID:0000-0003-2620-0345
imported from: Ontology for Biomedical Investigations

lower respiratory tract aspirate specimen
type: Class
equivalent class: Class
  intersection of: lower respiratory tract specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: aspiration specimen collection
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: lower respiratory tract
subclass of: lower respiratory tract specimen
editor preferred label: lower respiratory tract aspirate specimen
has curation status: metadata complete
definition: A specimen that is collected with a suctioning tube from the lower respiratory tract.
definition editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
alternative term: lower respiratory tract wash specimen
definition source: Asiyah Yu Lin ORCID:0000-0003-2620-0345
imported from: Ontology for Biomedical Investigations

lower respiratory tract specimen
type: Class
equivalent class: Class
  intersection of: respiratory system specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: lower respiratory tract
subclass of: respiratory system specimen
editor preferred label: lower respiratory tract specimen
has curation status: metadata complete
definition: A specimen that is derived from the lower respiratory tract.
definition editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
definition source: Asiyah Yu Lin ORCID:0000-0003-2620-0345
imported from: Ontology for Biomedical Investigations

anterior nasal swab specimen
type: Class
equivalent class: Class
  intersection of: nasal swab specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen with swab
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: anterior nasal wall
subclass of: nasal swab specimen
editor preferred label: anterior nasal swab specimen
has curation status: metadata complete
definition: A specimen that is derived from the anterior nasal wall
definition editor: Asiyah Yu Lin ORCID:0000-0003-2620-0345
definition source: Asiyah Yu Lin ORCID:0000-0003-2620-0345
imported from: Ontology for Biomedical Investigations

aspiration specimen collection
type: Class
subclass of: specimen collection process
editor preferred label: aspiration specimen collection
has curation status: metadata complete
definition: Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.
definition editor: Asiyah Yu Lin|ORCID:0000-0003-2620-0345
alternative term: aspiration procedure
definition source: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
imported from: Ontology for Biomedical Investigations

endotracheal tube specimen
type: Class
subclass of: lower respiratory tract specimen
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: respiratory system fluid/secretion
subclass of: Restriction
  on property: is specified output of
  some values from: collecting specimen from organism
editor preferred label: endotracheal tube specimen
has curation status: metadata complete
definition: A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea.
definition editor: John Judkins ORCID:0000-0001-6595-0902
definition source: https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3
imported from: Ontology for Biomedical Investigations

endotracheal aspirate specimen
type: Class
subclass of: lower respiratory tract aspirate specimen
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: respiratory system fluid/secretion
subclass of: Restriction
  on property: is specified output of
  some values from: aspiration specimen collection
editor preferred label: endotracheal aspirate specimen
has curation status: metadata complete
definition: A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube.
definition editor: John Judkins ORCID:0000-0001-6595-0902
definition source: https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3
imported from: Ontology for Biomedical Investigations

blood specimen in vacutainer
type: Class
subclass of: blood specimen
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: blood
subclass of: Restriction
  on property: is specified output of
  some values from: collecting specimen from organism
editor preferred label: blood specimen in vacutainer
has curation status: metadata complete
definition: A blood specimen that is located in a vacutainer.
definition editor: John Judkins
alternative term: Vacutainer sample
definition source: VEuPathDB
imported from: Ontology for Biomedical Investigations

blood specimen on filter paper
type: Class
subclass of: blood specimen
subclass of: Class
  intersection of: Restriction
    on property: is specified output of
    some values from: specimen collection process
  intersection of: Restriction
    on property: derives from
    some values from: blood
subclass of: Restriction
  on property: is specified output of
  some values from: collecting specimen from organism
editor preferred label: blood specimen on filter paper
has curation status: metadata complete
definition: A blood specimen that is located on a filter paper.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
alternative term: Filter paper sample
definition source: Penn Group
imported from: Ontology for Biomedical Investigations

placental blood specimen
type: Class
equivalent class: Class
  intersection of: blood specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: placental blood
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: blood specimen
editor preferred label: placental blood specimen
has curation status: metadata complete
definition: A specimen that is derived from placental blood.
definition editor: John Judkins
definition source: VEuPathDB
imported from: Ontology for Biomedical Investigations

peripheral blood mononuclear cell specimen
type: Class
equivalent class: Class
  intersection of: blood specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: peripheral blood mononuclear cell
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: blood specimen
editor preferred label: peripheral blood mononuclear cell specimen
has curation status: metadata complete
definition: A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system.
definition editor: Chris Stoeckert
definition editor: Jie Zheng
alternative term: PBMC specimen
definition source: http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell
imported from: Ontology for Biomedical Investigations

lymph specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: lymph specimen
has curation status: metadata complete
definition: A specimen that is derived from a portion of lymph collected from an organism.
definition editor: John Judkins ORCID:0000-0001-6595-0902
definition source: VEuPathDB
imported from: Ontology for Biomedical Investigations

digestive tract specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: digestive tract specimen
has curation status: metadata complete
definition: A specimen that is derived from part of a digestive tract.
definition editor: John Judkins ORCID:0000-0001-6595-0902
definition source: VEuPathDB
imported from: Ontology for Biomedical Investigations

nasal lavage fluid
type: Class
equivalent class: Class
  intersection of: lavage fluid specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: lavage
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: nasal cavity mucosa
subclass of: lavage fluid specimen
editor preferred label: nasal lavage fluid
has curation status: metadata incomplete
definition: A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.
definition editor: Randi Vita
definition editor: Sebastian Duesing
imported from: Ontology for Biomedical Investigations

reactant role
type: Class
subclass of: role
editor preferred label: reactant role
has curation status: metadata incomplete
definition: A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction.
definition editor: Sebastian Duesing
imported from: Ontology for Biomedical Investigations

albumin-free serum
type: Class
equivalent class: Class
  intersection of: blood serum specimen
  intersection of: Restriction
    on property: has part
    all values from: Class
      complement of: albumin
subclass of: blood serum specimen
editor preferred label: albumin-free serum
has curation status: metadata incomplete
definition: A blood serum specimen that contains no albumin.
definition editor: Sebastian Duesing
term tracker item: https://github.com/obi-ontology/obi/issues/493
ontology term requester: Philippe Rocca-Serra
imported from: Ontology for Biomedical Investigations

lavage fluid specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Restriction
    on property: is specified output of
    some values from: lavage
subclass of: processed specimen
subclass of: specimen from organism
editor preferred label: lavage fluid specimen
example of usage: The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present.
has curation status: metadata incomplete
definition: A specimen obtained through a lavage process which includes fluid in addition to cells and/or cellular secretions.
definition editor: Sebastian Duesing
term tracker item: https://github.com/obi-ontology/obi/issues/1803
imported from: Ontology for Biomedical Investigations

oral lavage fluid
type: Class
equivalent class: Class
  intersection of: lavage fluid specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: lavage
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: mouth
subclass of: lavage fluid specimen
editor preferred label: oral lavage fluid
has curation status: metadata incomplete
definition: A specimen collected through oral cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the oral cavity space.
definition editor: Sebastian Duesing
alternative term: mouth rinse specimen
term tracker item: https://github.com/obi-ontology/obi/issues/1803
ontology term requester: Anna Maria Masci
imported from: Ontology for Biomedical Investigations

blood plasma specimen
type: Class
subclass of: blood specimen
subclass of: processed specimen
subclass of: Restriction
  on property: is specified output of
  some values from: Class
    intersection of: material component separation
    intersection of: Restriction
      on property: has specified input
      some values from: blood specimen
editor preferred label: blood plasma specimen
example of usage: PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
has curation status: metadata complete
definition: a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
editor note: 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
definition editor: PERSON: Maura Gasparetto
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: plasma
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
imported from: Ontology for Biomedical Investigations

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

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: organizational term
has curation status: ready for release
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
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 source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: Ontology for Biomedical Investigations

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site.
has curation status: ready for release
definition: A material entity that is collected for potential use as an input upon which measurements or observations are performed.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: Ontology for Biomedical Investigations

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is specified output of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: metadata complete
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
definition editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
imported from: Ontology for Biomedical Investigations
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

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

bronchial alveolar lavage
type: Class
equivalent class: Class
  intersection of: lavage fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: lung
  intersection of: Restriction
    on property: is specified output of
    some values from: lavage
subclass of: lavage fluid specimen
editor preferred label: bronchial alveolar lavage
example of usage: solution containing lung derived T cells, eosinophils, and TNFa.
has curation status: metadata complete
definition: Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
definition editor: PERSON: Bjoern Peters
alternative term: BAL
definition source: GROUP: IEDB
imported from: Ontology for Biomedical Investigations

data transformation
type: Class
subclass of: planned process
editor preferred label: data transformation
definition: A planned process that produces output data from input data.
imported from: Ontology for Biomedical Investigations

pool of specimens
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: material combination
      intersection of: Restriction
        on property: has specified input
        all values from: specimen
subclass of: processed specimen
editor preferred label: pool of specimens
has curation status: metadata complete
definition: A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
editor note: check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
definition editor: PERSON: Jennifer Fostel
definition source: GROUP: CEBS
imported from: Ontology for Biomedical Investigations

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: metadata incomplete
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
definition editor: Person:Bjoern Peters
definition editor: Philippe Rocca-Serra
imported from: Ontology for Biomedical Investigations

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

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

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

storage
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: storage
example of usage: PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
has curation status: metadata complete
definition: A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.
definition editor: Philippe Rocca-Serra
definition source: OBI-Branch
imported from: Ontology for Biomedical Investigations

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

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

study design
type: Class
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
editor preferred label: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: ready for release
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
definition editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: Ontology for Biomedical Investigations

eligibility criterion
type: Class
subclass of: directive information entity
editor preferred label: eligibility criterion
example of usage: PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
has curation status: ready for release
definition: an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
definition editor: Person: Philippe Rocca-Serra
alternative term: eligibility rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: Ontology for Biomedical Investigations

inclusion criterion
type: Class
subclass of: eligibility criterion
editor preferred label: inclusion criterion
example of usage: PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
has curation status: pending final vetting
definition: an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
definition editor: Person: Philippe Rocca-Serra
alternative term: inclusion condition
alternative term: inclusion rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: Ontology for Biomedical Investigations

exclusion criterion
type: Class
subclass of: eligibility criterion
editor preferred label: exclusion rule
example of usage: PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
has curation status: pending final vetting
definition: an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
definition editor: Person: Philippe Rocca-Serra
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: Ontology for Biomedical Investigations

collecting specimen from organism
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has specified input
  some values from: organism
subclass of: Restriction
  on property: has specified output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
definition editor: PERSON:Bjoern Peters
definition source: IEDB
imported from: Ontology for Biomedical Investigations

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: material entity
subclass of: Restriction
  on property: has specified output
  some values from: material entity
editor preferred label: material component separation
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
definition editor: Bjoern Peters
definition source: IEDB
imported from: Ontology for Biomedical Investigations

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has specified input
  some values from: cultured cell population
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has specified output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: pending final vetting
definition: A planned process with the objective to keep cells alive in a defined environment outside of an organism.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigations

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: cell
subclass of: Restriction
  on property: has specified input
  some values from: culture medium
subclass of: Restriction
  on property: has specified output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: 'establishing cell culture'
has curation status: metadata complete
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: Ontology for Biomedical Investigations
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

addition of molecular label
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has specified input
  some values from: molecular label
subclass of: Restriction
  on property: has specified input
  some values from: target of material addition
subclass of: Restriction
  on property: has specified output
  some values from: molecular-labeled material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: addition of molecular label
example of usage: The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
has curation status: pending final vetting
definition: a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
definition editor: PERSON:Matthew Brush
alternative term: labeling
definition source: OBI developer call, 3-12-12
imported from: Ontology for Biomedical Investigations

lavage
type: Class
subclass of: collecting specimen from organism
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
editor preferred label: lavage
example of usage: the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
has curation status: metadata complete
definition: A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
editor note: This is not washing, in which case the material of interest is not the resulting fluid
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: Ontology for Biomedical Investigations

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

RNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has specified output
  some values from: RNA extract
editor preferred label: RNA extraction
has curation status: pending final vetting
definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO
imported from: Ontology for Biomedical Investigations

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has specified input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
subclass of: Restriction
  on property: has specified output
  some values from: nucleic acid extract
editor preferred label: nucleic acid extraction
example of usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
has curation status: pending final vetting
definition: a material separation to recover the nucleic acid fraction of an input material
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO. Could be defined class
imported from: Ontology for Biomedical Investigations

whole mount tissue
type: Class
subclass of: whole organism preparation
subclass of: processed specimen
subclass of: Restriction
  on property: is specified output of
  some values from: histological sample preparation
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred label: whole mount tissue
has curation status: metadata complete
definition: A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Philippe Rocca-Serra
alternative term: whole mount sample
definition source: GROUP: OBI
curator note: PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
curator note: PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
imported from: Ontology for Biomedical Investigations

lymph node cell specimen
type: Class
equivalent class: Class
  intersection of: cell specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: organ harvesting
      intersection of: Restriction
        on property: has specified input
        some values from: lymph node
subclass of: processed specimen
subclass of: cell specimen
editor preferred label: lymph node cell specimen
has curation status: metadata incomplete
definition: A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
definition editor: IEDB
definition source: IEDB
imported from: Ontology for Biomedical Investigations

organ harvesting
type: Class
subclass of: material component separation
editor preferred label: organ harvesting
has curation status: metadata incomplete
definition: The process of removing an organ from its source organism
definition editor: IEDB
definition source: IEDB
imported from: Ontology for Biomedical Investigations

target of material addition
type: Class
equivalent class: Restriction
  on property: has role
  some values from: target of material addition role
subclass of: material entity
editor preferred label: target of material addition
example of usage: A cell culture into which a mixture of peptides is being added.
has curation status: ready for release
definition: A material entity that receives the addition of another material entity in an “adding a material entity into a target” process.
editor note: 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
definition source: IEDB
imported from: Ontology for Biomedical Investigations

splenocyte specimen
type: Class
equivalent class: Class
  intersection of: cell specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: organ harvesting
      intersection of: Restriction
        on property: has specified input
        some values from: spleen
subclass of: processed specimen
subclass of: cell specimen
editor preferred label: splenocyte specimen
has curation status: metadata complete
definition: A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
definition editor: IEDB
definition source: IEDB
imported from: Ontology for Biomedical Investigations

FFPE specimen
type: Class
subclass of: paraffin specimen
editor preferred label: FFPE specimen
example of usage: Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/
has curation status: metadata complete
definition: A specimen that has been fixed in formalin and embedded in paraffin.
definition editor: MIABIS
alternative term: formalin-fixed paraffin-embeded specimen
definition source: https://www.biochain.com/general/what-is-ffpe-tissue/
term tracker item: https://github.com/obi-ontology/obi/issues/1019
imported from: Ontology for Biomedical Investigations

uterine cervix specimen
type: Class
equivalent class: Class
  intersection of: uterus specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: uterus specimen
editor preferred label: uterine cervix specimen
has curation status: metadata complete
definition: A specimen that is derived from some uterine cervix
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

urethra specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: urethra specimen
has curation status: metadata complete
definition: A specimen that is derived from some urethra
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

cervical mucus specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: cervical mucus
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: cervical mucus specimen
has curation status: metadata complete
definition: A specimen that is derived from some cervical mucus
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

throat specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: throat specimen
has curation status: metadata complete
definition: A specimen that is derived from some throat
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

eye specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: eye specimen
has curation status: metadata complete
definition: A specimen that is derived from some eye
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

respiratory system specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: respiratory system specimen
has curation status: metadata complete
definition: A specimen that is derived from some respiratory system
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

upper respiratory tract specimen
type: Class
equivalent class: Class
  intersection of: respiratory system specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: respiratory system specimen
editor preferred label: upper respiratory tract specimen
has curation status: metadata complete
definition: A specimen that is derived from some upper respiratory tract
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

nasopharynx specimen
type: Class
equivalent class: Class
  intersection of: upper respiratory tract specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: upper respiratory tract specimen
editor preferred label: nasopharynx specimen
has curation status: metadata complete
definition: A specimen that is derived from some nasopharynx
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

semen specimen
type: Class
equivalent class: Class
  intersection of: bodily fluid specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: semen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: bodily fluid specimen
editor preferred label: semen specimen
has curation status: metadata complete
definition: A specimen that is derived from some semen
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

bodily fluid specimen
type: Class
equivalent class: Class
  intersection of: specimen from organism
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: bodily fluid
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: specimen from organism
editor preferred label: bodily fluid specimen
has curation status: metadata complete
definition: A specimen that is derived from some bodily fluid
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

chorionic villus specimen
type: Class
equivalent class: Class
  intersection of: placenta specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: Class
        intersection of: tissue
        intersection of: Restriction
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: placenta specimen
editor preferred label: chorionic villus specimen
has curation status: metadata complete
definition: A specimen that is derived from some chorionic villus
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

meconium specimen
type: Class
equivalent class: Class
  intersection of: feces specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: meconium
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: feces specimen
editor preferred label: meconium specimen
has curation status: metadata complete
definition: A specimen that is derived from some meconium
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

umbilical cord blood specimen
type: Class
equivalent class: Class
  intersection of: blood specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: umbilical cord blood
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: arterial blood specimen
editor preferred label: umbilical cord blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some umbilical cord blood
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

arterial blood specimen
type: Class
equivalent class: Class
  intersection of: blood specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: arterial blood
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: blood specimen
editor preferred label: arterial blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some arterial blood
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

venous blood specimen
type: Class
equivalent class: Class
  intersection of: blood specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: venous blood
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: blood specimen
editor preferred label: venous blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some venous blood
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

capillary blood specimen
type: Class
equivalent class: Class
  intersection of: blood specimen
  intersection of: Class
    intersection of: Restriction
      on property: is specified output of
      some values from: specimen collection process
    intersection of: Restriction
      on property: derives from
      some values from: capillary blood
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
subclass of: blood specimen
editor preferred label: capillary blood specimen
has curation status: metadata complete
definition: A specimen that is derived from some capillary blood
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

erythrocyte specimen
type: Class
equivalent class: Class
  intersection of: cell specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: erythrocyte
subclass of: cell specimen
editor preferred label: erythrocyte specimen
has curation status: metadata complete
definition: A specimen that is derived from some erythrocytes
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

reticulocyte specimen
type: Class
equivalent class: Class
  intersection of: cell specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: reticulocyte
subclass of: cell specimen
editor preferred label: reticulocyte specimen
has curation status: metadata complete
definition: A specimen that is derived from some reticulocytes
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

leukocyte specimen
type: Class
equivalent class: Class
  intersection of: cell specimen
  intersection of: Restriction
    on property: is specified output of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: is specified output of
    some values from: Class
      intersection of: specimen collection process
      intersection of: Restriction
        on property: has specified input
        some values from: leukocyte
subclass of: cell specimen
editor preferred label: leukocyte specimen
has curation status: metadata complete
definition: A specimen that is derived from some leukocytes
definition editor: Christian Stoeckert ORCID:0000-0002-5714-991X
definition editor: Mark A. Miller ORCID:0000-0001-9076-6066
definition source: Christian Stoeckert ORCID:0000-0002-5714-991X
definition source: Mark A. Miller ORCID:0000-0001-9076-6066
imported from: Ontology for Biomedical Investigations

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
imported from: ogms.owl

laboratory finding
type: Class
subclass of: clinical finding
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 editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T10:21:58Z
imported from: ogms.owl
term_mapping_to_UMLS: C0456984
term_mapping_to_NCIT: C77140

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

clinical laboratory test
type: Class
subclass of: planned process
definition: A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:49:49Z
imported from: ogms.owl

bodily process
type: Class
subclass of: process
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:53:49Z
imported from: oae.owl
imported from: ogms.owl

treatment
type: Class
subclass of: planned process
definition: A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z
imported from: ogms.owl

health care process
type: Class
subclass of: planned process
definition: A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18
imported from: ogms.owl

injury
type: Class
subclass of: disorder
definition: A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
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'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
definition editor: Albert Goldfain Sagar Jain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
curator note: creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015
imported from: ogms.owl

diagnostic process
type: Class
subclass of: health care process
definition: A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
curator note: creation date: 2011-09-20T09:57:44Z
imported from: ogms.owl

fixed tissue specimen
type: Class
subclass of: processed specimen
editor preferred label: fixed tissue specimen
definition: A processed specimen that is the output of a fixation process.
imported from: Ontology for Biomedical Investigations
imported from: omiabis.owl

fixed tissue slide specimen
type: Class
subclass of: fixed tissue specimen
editor preferred label: fixed tissue slide specimen
definition: A fixed tissue specimen that is placed in a slide.
imported from: Ontology for Biomedical Investigations
imported from: omiabis.owl

health care provider organization role
type: Class
subclass of: organization health care role
definition: A role that inheres in an organization and that is realized by the providing of services in a health care encounter.
imported from: omrse.owl
Contributor: Mathias Brochhausen
creator: Amanda Hicks

collection of organisms
type: Class
equivalent class: Restriction
  on property: is-aggregate-of
  some values from: organism
subclass of: material entity
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.

obsolete 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
imported from: omrse.owl
comment: Previous definition: A role played by an entity in human social processes.
deprecated: true

organization social role
type: Class
subclass of: obsolete role in human social processes
definition: A role in human social processes that inheres in an organization.
definition editor: William R. Hogan
imported from: omrse.owl
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.

organization health care role
type: Class
subclass of: organization social role
definition: An organization social role that, if realized, is realized by either a health care process or an ancillary health care process
imported from: omrse.owl
comment: Previous definition: An organization social role played by an organization in health care processes.

aggregate of organizations
type: Class
equivalent class: Restriction
  on property: is-aggregate-of
  some values from: organization
subclass of: material entity
definition: An aggregate of organizations that have some feature in common, but is not itself an organization.
definition editor: William R. Hogan
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

legal person role
type: Class
subclass of: role
definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
definition editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
imported from: omrse.owl
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.

hospital role
type: Class
subclass of: health care provider organization role
definition: A healthcare provider role that inheres in an organization and is realized by providing inpatient care.
definition editor: Mathias Brochhausen
imported from: omrse.owl

hospital organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: bearer of
    some values from: hospital role
subclass of: organization
definition: An organization that is the bearer of a hospital role.
definition editor: Mathias Brochhausen
imported from: omrse.owl

employer role
type: Class
subclass of: obsolete role in human social processes
definition: a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration
imported from: omrse.owl

obsolete communication
type: Class
subclass of: process
definition: A process in which some participant shares some information content entity about some state of that participant with some other participant.
definition editor: S. Clint Dowland
imported from: omrse.owl
Contributor: Mathias Brochhausen
Contributor: Matthew Diller
Contributor: William R. Hogan
comment: The term 'participant' in the definition need not refer to a human agent.
deprecated: true

information content entity-request process
type: Class
subclass of: obsolete communication
definition: a communication in which some participant requests of some other participant an information content entity about some portion of reality
definition editor: S. Clint Dowland
imported from: omrse.owl
comment: As with the parent class, 'participant' in the definition need not refer to a human agent.
comment: The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be.

education process
type: Class
subclass of: planned process
editor preferred label: educating
definition: A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs either (1) becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability, (2) "improves" an existing capability as demonstrated through realization(s) of that capability, and/or (3) loses a capability whose realization is considered negative.
definition editor: William R. Hogan
alternative term: learning process
imported from: omrse.owl
elucidation: An act of acquiring new information and repeatedly applying that information to develop a new skill, improve an existing skill, and/or losing a skill at doing something "bad".
comment: An interesting question is whether there must be another participant who is the "educator". Some might object that many people are "self taught". A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the tip of a finger. There was no previous information about that type of skill. The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.). On the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow "plays a role" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).
comment: The loss of a "bad" capability is something like losing a bad golf swing and replacing it with a good one. Also a capability to disrupt the classroom might be something an educating process diminishes possibly to the point of "removal" in a student. This addition to the definition notwithstanding, we do not intend to incorporate the receipt of punishment into the definition of educating.

hospital governing body role
type: Class
subclass of: role
definition: A role that inheres in an organization and that, if realized, is realized by its bearer overseeing the overall operation of a hospital.
date: Imported 8.30.2018

committee member role
type: Class
subclass of: role
definition: A role that, if realized, is realized in the organizational context of a committee.
date: Imported 8.30.2018.

morphology
type: Class
subclass of: physical object quality
editor preferred label: morphology
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
imported from: pato.owl

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

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

temperature
type: Class
subclass of: physical quality
editor preferred label: temperature
definition: A physical quality of the thermal energy of a system.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

viability
type: Class
subclass of: organismal quality
editor preferred label: viability
definition: An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

physical quality
type: Class
subclass of: physical object quality
editor preferred label: physical quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
editor preferred label: physical object quality
definition: A quality which inheres in a continuant.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

alive
type: Class
subclass of: viability
editor preferred label: alive
definition: A viability quality inhering in a bearer by virtue of the bearer's condition before death.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

dead
type: Class
subclass of: viability
editor preferred label: dead
definition: A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

frozen
type: Class
subclass of: temperature
editor preferred label: frozen
definition: A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

organismal quality
type: Class
subclass of: physical object quality
editor preferred label: organismal quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: Ontology for Biomedical Investigations
imported from: pato.owl

protein
type: Class
subclass of: peptide
editor preferred label: protein
example of usage: antithrombin III is a protein
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: Ontology for Biomedical Investigations
imported from: pr.owl

albumin
type: Class
subclass of: protein
editor preferred label: albumin
definition: A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof.
imported from: Ontology for Biomedical Investigations
imported from: pr.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: Ontology for Biomedical Investigations
imported from: so.owl

uterine cervix
type: Class
subclass of: material anatomical entity
editor preferred label: uterine cervix
definition: Lower, narrow portion of the uterus where it joins with the top end of the vagina.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

pituitary gland
type: Class
subclass of: material anatomical entity
editor preferred label: pituitary gland
definition: The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

lymph node
type: Class
subclass of: material anatomical entity
editor preferred label: lymph node
definition: Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

urethra
type: Class
subclass of: material anatomical entity
editor preferred label: urethra
definition: The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cloaca
type: Class
subclass of: material anatomical entity
editor preferred label: cloaca
definition: Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

mouth
type: Class
subclass of: material anatomical entity
editor preferred label: mouth
definition: The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

amniotic fluid
type: Class
subclass of: organism substance
editor preferred label: amniotic fluid
definition: Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

blood
type: Class
subclass of: bodily fluid
editor preferred label: blood
definition: A fluid that is composed of blood plasma and erythrocytes.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

breast
type: Class
subclass of: material anatomical entity
editor preferred label: breast
definition: The upper ventral region of the torso of an organism.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cervical mucus
type: Class
subclass of: bodily fluid
editor preferred label: cervical mucus
definition: A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

throat
type: Class
subclass of: material anatomical entity
editor preferred label: throat
definition: In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

renal medulla
type: Class
subclass of: multi-tissue structure
editor preferred label: renal medulla
definition: The inner portion of the kidney consisting of the renal pyramids.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

organism substance
type: Class
subclass of: material anatomical entity
editor preferred label: organism substance
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

material anatomical entity
type: Class
subclass of: material entity
editor preferred label: material anatomical entity
definition: Anatomical entity that has mass.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

testis
type: Class
subclass of: material anatomical entity
editor preferred label: testis
definition: A gonad of a male animal. A gonad produces and releases sperm.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

anatomical cluster
type: Class
subclass of: material entity
editor preferred label: anatomical cluster
definition: Anatomical group whose component anatomical structures lie in close proximity to each other.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

tissue
type: Class
subclass of: material anatomical entity
editor preferred label: tissue
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

multi-tissue structure
type: Class
subclass of: material anatomical entity
editor preferred label: multi-tissue structure
definition: Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

stomach
type: Class
subclass of: material anatomical entity
editor preferred label: stomach
definition: An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

aorta
type: Class
subclass of: material anatomical entity
editor preferred label: aorta
definition: The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

heart
type: Class
subclass of: material anatomical entity
editor preferred label: heart
definition: A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

brain
type: Class
subclass of: material anatomical entity
editor preferred label: brain
definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cerebral cortex
type: Class
subclass of: material anatomical entity
editor preferred label: cerebral cortex
definition: The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

eye
type: Class
subclass of: material anatomical entity
editor preferred label: eye
definition: An organ that detects light.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

ovary
type: Class
subclass of: material anatomical entity
editor preferred label: ovary
definition: The gonad of a female organism which contains germ cells.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

uterus
type: Class
subclass of: material anatomical entity
editor preferred label: uterus
definition: The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

vagina
type: Class
subclass of: material anatomical entity
editor preferred label: vagina
definition: A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

respiratory system
type: Class
subclass of: material anatomical entity
editor preferred label: respiratory system
definition: Functional system which consists of structures involved in respiration.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

adipose tissue
type: Class
subclass of: tissue
editor preferred label: adipose tissue
definition: Portion of connective tissue composed of adipocytes enmeshed in areolar tissue.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

strand of hair
type: Class
subclass of: material anatomical entity
editor preferred label: strand of hair
definition: A filament, mostly protein, that grows from follicles found in the dermis[WP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

rectum
type: Class
subclass of: material anatomical entity
editor preferred label: rectum
definition: The terminal portion of the intestinal tube, terminating with the anus.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

pleural fluid
type: Class
subclass of: bodily fluid
editor preferred label: pleural fluid
definition: Transudate contained in the pleural cavity.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

urine
type: Class
subclass of: organism substance
editor preferred label: urine
definition: Excretion that is the output of a kidney.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

sweat
type: Class
subclass of: bodily fluid
editor preferred label: sweat
definition: Secretion produced by a sweat gland.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

synovial fluid
type: Class
subclass of: bodily fluid
editor preferred label: synovial fluid
definition: Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

skeletal muscle tissue
type: Class
subclass of: tissue
editor preferred label: skeletal muscle tissue
definition: Muscle tissue that consists primarily of skeletal muscle fibers.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

colon
type: Class
subclass of: material anatomical entity
editor preferred label: colon
definition: A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

sigmoid colon
type: Class
subclass of: material anatomical entity
editor preferred label: sigmoid colon
definition: The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cortex of kidney
type: Class
subclass of: material anatomical entity
editor preferred label: cortex of kidney
definition: Outer cortical portion of the kidney, between the renal capsule and the renal medulla.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

urinary bladder
type: Class
subclass of: material anatomical entity
editor preferred label: urinary bladder
definition: Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

pancreas
type: Class
subclass of: material anatomical entity
editor preferred label: pancreas
definition: An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

peritoneal fluid
type: Class
subclass of: bodily fluid
editor preferred label: peritoneal fluid
definition: Transudate contained in the peritoneal cavity.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

tibial nerve
type: Class
subclass of: material anatomical entity
editor preferred label: tibial nerve
definition: The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cerebrospinal fluid
type: Class
subclass of: bodily fluid
editor preferred label: cerebrospinal fluid
definition: A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

digestive tract
type: Class
subclass of: material anatomical entity
editor preferred label: digestive tract
definition: A tube extending from the mouth to the anus.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

upper respiratory tract
type: Class
subclass of: material anatomical entity
editor preferred label: upper respiratory tract
definition: The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

lower respiratory tract
type: Class
subclass of: material anatomical entity
editor preferred label: lower respiratory tract
definition: The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cheek
type: Class
subclass of: material anatomical entity
editor preferred label: cheek
definition: A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

coronary artery
type: Class
subclass of: artery
editor preferred label: coronary artery
definition: An artery that supplies the myocardium.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

artery
type: Class
subclass of: material anatomical entity
editor preferred label: artery
definition: An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

tongue
type: Class
subclass of: material anatomical entity
editor preferred label: tongue
definition: A muscular organ in the floor of the mouth.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

nasopharynx
type: Class
subclass of: material anatomical entity
editor preferred label: nasopharynx
definition: The section of the pharynx that lies above the soft palate.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

oropharynx
type: Class
subclass of: material anatomical entity
editor preferred label: oropharynx
definition: The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

vitreous humor
type: Class
subclass of: organism substance
editor preferred label: vitreous humor
definition: A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

nasal cavity mucosa
type: Class
subclass of: material anatomical entity
editor preferred label: nasal cavity mucosa
definition: The mucous membrane that lines the nasal cavity[MP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

minor salivary gland
type: Class
subclass of: material anatomical entity
editor preferred label: minor salivary gland
definition: One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

saliva
type: Class
subclass of: organism substance
editor preferred label: saliva
definition: A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

milk
type: Class
subclass of: bodily fluid
editor preferred label: milk
definition: An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

semen
type: Class
subclass of: organism substance
editor preferred label: semen
definition: Organism substance that is composed of sperm cells suspended in seminal fluid.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

bile
type: Class
subclass of: bodily fluid
editor preferred label: bile
definition: Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

placenta
type: Class
subclass of: material anatomical entity
editor preferred label: placenta
definition: Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

feces
type: Class
subclass of: organism substance
editor preferred label: feces
definition: Portion of semisolid bodily waste discharged through the anus[MW,modified].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

areola
type: Class
subclass of: material anatomical entity
editor preferred label: areola
definition: Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

cerebellum
type: Class
subclass of: multi-tissue structure
editor preferred label: cerebellum
definition: Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

thyroid gland
type: Class
subclass of: material anatomical entity
editor preferred label: thyroid gland
definition: A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

lung
type: Class
subclass of: material anatomical entity
editor preferred label: lung
definition: Respiration organ that develops as an outpocketing of the esophagus.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

skin of body
type: Class
subclass of: material anatomical entity
editor preferred label: skin of body
definition: The organ covering the body that consists of the dermis and epidermis.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

spleen
type: Class
subclass of: material anatomical entity
editor preferred label: spleen
definition: The organ that functions to filter blood and to store red corpuscles and platelets.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

liver
type: Class
subclass of: material anatomical entity
editor preferred label: liver
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

ileum
type: Class
subclass of: material anatomical entity
editor preferred label: ileum
definition: The portion of the small intestine that extends from the jejunum to the colon.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

prostate gland
type: Class
subclass of: material anatomical entity
editor preferred label: prostate gland
definition: The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

adrenal gland
type: Class
subclass of: material anatomical entity
editor preferred label: adrenal gland
definition: Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

bone marrow
type: Class
subclass of: tissue
editor preferred label: bone marrow
definition: The soft tissue that fills the cavities of bones.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

lymph
type: Class
subclass of: bodily fluid
editor preferred label: lymph
definition: Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

pericardial fluid
type: Class
subclass of: bodily fluid
editor preferred label: pericardial fluid
definition: Transudate contained in the pericardial cavity.[FMA].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

esophagus mucosa
type: Class
subclass of: material anatomical entity
editor preferred label: esophagus mucosa
definition: A mucosa that is part of a esophagus [Automatically generated definition].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

trachea
type: Class
subclass of: material anatomical entity
editor preferred label: trachea
definition: The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

omentum
type: Class
subclass of: material anatomical entity
editor preferred label: omentum
definition: A fold of peritoneum originating at the stomach and supporting the viscera.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

esophagus muscularis mucosa
type: Class
subclass of: tissue
editor preferred label: esophagus muscularis mucosa
definition: A muscularis mucosa that is part of a esophagus.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

middle nasal concha
type: Class
subclass of: material anatomical entity
editor preferred label: middle nasal concha
definition: The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

bodily fluid
type: Class
subclass of: organism substance
editor preferred label: bodily fluid
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

respiratory system fluid/secretion
type: Class
subclass of: organism substance
editor preferred label: respiratory system fluid/secretion
definition: A portion of organism substance that secreted_by a respiratory system.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

atrium auricular region
type: Class
subclass of: multi-tissue structure
editor preferred label: atrium auricular region
definition: A small conical pouch projections located on the upper anterior portion of each atrium of the heart.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

digestive system secreted substance
type: Class
subclass of: organism substance
editor preferred label: digestive system secreted substance
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

chorionic villus
type: Class
subclass of: material anatomical entity
editor preferred label: chorionic villus
definition: One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

meconium
type: Class
subclass of: feces
editor preferred label: meconium
definition: A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

sputum
type: Class
subclass of: respiratory system fluid/secretion
editor preferred label: sputum
definition: Matter ejected from the lungs, bronchi, and trachea, through the mouth.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

tibial artery
type: Class
subclass of: artery
editor preferred label: tibial artery
definition: The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

esophagogastric junction
type: Class
subclass of: material anatomical entity
editor preferred label: esophagogastric junction
definition: The junction between the esophagus and the stomach epithelium.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

umbilical cord blood
type: Class
subclass of: arterial blood
editor preferred label: umbilical cord blood
definition: Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP].
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

arterial blood
type: Class
subclass of: blood
editor preferred label: arterial blood
definition: A blood that is part of a artery.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

venous blood
type: Class
subclass of: blood
editor preferred label: venous blood
definition: A blood that is part of a vein.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

capillary blood
type: Class
subclass of: blood
editor preferred label: capillary blood
definition: A blood that is part of a capillary.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

suprapubic skin
type: Class
subclass of: material anatomical entity
editor preferred label: suprapubic skin
definition: Area of skin in the hypoastric region of the abdomen.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

anterior nasal wall
type: Class
subclass of: material anatomical entity
editor preferred label: anterior nasal wall
definition: Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

placental blood
type: Class
subclass of: blood
editor preferred label: placental blood
definition: Blood located in the placenta.
imported from: Ontology for Biomedical Investigations
imported from: uberon.owl

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: uo.owl

Topic
type: Class
subclass of: information content entity
definition: A category denoting a rather broad domain or field of interest, study, application, work, data, or technology. Topics have no clearly defined borders between each other.
id: topic:0003

obsolete ICO Classes to Move to RUBRIC
type: Class
subclass of: Obsolete Class
comment: This is a dummy class to be deprecated after it has fulfilled its organization purposes
deprecated: true

obsolete ICO Classes to Move to D-Acts
type: Class
subclass of: Obsolete Class
comment: This is a dummy class to be deprecated after it has fulfilled its organization purposes
deprecated: true

vulnerability
type: Class
subclass of: disposition
example of usage: Editors Note: E.g., "There are several definitions available for the term 'vulnerable population', the words simply imply the disadvantaged sub-segment of the community requiring utmost care, specific ancillary considerations and augmented protections in research. The vulnerable individuals’ freedom and capability to protect one-self from intended or inherent risks is variably abbreviated, from decreased freewill to inability to make informed choices." Preethi Shivayogi (2013). Vulnerable population and methods for their safeguard. Perspectives in clinical research, 4(1), 53-7.
definition: A disposition of an entity to undergo undesirable change in response to some exposure.
date: Imported 08.22.2018

legal name
type: Class
subclass of: author identification
definition: A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate.
curator note: from http://semanticscience.org/resource/SIO_000184

Obsolete Class
type: Class
subclass of: Thing

descriptive information content entity
type: Class
subclass of: information content entity
definition: An information content entity that consists of a set of propositions that describe some entity.
definition source: https://github.com/CommonCoreOntology/CommonCoreOntologies
date: Retrieved from Common Core Ontologies 7/17/2018
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Designative Information Content Entity
type: Class
subclass of: information content entity
definition: An Information Content Entity that consists of a set of symbols that denote some Entity.
definition source: https://github.com/CommonCoreOntology/CommonCoreOntologies
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
comment: [Merriam-Webster] (1) Definition of 'designate as' : to choose (someone or something) for (a particular role or purpose) (2) Definition of 'designate': (Entry 2 of 2) <transitive verb> 1: to indicate and set apart for a specific purpose, office, or duty (3) Definition of 'denote': <transitive verb> 1: to serve as an indication of : BETOKEN 2: to serve as an arbitrary mark for red flares denoting danger, 3: to make known : ANNOUNCE (4) Also 'demarcate' or 'delimit'

government
type: Class
subclass of: organization
definition: An Organization that exercises executive, legislative, or judicial authority over a Geopolitical Entity.
editor note: https://en.wikipedia.org/wiki/Government
editor note: is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology
date: Imported 8.30.2018
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

stasis
type: Class
subclass of: process
definition: A process in which some independent continuant endures and one or more of the dependent entities it bears does not change in kind or intensity.
definition source: https://github.com/CommonCoreOntology/CommonCoreOntologies
date: Retrieved from Common Core Ontologies 7/17/2018
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

stasis of generically dependent continuant
type: Class
subclass of: stasis
definition: A stasis in which some independent continuant bears some generically dependent continuant that remains unchanged during a temporal interval.
definition source: https://github.com/CommonCoreOntology/CommonCoreOntologies
curator note: At this time only stasis of genetically dependent continuant will be represented, leaving open the possibility of modeling other types of stasis as represented in the Common Core Ontologies. An example use case would be the transition of law enumerated by one document to a new iteration of the document for the same law. In this case, the old document would no longer be ‘legally effective’ and the corresponding stasis would cease.
date: Retrieved from Common Core Ontologies 7/17/2018
license: BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred label: example to be eventually removed

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

metadata complete
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release
definition editor: PERSON:Alan Ruttenberg

ready for release
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: ready for release
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

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

pending final vetting
type: Thing
type: NamedIndividual
type: curation status specification
editor preferred label: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

obsolete_core
type: NamedIndividual
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
has obsolescence reason: placeholder removed
deprecated: true

placeholder removed
type: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred label: terms merged
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 preferred label: term imported
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 preferred label: term split
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.

obsolete_other
type: NamedIndividual
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.
deprecated: true

universal
type: NamedIndividual
type: denotator type
editor preferred label: universal
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
definition editor: Alan Ruttenberg
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
editor preferred label: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
editor preferred label: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
definition editor: Alan Ruttenberg

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

requires discussion
type: NamedIndividual
type: curation status specification
editor preferred label: requires discussion
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

Ontology for Biomedical Investigations
type: NamedIndividual
default language: en
OBO foundry unique label: Ontology for Biomedical Investigations
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Alan Ruttenberg
creator: Allyson Lister
creator: Barry Smith
creator: Bill Bug
creator: Bjoern Peters
creator: Carlo Torniai
creator: Chris Mungall
creator: Chris Stoeckert
creator: Chris Taylor
creator: Christian Bolling
creator: Cristian Cocos
creator: Daniel Rubin
creator: Daniel Schober
creator: Dawn Field
creator: Dirk Derom
creator: Elisabetta Manduchi
creator: Eric Deutsch
creator: Frank Gibson
creator: Gilberto Fragoso
creator: Helen C. Causton
creator: Helen Parkinson
creator: Holger Stenzhorn
creator: James A. Overton
creator: James Malone
creator: Jay Greenbaum
creator: Jeffrey Grethe
creator: Jennifer Fostel
creator: Jessica Turner
creator: Jie Zheng
creator: Joe White
creator: John Westbrook
creator: Kevin Clancy
creator: Larisa Soldatova
creator: Lawrence Hunter
creator: Liju Fan
creator: Luisa Montecchi
creator: Matthew Brush
creator: Matthew Pocock
creator: Melanie Courtot
creator: Melissa Haendel
creator: Mervi Heiskanen
creator: Monnie McGee
creator: Norman Morrison
creator: Philippe Rocca-Serra
creator: Phillip Lord
creator: Pierre Grenon
creator: Richard Bruskiewich
creator: Richard Scheuermann
creator: Robert Stevens
creator: Ryan R. Brinkman
creator: Stefan Wiemann
creator: Susanna-Assunta Sansone
creator: Tanya Gray
creator: Tina Hernandez-Boussard
creator: Trish Whetzel
creator: Yongqun He
date: 2009-07-31
description: An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.
Format: OWL-DL
subject: An ontology for the annotation of biomedical and functional genomics experiments.
license: http://creativecommons.org/licenses/by/4.0/
comment: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
version info: 2025-01-09

C70958
term_mapping_to_UMLS: C2348583

bfo.owl
editor note: BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.
editor note: BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science.
editor note: BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that 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.
Contributor: Alan Ruttenberg
Contributor: Albert Goldfain
Contributor: Barry Smith
Contributor: Bill Duncan
Contributor: Bjoern Peters
Contributor: Chris Mungall
Contributor: David Osumi-Sutherland
Contributor: Fabian Neuhaus
Contributor: Holger Stenzhorn
Contributor: James A. Overton
Contributor: Janna Hastings
Contributor: Jie Zheng
Contributor: Jonathan Bona
Contributor: Larry Hunter
Contributor: Leonard Jacuzzo
Contributor: Ludger Jansen
Contributor: Mark Ressler
Contributor: Mathias Brochhausen
Contributor: Mauricio Almeida
Contributor: Melanie Courtot
Contributor: Pierre Grenon
Contributor: Randall Dipert
Contributor: Ron Rudnicki
Contributor: Selja Seppälä
Contributor: Stefan Schulz
Contributor: Thomas Bittner
Contributor: Werner Ceusters
Contributor: Yongqun "Oliver" He
license: http://creativecommons.org/licenses/by/4.0/
comment: Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.
comment: The BSD license on the BFO project site refers to code used to build BFO.
comment: This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.