Apollo Structured Vocabulary (Apollo-SV)
type: Ontology
version IRI: apollo sv.owl
contributor: Amanda Hicks
contributor: John Levander
contributor: Josh Hanna
contributor: Matt Diller
contributor: Mike Wagner
contributor: Shawn T. Brown
contributor: William R. Hogan
creator: Mathias Brochhausen
contributor: https://orcid.org/0000-0002-9881-1017
description: An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.
license: https://creativecommons.org/licenses/by/4.0/
comment: When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI).
version info: 2024-12-24

NLM ID
type: AnnotationProperty
alternative label: National Library of Medicine Identifier
comment: This identifier is the one that the National Library of Medicine uses to identify journals uniquely in PubMed.

ISSN Linking
type: AnnotationProperty
editor preferred term: linking ISSN
alternative label: International Standard Serial Number, Linking
comment: The linking ISSN is a single number assigned to all formats of a journal. The online and print versions of a journal, for example, are typically different. The linking ISSN refers to the journal regardless of format.

ISO Title Abbreviation
type: AnnotationProperty
alternative label: Iso Abbr
comment: ISO Abbreviations are constructed at NLM to assist NCBI in linking from GenBank to PubMed.

NLM Title Abbreviation
type: AnnotationProperty
comment: The abbreviated journal title assigned by the National Library of Medicine. Typically, it's the ISO title abbreviation without periods.

URI creation date
type: AnnotationProperty
definition: The date on which a URI annotated with this property was created.
definition editor: William R. Hogan
comment: This is the date that you created the URI that represents something, NOT the date that the thing referenced by the URI was created. For example, if you create a URI on 2014-09-24 to represent a book published on 1982-10-17, then this annotation property should have the value 2014-09-24. In other words, this annotation refers to the representation, not the represented thing. For the 1982-10-17 date, we suggest the dc:created annotation.

author list
type: AnnotationProperty
editor preferred term: author list
definition editor: William R. Hogan
comment: an annotation property for capturing the list of authors on the publication or other document to which the entity to which the annotation is attached refers. That is, this annotation should be attached only to individuals that represent information content entities, and its values must denote the people that authored the ICE.

source code repository URL
type: AnnotationProperty
editor preferred term: source code version control repository URL
definition editor: WIlliam R. Hogan
comment: This annotation is intended for annotating instances of software application, software module, ontology (artifact), etc. with a uniform resource locator that points to the source code version control repository where they are managed. Note that for OWL individuals that reference a particular version of the software or ontology, this URL should point to the place in the repository where that version is located, rather than the general main page of the repository.

human readable synopsis
type: AnnotationProperty
editor preferred term: human readable synopsis
definition: A comment that summarizes the most relevant or salient features and history of the entity for human readers.
definition editor: William R. Hogan
sub property of: comment

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

hasURL
type: AnnotationProperty
imported from: VIVO-ISF
comment: There are several URL and hasURL annotation properties out there in the ontology world. This one had the most sensible source ontology and OBO ID URI combination out there.

US State Two Digit Identifier
type: AnnotationProperty

US State Two Letter Abbreviation
type: AnnotationProperty

US State Ens Identifier
type: AnnotationProperty

UN Numerical Code
type: AnnotationProperty

ISO 3166-1-alpha-3 code
type: AnnotationProperty

ISO 3166-1-alpha-2 code
type: AnnotationProperty

Proposed Apollo Location Code
type: AnnotationProperty

ISO 3166-2 code
type: AnnotationProperty

geonameid
type: AnnotationProperty
editor preferred term: geonameid
comment: integer id of record in geonames database

admin1 code
type: AnnotationProperty
editor preferred term: geonames admin1 code
comment: fipscode (subject to change to iso code), see exceptions below, see file admin1Codes.txt for display names of this code; varchar(20)

admin2 code
type: AnnotationProperty
editor preferred term: geonames admin2 code
comment: code for the second administrative division, a county in the US, see file admin2Codes.txt; varchar(80)

admin3 code
type: AnnotationProperty
editor preferred term: geonames admin3 code
comment: code for third level administrative division, varchar(20)

admin4 code
type: AnnotationProperty
editor preferred term: geonames admin4 code
comment: code for fourth level administrative division, varchar(20)

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
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 label
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred term: example
editor preferred term: 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 term: 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 term: 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 term: definition
has curation status: ready for release
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>
label: textual definition

editor note
type: AnnotationProperty
editor preferred term: 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>

definition editor
type: AnnotationProperty
editor preferred term: 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 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 label
type: AnnotationProperty
editor preferred term: alternative label
editor preferred term: 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 term

definition source
type: AnnotationProperty
editor preferred term: 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 term: 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 term: 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

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

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

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

ISA alternative term
type: AnnotationProperty

NIAID GSCID-BRC alternative term
type: AnnotationProperty

logical characteristic of object property
type: AnnotationProperty
definition: This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.
definition source: OBO Operations call
created by: http://orcid.org/0000-0001-5208-3432

defined by construct
type: AnnotationProperty
example of usage: 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
definition: Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
term tracker item: https://github.com/ontodev/robot/issues/963
contributor: https://orcid.org/0000-0002-7356-1779
contributor: https://orcid.org/0000-0002-8688-6599

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.

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

STATO alternative term
type: AnnotationProperty
definition: an alternative term used for STATO statistical ontology and ISA team
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
sub property of: alternative label

external_definition
type: AnnotationProperty

homology_notes
type: AnnotationProperty

Unique Apollo Label
type: AnnotationProperty
definition: This annotation property gives the unique label of all Apollo_SV entities that are refered to in the schema. The UAL is the denotator for the Apollo_SV class in the schema. There can at all times only be ONE value of UAL for each class.
alternative label: UAL

has_rank
type: AnnotationProperty
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy
comment: This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored

eco subset
type: AnnotationProperty
sub property of: SubsetProperty

Creator
type: AnnotationProperty

Source
type: AnnotationProperty

dc:type
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
label: has broad synonym
sub property of: alternative label

database_cross_reference
type: AnnotationProperty

has_definition
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
label: has exact synonym
sub property of: alternative label

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
label: has narrow synonym
sub property of: alternative label

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
label: has related synonym
sub property of: alternative label

has_synonym_type
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

ontology IUI
type: AnnotationProperty
editor preferred term: ontology instance unique identifier

ontology version IUI
type: AnnotationProperty
editor preferred term: ontology version instance unique identifier

label
type: AnnotationProperty

basis of
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

obsolete is based on
type: ObjectProperty
sub property of: ObsoleteProperty
comment: p is based on e, if p is a purely intentional entity, e is an entity and p assumption/simulation that e exists regardless of the truth of this assumption.
deprecated: true

commissions
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: Class
  union of: Homo sapiens
  union of: organization
range: Class
  union of: independent continuant
  union of: process
  union of: information content entity
definition: a commissions b, iff a does not participate in the creation or execution of b and participates in a legal agreement that c participates on the creation or execution of b and c getting something in exchange for that participation.
elucidation: A relation between two entities where the first entity formally requests a third party to create or execute the second entity.
Unique Apollo Label: commissions

instantiates
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: entity
definition: A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times.
comment: Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.

simulates
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: simulation
range: entity
definition: a simulates b, iff a is a purely intentional entity that is representing a fictional individual or fact b and a participates in a simulating.

causally_precedes
type: ObjectProperty
sub property of: ObsoleteProperty
definition editor: Mathias Brochhausen
deprecated: true

obsoleted_administrated by
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

has basis in
type: ObjectProperty
domain: disposition
range: quality
editor preferred term: has basis in quality
definition: (Q is_a Quality ⋀ D is_a Disposition ⋀ Q base of D) ® ∀q (q instance_of Q ® b (q inheres_in b ⋀ d (d instance_of D ⋀ d inheres_in b)))
definition source: Representing dispositions Johannes Röhl and Ludger Jansen Journal of Biomedical Semantics 2011 2(Suppl 4):S4 DOI: 10.1186/2041-1480-2-S4-S4
comment: The relationship between a disposition and the quality that confers the disposition on the material entity in which they both inhere. For example, the disposition of a piece of glass to bend light and the lattice structure of the glass (quality) that results in the bending of the light.

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
type: ReflexiveProperty
editor preferred term: 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 label: part_of
temporal interpretation: axiom holds for all times
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable
RO_0040042: quality
RO_0040042: characteristic
RO_0040042: generically dependent continuant
database_cross_reference: BFO:0000050
has_obo_namespace: external
id: part_of
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: part_of
label: part_of

has part
type: ObjectProperty
sub property of: overlaps
sub property of: topObjectProperty
type: TransitiveProperty
type: ReflexiveProperty
editor preferred term: 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 label: has_part
temporal interpretation: axiom holds for all times
database_cross_reference: BFO:0000051
has_obo_namespace: external
id: has_part
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: has_part

is realized by
type: ObjectProperty
sub property of: topObjectProperty
inverse of: realizes
domain: realizable
range: process
TV pl: BFO_0000054
TV sg: BFO_0000054s
TV vbg: BFO_0000054ed
editor preferred term: obsolete_is_realized_by
editor preferred term: 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
has curation status: ready for release
definition: Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
editor note: replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungall
alternative label: executed_during
alternative label: has_realization
alternative label: is realized by
alternative label: is_realized_as
alternative label: realized by
alternative label: realized_by
alternative label: realized_in
has obsolescence reason: term imported
imported from: http://purl.obolibrary.org/obo/obi.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
label: realized in

realizes
type: ObjectProperty
domain: process
range: realizable
TV pl: BFO_0000055
TV sg: BFO_0000055s
TV vbg: BFO_0000055ed
editor preferred term: 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
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
sub property of: ends after
sub property of: topObjectProperty
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred term: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative label: is preceded by
alternative label: preceded_by
imported from: http://purl.obolibrary.org/obo/ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: eco subset

precedes
type: ObjectProperty
sub property of: temporal relation
sub property of: topObjectProperty
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
editor preferred term: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
imported from: http://purl.obolibrary.org/obo/ro.owl
in_subset: eco subset

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred term: 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 label: occurs_in
alternative label: unfolds in
alternative label: unfolds_in
imported from: http://purl.obolibrary.org/obo/ido.owl
imported from: http://purl.obolibrary.org/obo/obi.owl
database_cross_reference: BFO:0000066
has_obo_namespace: external
has_obo_namespace: relationship
id: occurs_in
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: occurs_in
comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
label: unfolds_in

contains process
type: ObjectProperty
sub property of: topObjectProperty
BFO OWL specification label: contains-process
BFO CLIF specification label: containsProcess
editor preferred term: 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
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 [XXX-001
imported from: http://purl.obolibrary.org/obo/bfo.owl
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 aggregate of
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is in aggregate
editor preferred term: is aggregate of
alternative label: aggregate of
alternative label: aggregate_of
imported from: http://purl.obolibrary.org/obo/obi.owl
imported from: http://purl.obolibrary.org/obo/omrse.owl

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

exists at
type: ObjectProperty

has continuant part at all times
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
TV pl: BFO_0000110
TV sg: BFO_0000110s
TV vbg: BFO_0000110ed
BFO OWL specification label: c-has-part_at
BFO CLIF specification label: hasContinuantPartAt
definition: [copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
definition: b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
editor note: [copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
imported from: http://purl.obolibrary.org/obo/bfo.owl
has associated axiom(fol): (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]

has proper continuant part at all times
type: ObjectProperty
sub property of: has continuant part at all times
type: TransitiveProperty
TV pl: BFO_0000111
TV sg: BFO_0000111s
TV vbg: BFO_0000111ed
BFO OWL specification label: c-has-ppart_at
BFO CLIF specification label: hasProperContinuantPartAt
definition: b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has proper continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has proper continuant part@en(x,y,t)'.
imported from: http://purl.obolibrary.org/obo/bfo.owl

has material basis at all times
type: ObjectProperty
sub property of: topObjectProperty
BFO OWL specification label: has-material-basis_at
BFO CLIF specification label: hasMaterialBasisAt
example of usage: the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract
example of usage: the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car.
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'.
imported from: http://purl.obolibrary.org/obo/bfo.owl
elucidation: b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002])
has associated axiom(fol): (forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002]

has occurrent part
type: ObjectProperty
sub property of: topObjectProperty
inverse of: part of occurrent
type: TransitiveProperty
TV pl: BFO_0000117
TV sg: BFO_0000117s
TV vbg: BFO_0000117ed
BFO OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
example of usage: [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
imported from: http://purl.obolibrary.org/obo/bfo.owl
elucidation: [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]

has proper occurrent part
type: ObjectProperty
sub property of: has occurrent part
type: TransitiveProperty
TV pl: BFO_0000118
TV sg: BFO_0000118s
TV vbg: BFO_0000118ed
BFO OWL specification label: o-has-ppart
BFO CLIF specification label: hasProperOccurrentPart
definition: [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
definition: b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
imported from: http://purl.obolibrary.org/obo/bfo.owl

has temporal part
type: ObjectProperty
sub property of: has occurrent part
BFO OWL specification label: has-t-part
example of usage: [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
example of usage: [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
example of usage: [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
definition: [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
imported from: http://purl.obolibrary.org/obo/bfo.owl

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

part of occurrent
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
TV pl: BFO_0000132
TV sg: BFO_0000132s
TV vbg: BFO_0000132ed
BFO OWL specification label: o-part-of
BFO CLIF specification label: occurrentPartOf
example of usage: Mary’s 5th birthday occurrent_part_of Mary’s life
example of usage: The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
example of usage: the first set of the tennis match occurrent_part_of the tennis match.
definition: [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
editor note: BFO2 Reference: occurrent
imported from: http://purl.obolibrary.org/obo/bfo.owl
elucidation: b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
has associated axiom(nl): occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
has associated axiom(nl): occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
has associated axiom(nl): occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
has associated axiom(nl): occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
has associated axiom(nl): occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
has associated axiom(fol): (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
has associated axiom(fol): (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
has associated axiom(fol): (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]

proper temporal part of
type: ObjectProperty
sub property of: proper part of occurrent
sub property of: temporal part of
BFO OWL specification label: t-ppart-of
BFO CLIF specification label: properTemporalPartOf
imported from: http://purl.obolibrary.org/obo/bfo.owl

proper part of continuant at all times
type: ObjectProperty
sub property of: part of continuant at all times
inverse of: has continuant part at all times that part exists
type: TransitiveProperty
BFO OWL specification label: c-ppart-of_at
BFO CLIF specification label: properContinuantPartOfAt
definition: b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'.
imported from: http://purl.obolibrary.org/obo/bfo.owl
has associated axiom(fol): (iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001]

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

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

occupies temporal region
type: ObjectProperty
sub property of: exists at
domain: occurrent
range: temporal region
BFO OWL specification label: spans
BFO CLIF specification label: occupiesTemporalRegion
imported from: http://purl.obolibrary.org/obo/bfo.owl
elucidation: p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])

has temporal occupant
type: ObjectProperty
sub property of: during which exists
sub property of: topObjectProperty
domain: temporal region
range: occurrent
BFO OWL specification label: span-of
BFO CLIF specification label: spanOf
imported from: http://purl.obolibrary.org/obo/bfo.owl
elucidation: [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])

during which exists
type: ObjectProperty

has participant at all times
type: ObjectProperty
TV pl: BFO_0000167
TV sg: BFO_0000167s
TV vbg: BFO_0000167ed

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

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

has proper temporal part
type: ObjectProperty
sub property of: has proper occurrent part
sub property of: has temporal part
BFO OWL specification label: has-t-ppart
imported from: http://purl.obolibrary.org/obo/bfo.owl

history of
type: ObjectProperty
sub property of: occurs in
domain: process
range: material entity

has history
type: ObjectProperty
domain: material entity
range: process

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

is in aggregate
type: ObjectProperty

is subordinate authority of
type: ObjectProperty
type: IrreflexiveProperty
domain: governmental organization
range: governmental organization
definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2.
comment: 'is subordinate authority of' Domain: governing organization Range: governing organization Formal properties: transitive, anti-symmetric, irreflexive Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2.

has jurisdiction in
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
domain: governmental organization
range: land mass
comment: It is not intended to be maximal, in the sense that if a has_jurisdiction_in b, and b is not part of c, then a NOT has_jurisdiction_in c. in other words, it is perfectly fine to say: a disjoint b c has_jurisdiction_in a c has_jurisdiction_in b otherwise, we'd end up creating some mereological sum of all the islands, contiguous land masses, etc. of the United States, calling it "United States territory", asserting United States has_jurisdiction_in United States territory, then figuring out all the parts of that territory like islands, etc. We'd end up doing the same thing for every sovereign state, major administrative subdivision (at least those like Hawaii that are multiple), etc. Seems like an unnecessary duplication of entities.
comment: a governmental organization has jurisdiction in particular territories (areas of land), which means that it can make and enforce laws that govern peoples living in those territories.
comment: if a has_jurisdiction_in b, then a has_jurisdiction_in all parts of b.

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label
editor preferred term: has measurement unit label
definition: A relation between a value specification and its unit of measurement.
imported from: http://purl.obolibrary.org/obo/obi.owl

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
sub property of: topObjectProperty
domain: information content entity
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.
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: http://purl.obolibrary.org/obo/iao.owl

mentions
type: ObjectProperty
sub property of: is about
inverse of: mentioned by
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

mentioned by
type: ObjectProperty
definition: Inverse of the relation 'mentions'
definition editor: http://orcid.org/0000-0002-8844-9165
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/250
date: 2022-01-28T07:20:08Z

denotes
type: ObjectProperty
sub property of: is about
inverse of: denoted by
domain: information content entity
range: entity
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

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

results_in
type: ObjectProperty

owns
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is owned by
type: AsymmetricProperty
definition editor: Mathias Brochhausen
elucidation: This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.

is owned by
type: ObjectProperty
type: AsymmetricProperty
definition: a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has_participant
domain: planned process
editor preferred term: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
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: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
editor preferred term: 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 editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: http://purl.obolibrary.org/obo/obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has_participant
sub property of: topObjectProperty
inverse of: is_specified_output_of
domain: planned process
editor preferred term: has_specified_output
has curation status: ready for release
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: obi.owl

OBI_0000308
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

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

achieves_planned_objective
type: ObjectProperty
sub property of: topObjectProperty
editor preferred term: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
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: http://purl.obolibrary.org/obo/obi.owl

has value specification
type: ObjectProperty
sub property of: topObjectProperty
editor preferred term: 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: http://purl.obolibrary.org/obo/obi.owl

obsolete owns
type: ObjectProperty
sub property of: ObsoleteProperty
sub property of: topObjectProperty
definition editor: Mathias Brochhausen
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
imported from: http://purl.obolibrary.org/obo/omrse.owl
elucidation: This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
term replaced by: owns
label: owns
deprecated: true

obsolete is owned by
type: ObjectProperty
sub property of: topObjectProperty
definition: a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
definition source: Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
definition source: Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204.
imported from: http://purl.obolibrary.org/obo/omrse.owl
term replaced by: is owned by
label: is owned by

is administered by
type: ObjectProperty
type: AsymmetricProperty

is enrolled in school
type: ObjectProperty
type: AsymmetricProperty
domain: Restriction
  on property: bearer of
  some values from: student role
range: school organization

is admitted to hospital
type: ObjectProperty
sub property of: topObjectProperty
domain: Restriction
  on property: bearer of
  some values from: patient role
range: hospital organization

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: bearer of
type: FunctionalProperty
editor preferred term: 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 label: inheres_in
temporal interpretation: axiom holds for all times
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
sub property of: topObjectProperty
type: InverseFunctionalProperty
range: characteristic
editor preferred term: 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 label: bearer of
alternative label: bearer_of
alternative label: is bearer of
imported from: http://purl.obolibrary.org/obo/omrse.owl
temporal interpretation: axiom holds for all times
label: bearer_of
label: has characteristic
label: is bearer of

participates in
type: ObjectProperty
sub property of: topObjectProperty
inverse of: has_participant
domain: continuant
range: occurrent
editor preferred term: 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 label: participates_in
imported from: http://purl.obolibrary.org/obo/obi.owl

has_participant
type: ObjectProperty
sub property of: topObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: characteristic of
editor preferred term: has participant
editor preferred term: 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 label: has_participant
imported from: http://purl.obolibrary.org/obo/obi.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
label: has participant

is concretized as
type: ObjectProperty
sub property of: topObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: characteristic
editor preferred term: is concretized as
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
imported from: http://purl.obolibrary.org/obo/obi.owl

concretizes
type: ObjectProperty
sub property of: topObjectProperty
domain: characteristic
range: generically dependent continuant
editor preferred term: concretizes
editor preferred term: is_concretization_of
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
imported from: http://purl.obolibrary.org/obo/obi.owl

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 label: function_of
alternative label: is function 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.

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 label: is quality of
alternative label: 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 label: is role of
alternative label: 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 label: has_function

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 label: has_quality

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 label: has_role

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
definition: inverse of has disposition
in_subset: RO_0002259
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
inverse of: derives into
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 label: derives_from

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 label: derives_into

location of
type: ObjectProperty
inverse of: located in
type: TransitiveProperty
editor preferred term: 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 label: location_of
temporal interpretation: axiom holds for all times

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
property chain axiom: part of
editor preferred term: 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 label: located_in
temporal interpretation: axiom holds for all times
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
in_subset: valid for go gp2term

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 label: 2D_boundary_of
alternative label: boundary of
alternative label: is 2D boundary of
alternative label: is boundary of
temporal interpretation: axiom holds for all times

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 label: has boundary
alternative label: has_2D_boundary
temporal interpretation: axiom holds for all times

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-05-24T09:49:21Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: https://orcid.org/0000-0002-7073-9172
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: https://orcid.org/0000-0002-7073-9172

during which ends
type: ObjectProperty
sub property of: temporal relation
inverse of: ends during
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
definition editor: David Osumi-Sutherland
in_subset: eco subset
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately_preceded_by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
definition: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
definition editor: David Osumi-Sutherland
alternative label: starts_at_end_of
imported from: http://purl.obolibrary.org/obo/uberon.owl
external_definition: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
database_cross_reference: RO:0002087
database_cross_reference: http://semanticscience.org/resource/SIO_000251
has_exact_synonym: directly preceded by
has_exact_synonym: is directly preceded by
has_exact_synonym: is immediately preceded by
has_exact_synonym: starts_at_end_of
has_obo_namespace: uberon
id: immediately_preceded_by
shorthand: immediately_preceded_by
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
label: immediately preceded by

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
definition editor: https://orcid.org/0000-0002-7073-9172
definition editor: David Osumi-Sutherland
alternative label: ends_at_start_of
alternative label: meets
RO_0002575: precedes
in_subset: eco subset
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
label: immediately_precedes

ends during
type: ObjectProperty
sub property of: temporal relation
definition editor: David Osumi-Sutherland
alternative label: o
alternative label: overlaps
database_cross_reference: RO:0002093
has_obo_namespace: external
id: ends_during
in_subset: eco subset
shorthand: ends_during
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
type: SymmetricProperty
property chain axiom: part of
property chain axiom: has part
has curation status: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: eco subset

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: topObjectProperty
has curation status: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
editor note: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
curator note: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
imported from: http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl
expand expression to: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
temporal interpretation: axiom holds for all times
in_subset: eco subset

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.
temporal interpretation: axiom holds for all times
in_subset: eco subset

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: ends with
property chain axiom: directly regulates
has curation status: pending final vetting
definition: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
definition: x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
definition editor: https://orcid.org/0000-0001-7476-6306
definition editor: https://orcid.org/0000-0002-3837-8864
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
definition editor: David Hill
definition editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
elucidation: false
database_cross_reference: RO:0002211
has_obo_namespace: external
id: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: regulates

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
sub property of: topObjectProperty
inverse of: negatively regulated by
property chain axiom: ends with
has curation status: pending final vetting
definition: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
definition: x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
definition source: causal-relations
imported from: http://purl.obolibrary.org/obo/ro.owl
OBO foundry unique label: negatively regulates (process to process)
RO_0004050: regulates
database_cross_reference: RO:0002212
has_obo_namespace: external
id: negatively_regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: negatively_regulates

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
definition: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
OBO foundry unique label: positively regulates (process to process)
RO_0004049: regulates
database_cross_reference: RO:0002213
has_obo_namespace: external
id: positively_regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
shorthand: positively_regulates

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in_subset: eco subset

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

obsolete 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: OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
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: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
alternative label: has agent
imported from: http://purl.obolibrary.org/obo/ro.owl
term replaced by: causal agent in process
in_subset: eco subset
label: has active participant
deprecated: true

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
domain: independent continuant
range: independent continuant
example of usage: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
has curation status: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
editor note: This relation acts as a join point with BSPO
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
imported from: http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl
temporal interpretation: axiom holds for all times
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

Axiom
annotated source: adjacent to
annotated property: example of usage
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

temporal relation
type: ObjectProperty
sub property of: topObjectProperty
domain: occurrent
range: occurrent
has curation status: pending final vetting
editor note: move to BFO?
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: Allen's interval algebra
definition source: Allen
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
imported from: http://purl.obolibrary.org/obo/obi.owl
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: eco subset
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
label: temporally related to

starts
type: ObjectProperty
sub property of: part of
sub property of: temporal relation
inverse of: starts with
has curation status: pending final vetting
definition: inverse of starts with
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
definition source: Allen
in_subset: eco subset

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporal relation
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: pending final vetting
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
alternative label: started by
imported from: http://purl.obolibrary.org/obo/obi.owl
in_subset: eco subset

ends
type: ObjectProperty
sub property of: part of
sub property of: temporal relation
inverse of: ends with
has curation status: pending final vetting
definition: inverse of ends with
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
Source: http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl
in_subset: eco subset

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporal relation
type: TransitiveProperty
has curation status: pending final vetting
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
alternative label: finished by
alternative label: finished with
Source: http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl
in_subset: eco subset

has start location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: starts with
property chain axiom: occurs in
has curation status: pending final vetting
definition: x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: starts with process that occurs in
in_subset: eco subset

has end location
type: ObjectProperty
sub property of: has part that occurs in
domain: process
range: independent continuant
property chain axiom: ends with
property chain axiom: occurs in
has curation status: pending final vetting
definition: x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: ends with process that occurs in
in_subset: eco subset

has input
type: ObjectProperty
sub property of: has_participant
inverse of: input of
domain: process
property chain axiom: starts with
has curation status: pending final vetting
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: consumes
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: eco subset

has output
type: ObjectProperty
sub property of: has_participant
inverse of: output of
property chain axiom: ends with
has curation status: pending final vetting
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
alternative label: produces
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: eco subset

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
example of usage: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in_subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
example of usage: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in_subset: valid for go gp2term

results in formation of
type: ObjectProperty
sub property of: results_in
example of usage: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
has curation status: pending final vetting
definition editor: Chris Mungall
definition source: GOC:mtg_berkeley_2013
shorthand: results_in_formation_of

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
definition: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
RO_0004049: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
definition: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO_0004050: causally upstream of
creator: https://orcid.org/0000-0002-6601-2165
in_subset: valid for go annotation extension
in_subset: valid for gocam

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: inheres in part of
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
temporal interpretation: axiom holds for all times

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
definition editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
temporal interpretation: axiom holds for all times

colocalizes with
type: ObjectProperty
sub property of: mereotopologically related to
sub property of: topObjectProperty
domain: material entity
range: material entity
example of usage: Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
definition source: http://www.geneontology.org/GO.annotation.conventions.shtml#colocalizes_with
curator note: In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
imported from: http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl
creator: Gene Ontology Consortium
in_subset: valid for go gp2term

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
example of usage: a particular instances of akt-2 enables some instance of protein kinase activity
definition: c enables p iff c is capable of p and c acts to execute p.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: catalyzes
alternative label: executes
alternative label: has
alternative label: is catalyzing
alternative label: is executing
curator note: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
in_subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
definition editor: https://orcid.org/0000-0002-6601-2165
curator note: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: actively involved in
alternative label: enables part of

enabled by
type: ObjectProperty
sub property of: has_participant
sub property of: functionally related to
definition: inverse of enables
definition editor: https://orcid.org/0000-0002-6601-2165
in_subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
definition editor: https://orcid.org/0000-0002-6601-2165
OBO foundry unique label: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
definition editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
definition editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259

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 label: is member of
alternative label: member part of
definition source: SIO
temporal interpretation: axiom holds for all times

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: axiom holds for all times

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
definition editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259
in_subset: eco subset

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has output
definition editor: https://orcid.org/0000-0002-6601-2165
in_subset: RO_0002259
in_subset: eco subset

spatially coextensive with
type: ObjectProperty
sub property of: overlaps
property chain axiom: located in
property chain axiom:
  inverse of: located in
example of usage: A lump of clay and a statue
definition: x spatially_coextensive_with y if and inly if x and y have the same location
definition editor: https://orcid.org/0000-0002-6601-2165
curator note: This relation is added for formal completeness. It is unlikely to be used in many practical scenarios

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
sub property of: causal relation between processes
inverse of: causally upstream of
has curation status: requires discussion
definition: inverse of upstream of
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
imported from: http://purl.obolibrary.org/obo/ro.owl

immediately causally downstream of
type: ObjectProperty
sub property of: immediately_preceded_by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: requires discussion
definition editor: https://orcid.org/0000-0002-6601-2165

indirectly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly positively regulates
property chain axiom: indirectly negatively regulates
definition: p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly activates
RO_0002579: positively regulates

indirectly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: indirectly regulates
type: TransitiveProperty
property chain axiom: directly negatively regulates
definition: p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: indirectly inhibits
RO_0002579: negatively regulates

causally related to
type: ObjectProperty
definition: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yie…
definition editor: https://orcid.org/0000-0002-6601-2165
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
sub property of: causal relation between processes
type: TransitiveProperty
has curation status: requires discussion
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
definition: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
imported from: http://purl.obolibrary.org/obo/ro.owl
in_subset: valid for go annotation extension
in_subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
definition: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
definition editor: https://orcid.org/0000-0002-6601-2165
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: influences (processual)
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
in_subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
definition editor: https://orcid.org/0000-0002-6601-2165

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
definition editor: https://orcid.org/0000-0002-6601-2165
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
definition editor: https://orcid.org/0000-0002-6601-2165
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
editor note: OWL does not allow defining object properties via a Union
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: involved in or reguates

is active in
type: ObjectProperty
sub property of: overlaps
sub property of: functionally related to
property chain axiom: enables
property chain axiom: occurs in
example of usage: A protein that enables activity in a cytosol.
definition: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: executes activity in
has_exact_synonym: enables activity in

Axiom
annotated source: is active in
annotated property: propertyChainAxiom
annotated target: enables
annotated target: occurs in
is a defining property chain axiom: true

Axiom
annotated source: is active in
annotated property: definition
annotated target: c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
database_cross_reference: https://orcid.org/0000-0002-6601-2165
database_cross_reference: https://orcid.org/0000-0002-7073-9172

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
editor note: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
editor note: Considering relabeling as 'pairwise interacts with'
definition editor: https://orcid.org/0000-0002-6601-2165
curator note: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has_exact_synonym: in pairwise interaction with
in_subset: eco subset

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: binds
alternative label: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
editor note: Axiomatization to GO to be added later
definition editor: https://orcid.org/0000-0002-6601-2165
alternative label: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: https://orcid.org/0000-0003-4639-4431
has_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly inhibits
has_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: https://orcid.org/0000-0003-4639-4431
alternative label: directly activates
has_exact_synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
definition editor: https://orcid.org/0000-0002-6601-2165
curator note: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

has part that occurs in
type: ObjectProperty
domain: occurrent
range: independent continuant
property chain axiom: has part
property chain axiom: occurs in
definition: p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
definition editor: https://orcid.org/0000-0002-6601-2165
in_subset: eco subset

Axiom
annotated source: has part that occurs in
annotated property: propertyChainAxiom
annotated target: has part
annotated target: occurs in
is a defining property chain axiom: true

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
definition editor: https://orcid.org/0000-0002-6601-2165

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
definition source: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
sub property of: topObjectProperty
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: http://purl.obolibrary.org/obo/ro.owl

depends on
type: ObjectProperty
definition editor: https://orcid.org/0000-0002-6601-2165

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
editor note: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
OBO foundry unique label: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
definition editor: https://orcid.org/0000-0002-6601-2165

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
definition editor: https://orcid.org/0000-0002-6601-2165

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
definition editor: https://orcid.org/0000-0002-6601-2165
definition editor: https://orcid.org/0000-0003-4639-4431
definition source: causal-relations
OBO foundry unique label: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations
OBO foundry unique label: directly regulates (processual)
RO_0002575: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
example of usage: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
definition editor: https://orcid.org/0000-0002-6601-2165

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
editor note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
example of usage: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
definition source: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
definition source: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
example of usage: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
definition source: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
definition source: causal-relations

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
definition source: causal-relations
OBO foundry unique label: directly positively regulates (process to process)
RO_0004049: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
definition source: causal-relations
OBO foundry unique label: directly negatively regulates (process to process)
RO_0004050: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

produces
type: ObjectProperty
inverse of: produced by
domain: material entity
range: material entity
property chain axiom:
  inverse of: occurs in
property chain axiom: has output
has curation status: pending final vetting
definition: a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
definition editor: https://orcid.org/0000-0001-9114-8737
in_subset: eco subset
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.

produced by
type: ObjectProperty
domain: material entity
range: material entity
has curation status: pending final vetting
definition: a produced_by b iff some process that occurs_in b has_output a.
definition editor: https://orcid.org/0000-0001-9114-8737
in_subset: eco subset

realized in response to stimulus
type: ObjectProperty
sub property of: causally related to
domain: realizable
range: material entity
property chain axiom: realized in response to
property chain axiom: has input
definition: A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2017-12-26T19:45:49Z

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:30Z
in_subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:49:51Z
in_subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:14Z
in_subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-01-26T23:53:22Z
in_subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: https://orcid.org/0000-0002-6601-2165
creation date: 2018-03-13T23:55:19Z

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

realized in response to
type: ObjectProperty
sub property of: causally related to
domain: realizable
range: process
property chain axiom: is realized by
property chain axiom: causally downstream of
example of usage: A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
example of usage: An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
example of usage: Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
definition: r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
contributor: https://orcid.org/0000-0001-6996-0040
contributor: https://orcid.org/0000-0002-6601-2165
contributor: https://orcid.org/0000-0002-7073-9172
contributor: https://orcid.org/0000-0002-8461-9745
has_exact_synonym: triggered by process

Axiom
annotated source: realized in response to
annotated property: has_exact_synonym
annotated target: triggered by process
database_cross_reference: https://orcid.org/0000-0002-6601-2165

generically depends on
type: ObjectProperty
inverse of: is carrier of
domain: generically dependent continuant
range: independent continuant
property chain axiom: characteristic of
property chain axiom: is concretized as
example of usage: Genetic information generically depend on molecules of DNA.
example of usage: The novel *War and Peace* generically depends on this copy of the novel.
example of usage: The pattern shared by chess boards generically depends on any chess board.
example of usage: The score of a symphony g-depends on a copy of the score.
example of usage: This pdf file generically depends on this server.
definition: A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
definition source: [072-ISO]
has_exact_synonym: g-depends on

is carrier of
type: ObjectProperty
domain: independent continuant
range: generically dependent continuant
property chain axiom: concretizes
property chain axiom: bearer of
example of usage: Molecules of DNA are carriers of genetic information.
example of usage: This copy of *War and Peace* is carrier of the novel written by Tolstoy.
example of usage: This hard drive is carrier of these data items.
definition: *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
definition source: [072-ISO]

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
definition editor: https://orcid.org/0000-0003-4639-4431

indirectly causally upstream of
type: ObjectProperty
sub property of: causally upstream of
definition: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:07:17Z

indirectly regulates
type: ObjectProperty
sub property of: regulates
sub property of: indirectly causally upstream of
definition: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
created by: https://orcid.org/0000-0003-1813-6857
creation date: 2022-09-26T06:08:01Z

device utilizes material
type: ObjectProperty
property chain axiom: capable of
property chain axiom: has input
example of usage: A diagnostic testing device utilizes a specimen.
definition: X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
curator note: A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
curator note: See github ticket https://github.com/oborel/obo-relations/issues/497
contributor: https://orcid.org/0000-0001-9625-1899
contributor: https://orcid.org/0000-0003-2620-0345
creation date: 2021-11-08T12:00:00Z
has_broad_synonym: utilizes

regulates characteristic
type: ObjectProperty
sub property of: causally related to
domain: process
range: quality
property chain axiom: regulates
definition: A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

positively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

negatively regulates characteristic
type: ObjectProperty
sub property of: regulates characteristic
property chain axiom: negatively regulates
property chain axiom: positively regulates characteristic
property chain axiom: positively regulates
definition: A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
contributor: https://orcid.org/0000-0002-8688-6599

obsolete has_disposition
type: ObjectProperty
sub property of: ObsoleteProperty
imported from: http://purl.obolibrary.org/obo/ido.owl
has_obo_namespace: relationship
deprecated: true

negatively_regulates
type: ObjectProperty
sub property of: ObsoleteProperty
imported from: http://purl.obolibrary.org/obo/ido.owl
has_obo_namespace: relationship
deprecated: true

obsolete_realized_by
type: ObjectProperty
sub property of: ObsoleteProperty
imported from: http://purl.obolibrary.org/obo/ido.owl
has_alternative_id: OBO_REL:0000035
has_alternative_id: OBO_REL:realized_as
has_obo_namespace: relationship
comment: NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
deprecated: true

regulates
type: ObjectProperty
sub property of: ObsoleteProperty
imported from: http://purl.obolibrary.org/obo/ido.owl
has_obo_namespace: relationship
deprecated: true

ObsoleteProperty
type: ObjectProperty

bearer of
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

obsolete has proper part
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

inheres in
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

location of
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

proper part of
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

topObjectProperty
type: ObjectProperty
definition: a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
comment: A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl

is expressed as
type: DatatypeProperty
domain: generically dependent continuant

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
definition: A relation between a scalar measurement data item and a number that quantifies it.
editor note: The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now.
imported from: http://purl.obolibrary.org/obo/obi.owl

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

Aedes albopictus
type: Class
subclass of: Stegomyia
alternative label: Stegomyia albopicta
alternative label: forest day mosquito

purely intentional entity
type: Class
subclass of: generically dependent continuant
definition: A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content.
elucidation: A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content.
Source: Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen.
Source: Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen.
Source: Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen.
Source: Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87
Source: Thomasson AL. "Ingarden and the Ontology of Cultural Objects." In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136.
comment: MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'.

epidemic model
type: Class
subclass of: disease transmission model
definition: A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic.
definition editor: William Hogan and Michael Wagner
elucidation: An algorithm the concretizations of which models the transmission of transmissible disease.

basic reproduction number
type: Class
subclass of: Class
  intersection of: reproduction number
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: infection acquisition
      intersection of: Restriction
        on property: has_participant
        some values from: Class
definition: The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population.
definition editor: William R. Hogan
elucidation: The number of organisms that each infected organism infects in a completely susceptible population during its infectious period.
Unique Apollo Label: basicReproductionNumbers
comment: MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to.

population immunity survey
type: Class
subclass of: population survey
definition: A population survey that assesses the level of immunity against a particular pathogen in a specified population.
definition editor: Mathias Brochhausen
elucidation: A population survey that assesses the level of immunity against a particular pathogen in a specified population.
comment: Comment from Mike (to do!): I checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.

simulating of process of type X
type: Class
subclass of: planned process
definition: a planned process that (1) has at least one process part that has as participants representations of participants (in place of those participants) of processes of type X, and where all such process parts substitute for parts of processes of type X, and (2) is carried out for the purpose of planning for processes of type X, learning more about processes of type X, or teaching about processes of type X.
elucidation: A process that replaces the essential participants of another type of process with representations of those participants.
Unique Apollo Label: simulating of process of type X
comment: For example, in a simulated volcano eruption, representations of lava, lava tubes, vents, etc. take the place of actual lava, lava tubes, vents, etc. Even in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones.

simulation requester identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: Class
      intersection of: Class
        union of: Homo sapiens
        union of: organization
      intersection of: Restriction
        on property: commissions
        some values from: simulating of process of type X
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: Class
      union of: Homo sapiens
      union of: organization
    intersection of: Restriction
      on property: commissions
      some values from: simulating of process of type X
definition: An identifier that refers to the legal person that commissions a simulation process.
elucidation: An identifier that refers to the person or organization who is requesting one or more executions of the simulator software.
comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.

simulation software application
type: Class
subclass of: software application
definition: A software application that provides a model of a real phenomenon based on a set of mathematical formulas.
definition source: http://en.wikipedia.org/wiki/Simulation_software
elucidation: A software application that provides a model of a real phenomenon based on a set of mathematical formulas.
Unique Apollo Label: simulator

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
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: software
    union of: source code module
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.

simulator developer identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: Class
      intersection of: Class
        union of: Homo sapiens
        union of: organization
      intersection of: Restriction
        on property: participates in
        some values from: Class
subclass of: software developer identifier
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: Class
      union of: Homo sapiens
      union of: organization
    intersection of: Restriction
      on property: participates in
      some values from: Class
        intersection of: software development
        intersection of: Restriction
definition: An identifier that refers to the legal person that creates and maintains a simulator.
elucidation: An identifier that refers to the person or organization who is responsible for the simulator. It is intended to uniquely identify a person or organization. That said, we do not plan to control the namespace for simulator developer at this point in development. We will add our ideas about alternatives at a future date.

simulator identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: simulation software application
subclass of: software identifier
subclass of: Restriction
  on property: part of
  some values from: complete simulator identifier
subclass of: Restriction
  on property: denotes
  some values from: simulation software application
definition: An identifier that refers to all version of a specific simulator.
elucidation: An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer.

control strategy reactive start time information
type: Class
definition: A control strategy start time information item that is based on a condition that triggers the control strategy.
definition editor: Mathias Brochhausen
elucidation: A control strategy start time information item that is based on a condition that triggers the control strategy.
deprecated: true

simulation time step value
type: Class
subclass of: numeral
definition: A numeral that is part of a simulation time step action specification.
elucidation: A number of time step units in a time step of a simulation. For example, if the time step is 6 hours, then this value is 6.
Unique Apollo Label: numberOfUnitsOfTimeInOneSimulatorStep

simulator version identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: part of
  some values from: complete simulator identifier
definition: An identifier that, as part of a complete simulator identifier, refers to one specific version of a simulator software.
elucidation: An identifier that refers to a unique version of a simulator. Simulator version distinguishes, for example, version “2.0” from “2.0.b”

simulation time step unit
type: Class
subclass of: time unit
definition: A time unit that is part of a simulation time step action specification.
elucidation: A unit of time for each time step of a simulation, such as “hours” or “days”.
Unique Apollo Label: unitOfTimeForSimulatorTimeStep

simulation run length
type: Class
subclass of: epidemic simulator action specification
subclass of: Restriction
  on property: has part
  some values from: simulation time step action specification
definition: The action specification that specifies the number of time steps a simulation is going to run.
elucidation: The number of time steps in a simulator run. For example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.
Unique Apollo Label: runLength

infectious period duration
type: Class
subclass of: duration
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: one-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: infectious period
definition: A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts.
definition editor: Mathias Brochhausen
elucidation: A period when an individual of a particular species, who is infected with a particular pathogen, is able to infect susceptible organisms of a particular species. Note that the susceptible and infectious organisms can be of different species.
Unique Apollo Label: infectiousPeriodDuration
comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs.

latent period duration
type: Class
subclass of: duration
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: one-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: latent period
definition: A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts.
definition editor: Mathias Brochhausen
elucidation: A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species. Note that the susceptible and infected organisms can be of different species.
Unique Apollo Label: latentPeriodDuration
comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs
comment: The duration of the period between when an organism becomes infected and when it becomes infectious.

count of simulated susceptible population
type: Class
subclass of: population count
definition editor: Mathias Brochhausen

count of simulated exposed population
type: Class
subclass of: population count
definition editor: Mathias Brochhausen

count of simulated contagious population
type: Class
subclass of: population count
definition editor: Mathias Brochhausen

count of simulated resistant population
type: Class
subclass of: population count
definition editor: Mathias Brochhausen

count of simulated population
type: Class
subclass of: Class
  intersection of: population count
  intersection of: Restriction
    on property: is about
    some values from: simulated population
definition: The count of (simulated organisms) in a simulated population.
definition editor: Mathias Brochhausen
elucidation: The number of simulated organisms in a simulated population. The number does not have to be an integer.
comment: MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’

vaccination dose schedule
type: Class
subclass of: control strategy dose schedule
definition: An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent.
elucidation: A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism.

vaccination compliance
type: Class
subclass of: calculated datum
definition: The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination.
elucidation: The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint.
comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
comment: MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy” and “control measure efficacy delay.” We could then post-coordinate particular control measures such as vaccine. It is worth noting that there are control measures such as closing schools that are not applied at the individual level. We have not represented those control measures yet.

vaccination efficacy
type: Class
subclass of: infectious disease treatment efficacy
definition: The infectious disease treatment efficacy of a vaccine.
elucidation: The degree to which a particular vaccination reduces the probability that a vaccinated individual will have a particular vaccination preventable outcome.
Unique Apollo Label: vaccinationEfficacies
comment: Notes: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’ 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer
comment: need to generate class restriction. Something like: 'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance')) we'd also like to say that the protective resistance disposition began to exist during the process. can't recall whether we should use process or processual_entity for future BFO compatibility.

facility survey
type: Class
subclass of: planned process
definition: A planned process involving counting numbers of facilities in a specific region.
elucidation: A planned process involving counting numbers of facilities in a specific region.

school facility census
type: Class
equivalent class: Class
  intersection of: census
  intersection of: Restriction
    on property: is about
    some values from: school facility
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: facility survey
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: facility survey
subclass of: census
subclass of: Restriction
  on property: is about
  some values from: school facility
subclass of: Restriction
  on property: is_specified_output_of
  some values from: facility survey
definition editor: Mathias Brochhausen
comment: Motivating use case is Synthia synthetic population data.

infectious disease control strategy 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: Class
        intersection of: plan specification
        intersection of: Restriction
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: has part
        some values from: infectious disease control objective specification
definition: A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.
elucidation: A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease.

hospital patient population
type: Class
equivalent class: Class
  intersection of: collection of humans
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: bearer of
        some values from: patient role
      intersection of: Restriction
        on property: is admitted to hospital
        qualified cardinality: 1
        on class: hospital organization
subclass of: collection of humans
definition editor: Mathias Brochhausen
comment: Key motivating use case was Synthia synthetic population data.

simulated population
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: simulates
    some values from: PCO:collection of organisms
  intersection of: Restriction
    on property: participates in
    some values from: simulating of process of type X
subclass of: simulation
subclass of: Restriction
  on property: simulates
  some values from: PCO:collection of organisms
subclass of: Restriction
  on property: participates in
  some values from: simulating of process of type X
definition: A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval.
definition editor: Mathias Brochhausen
elucidation: A simulated population is a set of simulated organisms. The set can be null (e.g., the set of 200 year-old H. sapiens). A simulated population can include more than one species, in which case it may be convenient to define each species as a simulated population and form the overall simulated population by set union. Similarly, it may be convenient to define sociodemographic or geographic strata within a simulated population as simulated populations and obtain the overall simulated population by set union. See examples in “Programmer’s Guide, page x)
Unique Apollo Label: simulatorReferencablePopulation

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
subclass of: Restriction
  on property: is_specified_output_of
  some values from: counting
definition: A measurement datum that is the output of counting.
definition editor: Mathias Brochhausen
elucidation: A measurement datum that is the output of counting.
Unique Apollo Label: count

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
subclass of: Restriction
  on property: has_specified_output
  some values from: count
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.

simulation of organism
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: simulation
    intersection of: Restriction
      on property: simulates
      some values from: organism
  intersection of: Restriction
    on property: participates in
    some values from: simulating of process of type X
subclass of: simulation
subclass of: Restriction
  on property: simulates
  some values from: organism
subclass of: Restriction
  on property: participates in
  some values from: simulating of process of type X
comment: a simulation that is about an organism

normal distribution
type: Class
subclass of: continuous parametric probability distribution
definition: A continuous parametric probability distribution that is uniform; centered around the mean, parameter μ​; and whose spread of standard deviations, parameter σ​, adheres to the empirical rule.
elucidation: A continuous probability distribution in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation
Unique Apollo Label: NormalDistribution

simulation of exposed organism
type: Class
subclass of: simulation of organism
definition: A simulation of an infectious agent host that is not contagious and is part of a simulated population.
elucidation: A simulated organism in a simulated population that has acquired a particular simulated disease but is not yet able to transmit the disease to another simulated organism.

simulated population location identifier
type: Class
subclass of: identifier
definition: An identifier that refers to a geographical location to be used as location of a population in a simulation.
definition editor: Mathias Brochhausen
elucidation: An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes.

simulation of infectious organism
type: Class
subclass of: simulation of organism
definition: A simulation of an infectious organism host that is contagious.
elucidation: A simulated organism in a simulated population that has acquired a particular simulated disease and is able to transmit the disease to another simulated organism.

simulation of recovered organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: simulates
    some values from: Class
      intersection of: organism
      intersection of: Class
        complement of: Restriction
  intersection of: Restriction
    on property: participates in
    some values from: simulating of process of type X
subclass of: simulation of organism
subclass of: Restriction
  on property: simulates
  some values from: Class
    intersection of: organism
    intersection of: Class
      complement of: Restriction
        on property: bearer of
        some values from: susceptibility
definition: A simulated organism in a simulated population that is not susceptible.
elucidation: A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. Note that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.

simulation of disease
type: Class
subclass of: simulation
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: identifier
    intersection of: Restriction
      on property: denotes
      some values from: disease
definition: A representation of a disposition realized in a represented disease course that at least part of the simulated population is represented as participating in.
definition editor: Mathias Brochhausen
elucidation: The disease being simulated.
Unique Apollo Label: disease

reproduction number
type: Class
subclass of: Class
  intersection of: average value
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: infection acquisition
      intersection of: Restriction
        on property: has_participant
        some values from: Class
definition: The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection.
definition editor: Mathias Brochhausen
elucidation: The number of susceptible organisms that each infected organism infects. ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation.
Unique Apollo Label: ReproductionNumber

nursery school student population
type: Class
equivalent class: Class
  intersection of: collection of humans
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: bearer of
        some values from: student role
      intersection of: Restriction
        on property: is enrolled in school
        qualified cardinality: 1
        on class: Class
subclass of: school student population
definition editor: Mathias Brochhausen
comment: Key motivating use case was Synthia synthetic population data.

obsolete asymptomatic infection fraction
type: Class
subclass of: Obsolete Class
definition: The fraction given to express the probability that an organism will become infected, but stay asymptomatic.
elucidation: The fraction of infectious individuals who do not develop symptoms during the course of their infections.
Unique Apollo Label: asymptomatic infection fraction
deprecated: true

vaccine supply schedule
type: Class
subclass of: individual treatment control strategy action specification
definition: An action specification giving the number of doses of vaccine to be made available over a specific time period.
elucidation: The counts of vaccine doses that become available in a specific population location during (at the start of would be unambiguous) each simulator time step.

vaccination administration capacity
type: Class
subclass of: individual treatment control strategy action specification
definition: An action specification giving the number of vaccinations possible in a population during a specific time interval.
elucidation: The counts of individuals that could be vaccinated in a population location per time step unit in the absence of any vaccine supply constraints. It represents the capacity of medical system to vaccinate individuals.

antiviral treatment efficacy
type: Class
subclass of: infectious disease treatment efficacy
definition: The infectious disease treatment efficacy of an antiviral drug.
elucidation: The degree to which a particular antiviral drug reduces the probability that a treated individual will have a particular preventable outcome. Preventable outcomes include but are not limited to infection, infectiousness, symptoms, and hospitalization.
Unique Apollo Label: AntiviralTreatmentEfficacy
comment: MB: For DL reasons the easiest way to formalize the definition was to assume only organism that are either host or not immune undergo antiviral treatment. Is that adequate? I assume this'll create problems…

antiviral efficacy delay
type: Class
subclass of: duration
definition: The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role.
elucidation: The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection.

antiviral compliance
type: Class
subclass of: calculated datum
definition: The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible.
elucidation: The fraction of individuals in a simulated population that will accept antiviral treatment if offered.
Unique Apollo Label: antiviral cm compliance
comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
comment: MW: Since the estimates that modelers use are from real populations, I have two questions: 1. Should we distinguish between real and simulated population? 2. If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population? MB: This issue will need to be taken care of in the axiomatization of simulated population

antiviral supply schedule
type: Class
subclass of: individual treatment control strategy action specification
definition: An action specification giving the number of doses of an antiviral to be made available during a specific time interval.
elucidation: Counts of antiviral doses that become available in a specific location per time step unit.

antiviral administration schedule
type: Class
subclass of: individual treatment control strategy action specification
definition: An action specification that tells the total number of antiviral doses available to be administered to a population during a specific time interval.
elucidation: Counts of antiviral doses that can be administered in a specific location per time step unit.

simulation of organism awaiting control measure
type: Class
subclass of: simulation of organism
disjoint with: simulation of organism not awaiting control measure
definition: A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure.
elucidation: A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure.
comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
comment: This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date.

complete simulator identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: epidemic model
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: epidemic model
definition: An identifier that refers to a specific simulator.
definition editor: Mathias Brochhausen
elucidation: The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results.
comment: MB: I am not 100% happy with the elucidation. Can't we just say that this is the full identifier identifying the simulator with both its name and its version number?

epidemic simulating
type: Class
subclass of: Class
  intersection of: simulating of process of type X
  intersection of: Restriction
    on property: has_participant
    some values from: epidemic model
definition: A simulating of a disease epidemic or pandemic.
definition editor: Mathias Brochhausen
elucidation: the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS.
Unique Apollo Label: epidemic simulation

hospital patient population census
type: Class
equivalent class: Class
  intersection of: population census
  intersection of: Restriction
    on property: is about
    some values from: hospital patient population
subclass of: population census
subclass of: Restriction
  on property: is about
  some values from: hospital patient population
definition editor: Mathias Brochhausen
comment: Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast).

simulation of organism not awaiting control measure
type: Class
subclass of: Class
  intersection of: simulation of organism
  intersection of: Class
    complement of: Restriction
      on property: participates in
      some values from: infectious disease control strategy execution
definition: A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure.
elucidation: A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure.
comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
comment: This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date.

simulation of organism awaiting effect of control measure
type: Class
subclass of: simulation of organism
definition: A simulated organism that participates in a particular control measure that has not yet been effective.
elucidation: This concept represents a simulated organism that has received a control measure such as vaccination in which a period of time must elapse before the benefit of the control measure accrues. A simulated organism is ‘awaiting efficacy’ if ‘efficacy delay’ (e.g. the concept ‘antiviral efficacy delay’ for the particular simulated control measure is greater than the elapsed time between application of the control measure and the current simulated time.

simulation of antiviral control measure
type: Class
subclass of: simulation
definition: The simulation of an antiviral control measure.
elucidation: A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism.
Unique Apollo Label: antiviral control measure
comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI). AND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess. Maybe we need to discuss this.

simulation of vaccination control measure
type: Class
subclass of: simulation
definition: A simulation of a vaccination control measure.
elucidation: A type of control measure that uses vaccination to create immunity in simulated organisms to specific pathogens.
Unique Apollo Label: simulation of vaccination control measure

primary school student population
type: Class
equivalent class: Class
  intersection of: collection of humans
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: bearer of
        some values from: student role
      intersection of: Restriction
        on property: is enrolled in school
        qualified cardinality: 1
        on class: Class
subclass of: school student population
comment: Key motivating use case was Synthia synthetic population data.

simulation of control measure participant
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: simulates
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: infectious disease control strategy execution
  intersection of: Restriction
    on property: participates in
    some values from: simulating of process of type X
subclass of: simulation of organism
subclass of: Restriction
  on property: simulates
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: infectious disease control strategy execution
definition: A simulation of an organism in a simulated population that has participated in an epidemic control measure.
elucidation: A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment)

simulation time series
type: Class
subclass of: time sampled measurement data set
definition: A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation.
elucidation: A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation.
comment: MB: The ontological status of simulations (Thoughts) One property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating. While in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.

simulation identifier numeral
type: Class
equivalent class: Class
  intersection of: numeral
  intersection of: Restriction
    on property: denotes
    some values from: simulating of process of type X
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: identifier creating process
subclass of: numeral
subclass of: Restriction
  on property: denotes
  some values from: simulating of process of type X
definition: A numeral that indexes a specific simulation.
elucidation: The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures. The simulator is responsible for generating a run id and ensuring its uniqueness.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

simulation of time step
type: Class
subclass of: simulation
subclass of: Class
  intersection of: Class
    intersection of: simulation
    intersection of: Restriction
      on property: simulates
      some values from: one-dimensional temporal region
  intersection of: Restriction
    on property: participates in
    all values from: simulating of process of type X
definition: A purely intentional entity that simulates a temporal interval of pre-specified length.
elucidation: A purely intentional entity that simulates a temporal interval of pre-specified length.
Unique Apollo Label: simulation time step

simulation time step action specification
type: Class
subclass of: epidemic simulator action specification
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: simulation software application
  intersection of: Restriction
    on property: is about
    some values from: simulation of time step
  intersection of: Restriction
    on property: has value specification
    some values from: scalar value specification
definition: An action specification that specifies the length of the time steps interval assumed in a simulation.
definition editor: Mathias Brochhausen
elucidation: An action specification that specifies the length of the time steps interval assumed in a simulation.
comment: simulation time step value simulation time step unit simulation run length The time step value and unit are specified using a scalar value specification.

time step identifying numeral
type: Class
equivalent class: Class
  intersection of: numeral
  intersection of: Restriction
    on property: denotes
    some values from: simulation of time step
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: identifier creating process
subclass of: numeral
subclass of: Restriction
  on property: denotes
  some values from: simulation of time step
definition: A numeral that indexes a specific time step of a simulation.
elucidation: The time step number of a simulation.
Unique Apollo Label: simulatorTime

simulation
type: Class
equivalent class: Class
  intersection of: purely intentional entity
  intersection of: Restriction
    on property: simulates
    some values from: entity
subclass of: purely intentional entity
subclass of: Restriction
  on property: simulates
  some values from: entity
definition: A purely intentional entity that simulates an entity and its properties.
elucidation: A purely intentional entity that simulates an entity and its properties.
Unique Apollo Label: simulation

obsolete simulation of population location
type: Class
subclass of: Obsolete Class
definition: The simulation of geographical location in which a population is assumed to be located.
elucidation: An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes.
Unique Apollo Label: simulated population location
deprecated: true

simulation of susceptible organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: simulates
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: susceptibility
  intersection of: Restriction
    on property: participates in
    some values from: simulating of process of type X
subclass of: simulation of organism
subclass of: Restriction
  on property: simulates
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: bearer of
      some values from: susceptibility
definition: A simulation of a susceptible organism in a simulated population.
elucidation: A simulated organism in a simulated population that is capable of acquiring a particular simulated disease.

simulation of symptomatic organism
type: Class
subclass of: simulation of organism
definition: A simulation of a symptomatic infectious agent host.
elucidation: A simulated organism in a simulated population that has at least one symptom caused by a particular simulated disease.

simulation of asymptomatic organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: simulates
    some values from: asymptomatic host
  intersection of: Restriction
    on property: participates in
    some values from: simulating of process of type X
subclass of: simulation of organism
subclass of: Restriction
  on property: simulates
  some values from: asymptomatic host
definition: A simulation of an asymptomatic infectious agent host.
elucidation: A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease.

infectious disease control objective specification
type: Class
subclass of: objective specification
definition: An objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population.
elucidation: an objective of achieving satisfactory control of epidemic spread through a population
comment: typically, the process endpoint is achievement of R0 < 1

μ
type: Class
subclass of: Obsolete Class
elucidation: the mean or expectation of a distribution
Unique Apollo Label: μ
deprecated: true

σ
type: Class
subclass of: Obsolete Class
elucidation: standard deviation
Unique Apollo Label: sigma
deprecated: true

beta distribution
type: Class
subclass of: continuous parametric probability distribution
elucidation: A continuous probability distribution whose characteristics and shape are determined by two parameters, alpha and beta.
Unique Apollo Label: beta distribution

deprecated log normal distribution
type: Class
subclass of: Obsolete Class
elucidation: a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm
deprecated: true

uniform distribution
type: Class
subclass of: continuous parametric probability distribution
elucidation: A continous probability distribution whose parameters a and b, denote its minimum and maximum values
Unique Apollo Label: UniformDistribution

triangular distribution
type: Class
subclass of: continuous parametric probability distribution
elucidation: a continuous probability distribution with lower limit a, upper limit b and mode c, where a < b and a <= c <= b.
Unique Apollo Label: triangular distribution

Bayesian network
type: Class
subclass of: joint probability distribution
elucidation: a discrete probability distribution
Unique Apollo Label: BayesianNetwork

temporal Bayesian network
type: Class
subclass of: TODO
elucidation: a discrete probability distribution that conditions on time
Unique Apollo Label: temporal Bayesian network

control strategy dose schedule
type: Class
subclass of: individual treatment control strategy action specification
subclass of: Restriction
  on property: part of
  some values from: infectious disease control strategy
definition: An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism.
elucidation: A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism.

age data in age brackets data set
type: Class
subclass of: data set
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: Class
editor preferred term: age structure data set
definition: A data set consisting of measurements of age organized in age brackets.
elucidation: A data set consisting of measurements of age organized in age brackets.

infectious disease control strategy
type: Class
equivalent class: Class
  intersection of: plan specification
  intersection of: Restriction
    on property: has part
    some values from: infectious disease control objective specification
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: infectious disease control objective specification
definition: A plan specification whose objective specification is an infectious disease control objective specification.
elucidation: A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens.
Unique Apollo Label: InfectiousDiseaseControlMeasure
comment: The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population.

count of susceptible population
type: Class
subclass of: population count
definition: The count of individuals in a susceptible population (empirical or virtual).
elucidation: The count of individuals in a susceptible population (empirical or virtual).

count of contacted population
type: Class
subclass of: population count
definition: The count of individuals in an exposed population (empirical or virtual).
elucidation: The count of individuals in an exposed population (empirical or virtual).

measured vaccination efficacy
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: vaccination efficacy
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: PCO:collection of organisms
      intersection of: Restriction
        on property: has member
        all values from: Class
definition: A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study.
elucidation: A vaccination efficacy that results from a vaccination efficacy study.
Unique Apollo Label: VaccinationEfficacyMeasured
comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’ 2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.

vaccination efficacy study design execution
type: Class
equivalent class: Class
  intersection of: study design execution
  intersection of: Restriction
    on property: has part
    some values from: vaccination
  intersection of: Restriction
    on property: has_specified_output
    some values from: measured vaccination efficacy
subclass of: study design execution
subclass of: Restriction
  on property: has part
  some values from: vaccination
subclass of: Restriction
  on property: has_specified_output
  some values from: measured vaccination efficacy
definition: a study design execution that has as its specified output one or more measured vaccination efficacy data items
elucidation: an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals
Unique Apollo Label: VaccinationEfficacyStudy

obsolete immune
type: Class
subclass of: Obsolete Class
elucidation: an organism that has the property of being immune to a specific disease agent
Unique Apollo Label: immune
deprecated: true

95% confidence interval
type: Class
subclass of: TODO
elucidation: a type of interval estimate of a population parameter used to indicate the reliability of an estimate. How frequently the observed interval contains the parameter is determined by the confidence level or confidence coefficient, in this type the confidence level is 95%
Unique Apollo Label: 95% confidence interval

Bayesian credible interval
type: Class
subclass of: TODO
elucidation: a type of interval estimate of a population parameter that has the property that the true value of the estimated populatin parameter has a (specified) particular probability of being in the confidence interval given the data on which the estimate is derived.
Unique Apollo Label: Baysesian credible interval

community
type: Class
subclass of: object_aggregate
subclass of: Class
  intersection of: object_aggregate
  intersection of: Restriction
    on property: has member
    some values from: population
  intersection of: Restriction
    on property: has member
    all values from: population
definition: Two or more distinct populations that are part of the same biotic ecosystem.
elucidation: Two or more distinct populations that are part of the same biotic ecosystem.
Unique Apollo Label: community
creator: William R. Hogan

deprecated discrete probability distribution
type: Class
subclass of: Obsolete Class
elucidation: a probability distribution over a discrete random variable
Unique Apollo Label: discrete probability distribution
deprecated: true

obsolete unit of measure
type: Class
elucidation: The increments of measurement for a measurable thing
deprecated: true

ecosystem
type: Class
subclass of: material entity
definition: The sum of all biotic and abiotic entities in a geographical region.
elucidation: The sum of all biotic and abiotic entities in a geographical region.
Unique Apollo Label: Ecosystem
creator: William R. Hogan

count of contagious population
type: Class
subclass of: population count
definition: The count of individuals in a contagious population (empirical or virtual).
elucidation: The count of individuals in a contagious population (empirical or virtual).

count of resistant population
type: Class
subclass of: population count
definition: The count of individuals in a resistant population (empirical or virtual).
elucidation: The count of individuals in a resistant population (empirical or virtual).

abiotic ecosystem
type: Class
subclass of: material entity
definition: The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms.
elucidation: The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms.
Unique Apollo Label: AbioticEcosystem
creator: William R. Hogan

fixed control strategy start time specification
type: Class
subclass of: infectious disease control strategy action specification
definition: An action specification that is part of a simulation software and specifies the time step numeral identifying the time step after which a simulation of a control strategy starts.
elucidation: The number of time steps after which a control strategy starts in a simulator.
Unique Apollo Label: FixedStartTime

control strategy reactive endpoint fraction
type: Class
subclass of: rule
subclass of: Restriction
  on property: part of
  some values from: infectious disease control strategy
definition: A rule that is part of an infectious disease control strategy specification and specifies at which fraction of a population a control strategy is to be discontinued.
elucidation: A fraction of a population that is targeted for treatment at which the control strategy is discontinued. The concept derives from the epidemiological notion of ‘herd immunity,’ which is a level of immunity in a population at which there are not enough susceptible individuals for a contagious disease to maintain the chain reaction. Technically, it is when the effective reproduction rate <= 1, which means that infectious individuals at most infect one person during the course of their illness.
Unique Apollo Label: controlStrategyReactiveEndpointFraction

biotic ecosystem
type: Class
subclass of: material entity
definition: The biotic ecosystem is the sum total of all organism populations in a particular geographical region.
elucidation: The biotic ecosystem is the sum total of all organism populations in a particular geographical region.
Unique Apollo Label: BioticEcosystem
creator: William R. Hogan

software developer identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: Class
      intersection of: Class
        union of: Homo sapiens
        union of: organization
      intersection of: Restriction
        on property: participates in
        some values from: software development
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: Class
      union of: Homo sapiens
      union of: organization
    intersection of: Restriction
      on property: participates in
      some values from: software development
definition: An identifier that refers to the legal person that creates and maintains software.
elucidation: An identifier that refers to the legal person that creates and maintains software.
Unique Apollo Label: softwareDeveloper

complete software identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    qualified cardinality: 1
    on class: software application
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: software application
definition: An identifier that refers to a specific piece of software.
elucidation: An identifier that refers to a specific piece of software.
Unique Apollo Label: SoftwareIdentification

atmosphere
type: Class
subclass of: fiat object
definition: a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force
elucidation: a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force
creator: William R. Hogan
comment: atmosphere of Earth, Earth's moon, Saturn, Titan, etc.
comment: outer, gaseous layers of exoplanets are called extraterrestrial atmosphere.

software version identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: part of
  some values from: complete software identifier
definition: An identifier that, as part of a complete software identifier, refers to one specific version of the software.
elucidation: An identifier that, as part of a complete software identifier, refers to one specific version of the software.
Unique Apollo Label: softwareVersion

software identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: software
subclass of: identifier
subclass of: Restriction
  on property: part of
  some values from: complete software identifier
subclass of: Restriction
  on property: denotes
  some values from: software
definition: An identifier that refers to all version of a specific software.
elucidation: An identifier that refers to all version of a specific software.
Unique Apollo Label: softwareName

atmosphere of geographical region
type: Class
equivalent class: Class
  intersection of: geographical feature
  intersection of: Restriction
    on property: part of
    has value: atmosphere of the Earth
subclass of: geographical feature

obsolete educational institution
type: Class
subclass of: Obsolete Class
definition: An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities.
definition source: http://en.wikipedia.org/wiki/Types_of_educational_institutions (amended)
elucidation: An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities.
deprecated: true

school closure target facilities
type: Class
subclass of: information content entity
subclass of: Class
  intersection of: Class
    intersection of: Restriction
      on property: part of
      some values from: school closure control strategy
    intersection of: Restriction
      on property: part of
      some values from: action specification
  intersection of: Restriction
    on property: is about
    some values from: school organization
definition: An information content entity about educational institutions that is part of the action sepcification of a school closure control measure.
elucidation: The specification of which facilities to target in a school closure control measure.

infection
type: Class
equivalent class: Class
  intersection of: reproduction
  intersection of: Restriction
    on property: occurs in
    some values from: Class
      intersection of: tissue
      intersection of: Restriction
        on property: part of
        some values from: organism
subclass of: reproduction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: tissue
    intersection of: Restriction
      on property: part of
      some values from: organism
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: infection acquisition
definition: A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon.
definition editor: William R. Hogan
alternative label: infection process
alternative label: process of infection
elucidation: A process of reproduction of a particular pathogen species inside some tissue of a particular host species.
creator: M. Brochhausen
comment: infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon.

infection acquisition
type: Class
equivalent class: Class
  intersection of: entry into host
  intersection of: Restriction
    on property: occurs in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: susceptibility
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      union of: contaminated thing
      union of: Class
        intersection of: host organism
        intersection of: Restriction
  intersection of: Restriction
    on property: causally upstream of
    some values from: infection
subclass of: entry into host
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: bearer of
      some values from: susceptibility
subclass of: Restriction
  on property: has_participant
  some values from: Class
    union of: contaminated thing
    union of: Class
      intersection of: host organism
      intersection of: Restriction
        on property: bearer of
        some values from: contagiousness
subclass of: Restriction
  on property: causally upstream of
  some values from: infection
definition: The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources
definition editor: Mathias Brochhausen
elucidation: A process where a susceptible organism from a particular species becomes infected by a particular pathogen. The infection is acquired from an infected organism of a particular species or from a contaminated thing. Note that the susceptible and infectious organisms can be of different species.
Unique Apollo Label: InfectionAcquisition
comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things. The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. An infection is acquired from an infectious organism or a contaminated thing.
comment: Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing

vaccine identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: material entity
definition: An identifier that refers to a type of vaccine, i.e., one of a class of manufactured vaccines that public health would consider interchangable.
elucidation: A unique identifier for a vaccine.
Unique Apollo Label: vaccineOntologyId

latent period
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: temporal part of
    some values from: infection
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: host organism
      intersection of: Class
        complement of: Restriction
subclass of: process
subclass of: Restriction
  on property: temporal part of
  some values from: infection
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: host organism
    intersection of: Class
      complement of: Restriction
        on property: bearer of
        some values from: contagiousness
definition editor: Mathias Brochhausen

vaccination identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: directive information entity
definition: a unique identifier that refers to a protocol for vaccinating one person
elucidation: A unique identifier for a vaccination protocol (the process of vaccinating one person)

vaccination course
type: Class
subclass of: individual treatment control strategy action specification
elucidation: the number of doses of vaccine that are recommended to achieve immunity

species
type: Class
subclass of: TODO
elucidation: an interbreeding population
Unique Apollo Label: species

antiviral identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: material entity
definition: a unique identifier that refers to an antiviral drug product
elucidation: A unique identifier for an antiviral drug
Unique Apollo Label: antiviralId

school closure control strategy
type: Class
subclass of: place closure control strategy
definition: A place closure control strategy whose action specification is realized in a school closure process.
elucidation: A control measure in which schools are closed in an attempt to reduce transmission of disease.
Unique Apollo Label: SchoolClosureControlStrategy

school closure duration
type: Class
subclass of: infectious disease control strategy action specification
elucidation: The number of time steps that a school closure control measure prescribes that schools will remain closed.
Unique Apollo Label: school closure duration

school calendar
type: Class
elucidation: The time steps that a school will be in session.
deprecated: true

control strategy target facilities
type: Class
subclass of: facility
elucidation: Faciilities that are the target of a control strategy
Unique Apollo Label: control strategy target facilities

control strategy target populations and prioritization
type: Class
subclass of: TODO
elucidation: A simulated population that is the target of a control strategy and its priority under triage conditions
Unique Apollo Label: ControlMeasureTargetPopulationsAndPrioritization

control strategy target population fraction
type: Class
subclass of: infectious disease control objective specification
elucidation: Fraction of organisms in a target population that a control strategy program seeks to enroll or prioritize
comment: a specification of a population that a control strategy applies to. It is intended to apply to a real population, so I don’t know whether you would consider it a simulated thing. I don’t.

obsolete Reactive control measure
type: Class
subclass of: Obsolete Class
definition: an epidemic control measure plan specification that has a conditional specification as part
elucidation: a control measure (program) that is initiated or modified by an epidemic-related event (or if you prefer, an event occurring within/during the simulation)
Unique Apollo Label: Reactive control measure
deprecated: true

reactive control strategy test
type: Class
subclass of: conditional specification
elucidation: An event in the ecosystem that triggers the starting or stopping of a control strategy.
Unique Apollo Label: reactiveControlMeasureTest

reactive control strategy threshold
type: Class
subclass of: data item
definition: A data item that specifies the fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy.
elucidation: A fraction of the population known to have undergone a specific event that results in starting or stopping an infectious disease control strategy. The event could be infection acquisition, vaccination, antiviral treatment, etc.
Unique Apollo Label: reactiveControlMeasureThreshold

secondary school student population
type: Class
equivalent class: Class
  intersection of: collection of humans
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: bearer of
        some values from: student role
      intersection of: Restriction
        on property: is enrolled in school
        qualified cardinality: 1
        on class: Class
subclass of: school student population
comment: Key motivating use case was Synthia synthetic population data.

control strategy response delay
type: Class
subclass of: measurement datum
definition: A measurement datum of the time interval from the decision to implement an infectious disease control strategy to the start of the control strategy expressed in number of time intervals.
elucidation: A period from the initiation of a control strategy until its disease-controlling actions actually begin. For example, once a vaccination control strategy starts, individual vaccinations may not occur right away: it might take some time until workers and vaccines are deployed and ready to begin.
Unique Apollo Label: controlMeasureResponseDelay

ascertainment delay
type: Class
subclass of: directive information entity
elucidation: Number of time steps it takes medical personnel to ascertain a symptomatic individual from onset of symptoms
comment: per Mike Wagner, this is input

ascertainment fraction
type: Class
subclass of: data item
elucidation: Fraction of all symptomatic individuals who will be ascertained
Unique Apollo Label: fractionInState
comment: fraction of organisms (usually infected) that a surveillance system detects out of the total population

vaccination control strategy
type: Class
subclass of: individual treatment control strategy
definition: An individual treatment control strategy that has as part an action specification that is realized in a vaccination process.
elucidation: An individual treatment control strategy that administers one or more vaccines to individuals in a population with the goal of inducing resistance to infection with a particular pathogen in those individuals.

vaccine valence
type: Class
subclass of: count
elucidation: the number of distinct antigenic strains in a vaccine product
Unique Apollo Label: valence

antiviral course
type: Class
subclass of: individual treatment control strategy action specification
definition: An action specification that tells how many doses of antiviral drug should be given to each individual that participates in the antiviral control measure.
elucidation: The quantity of antiviral drug used to treat one individual

control strategy compliance
type: Class
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: population
      intersection of: Restriction
        on property: participates in
        some values from: infectious disease control strategy execution
definition: A measurement datum about the fraction of individuals in a population that elect to participate in a control strategy when offered.
elucidation: A fraction of eligible individuals in a population who receive an intervention or participate in a control strategy.
Unique Apollo Label: compliance
comment: the class restriction can be made more precise AH
comment: the fraction of some population that is targeted for a control strategy that accepts it. It can obviously also be interpreted as a probability that the average individual in the targeted population accepts/complies with the control strategy. It is not simulated

infectious period
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: temporal part of
    some values from: infection
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: host organism
      intersection of: Restriction
        on property: bearer of
        some values from: contagiousness
  intersection of: Restriction
    on property: immediately_preceded_by
    some values from: latent period
subclass of: process
subclass of: Restriction
  on property: temporal part of
  some values from: infection
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: host organism
    intersection of: Restriction
      on property: bearer of
      some values from: contagiousness
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: latent period
definition editor: Mathias Brochhausen

protect against effect of pathogen
type: Class
subclass of: objective specification
definition editor: Mathias Brochhausen

vaccination
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: Class
        intersection of: plan specification
        intersection of: Restriction
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: bearer of
        some values from: vaccine function
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: susceptibility
subclass of: treatment
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: has part
        some values from: protect against effect of pathogen
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: bearer of
      some values from: vaccine function
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: bearer of
      some values from: susceptibility
definition: A treatment that consists of the administration of antigenic material to stimulate an individual's immune system to develop adaptive immunity to a pathogen.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Vaccination
elucidation: A treatment of an individual with antigenic material from a pathogen that has the goal of inducing resistance of the individual to infection with the pathogen.
Unique Apollo Label: Vaccination

vaccine disposition
type: Class
definition editor: Mathias Brochhausen
comment: replaced with VO 'vaccine function'
deprecated: true

disposition to become contaminated with a pathogen
type: Class
equivalent class: Class
  intersection of: disposition
  intersection of: Class
    intersection of: Restriction
      on property: characteristic of
      some values from: material entity
    intersection of: Restriction
      on property: is realized by
      all values from: contamination acquisition
subclass of: disposition
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
definition editor: Mathias Brochhausen

resistance to infection
type: Class
subclass of: disposition
definition: The dispostion of an organism of a particular biological taxon A that is realized by inhibiting the establishment of an infection by an organism of another particular biological taxon that bears an infectious disposition towards members of A
definition editor: Mathias Brochhausen @de
definition editor: William R. Hogan
curator note: Key issue with equivalent class axiom is how to say that this scattered molecular aggregate is both 1) not originally part of the organism and/or 2) is temporary. I suppose baby could be born with drug acquired from its mother's system. Somehow, it's not innate and it's temporary, ie, the body will eventually clear it.
elucidation: The dispostion of an organism of a particular biological taxon A that is realized by inhibiting the establishment of an infection by an organism of another particular biological taxon that bears an infectious disposition towards members of A

beta
type: Class
elucidation: Transmission parameter (sometime known as Ptrans). This value is multiplied by the inter-personal contact probability to determine the transmission probability between infected and susceptible persons.
comment: it is the same thing as transmission coefficient
deprecated: true

inter-personal contact probability
type: Class
subclass of: TODO
elucidation: Transmission parameter
Unique Apollo Label: inter-personal contact probability

random number seed
type: Class
elucidation: random number seed
deprecated: true

susceptibility measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: susceptibility
elucidation: A number between 0 and 1 indicating the degree of susceptibility of an organism

vaccination reactive end point fraction
type: Class
subclass of: control strategy reactive endpoint fraction
elucidation: a fraction of the target population, that once vaccinated, results in stopping further vaccination in the population

immune resistance to infection
type: Class
equivalent class: Class
  intersection of: resistance to infection
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: Restriction
        on property: has_participant
        some values from: immune system
      intersection of: Restriction
        on property: negatively regulates
        some values from: Restriction
subclass of: resistance to infection
definition: Resistance to infection that is conferred by immune system/immune mechansisms.
definition editor: Mathias Brochhausen
elucidation: Resistance to infection that is conferred by immune system/immune mechansisms.

population survey
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: counting
      intersection of: Restriction
        on property: has_specified_output
        some values from: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: counting
    intersection of: Restriction
      on property: has_specified_output
      some values from: Class
        intersection of: count
        intersection of: Restriction
definition: A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria, and that realizes some concretization of a census objective specification.
definition editor: Mathias Brochhausen
elucidation: A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria.

population census
type: Class
equivalent class: Class
  intersection of: census
  intersection of: Restriction
    on property: is about
    some values from: population
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: population survey
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: population survey
subclass of: census
subclass of: Restriction
  on property: is about
  some values from: population
subclass of: Restriction
  on property: is_specified_output_of
  some values from: population survey
definition: A census that is the outcome of a population survey.
elucidation: A census that is the outcome of a population survey.

exposed population
type: Class
equivalent class: Class
  intersection of: host population
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: host organism
      intersection of: Class
        complement of: Restriction
subclass of: host population
definition: A population of host organisms undergoing infection and that are not infectious.
elucidation: A population of host organisms undergoing infection and that are not infectious.
Unique Apollo Label: exposed population

population infection survey
type: Class
equivalent class: Class
  intersection of: population survey
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: counting
      intersection of: Restriction
        on property: has_specified_output
        some values from: Class
      intersection of: Restriction
        on property: has_specified_output
        some values from: Class
subclass of: population survey
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: counting
    intersection of: Restriction
      on property: has_specified_output
      some values from: Class
        intersection of: count
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_output
      some values from: Class
        intersection of: count
        intersection of: Restriction
definition: A population survey that counts the number of individuals in the population who are infected with a particular pathogen.
definition editor: Mathias Brochhausen
elucidation: A population survey that counts the number of individuals in the population who are infected with a particular pathogen.
Unique Apollo Label: PopulationInfectionSurvey
comment: Comment from Mike (to do!): I checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.
comment: Equivalent class was: 'population survey' and (has_part some (counting and (has_specified_output some (count and ('is about' some 'exposed population'))) and (has_specified_output some (count and ('is about' some 'infectious population'))) and (has_specified_output some (count and ('is about' some 'susceptible population'))) and (has_specified_output some (count and ('is about' some 'immune population')))))

contagious population
type: Class
subclass of: host population
definition: A population of host organisms undergoing infection that are contagious.
elucidation: A population of host organisms undergoing infection that are contagious.

population infection and immunity census
type: Class
equivalent class: Class
  intersection of: census
  intersection of: Class
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: population immunity survey
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: population infection survey
  intersection of: Class
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: population immunity survey
    intersection of: Restriction
      on property: is_specified_output_of
      all values from: population infection survey
subclass of: census
subclass of: Restriction
  on property: is_specified_output_of
  some values from: population immunity survey
subclass of: Restriction
  on property: is_specified_output_of
  some values from: population infection survey
definition: A census that is the result of a population infection survey and a population immunity survey.
definition editor: Mathias Brochhausen
alternative label: PII Census
elucidation: A census of the infection status (e.g., susceptible, infected, infectious, and immune/resistant) of organisms in a population, with respect to a particular pathogen.
Unique Apollo Label: PopulationInfectionAndImmunityCensus

population demographic survey
type: Class
subclass of: population survey

population demographic census
type: Class
equivalent class: Class
  intersection of: census
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: population demographic survey
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: population demographic survey
subclass of: census
subclass of: Restriction
  on property: is_specified_output_of
  some values from: population demographic survey
definition: A census that is the specific outcome of a population demographic survey.
definition editor: Mathias Brochhausen
elucidation: A census that is the specific outcome of a population demographic survey.

obsolete contamination
type: Class
subclass of: Obsolete Class
definition editor: Mathias Brochhausen
deprecated: true

MIDAS scenario
type: Class
definition: An ecosystem in which a population of hosts is undergoing at least one infection.
definition editor: Mathias Brochhausen
elucidation: An ecosystem in which a population of hosts is undergoing at least one infection.
deprecated: true

MIDAS scenario representation
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: ecosystem
      intersection of: Restriction
        on property: has proper continuant part at all times
        some values from: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: ecosystem
    intersection of: Restriction
      on property: has proper continuant part at all times
      some values from: Class
        intersection of: biotic ecosystem
        intersection of: Restriction
definition: An information content entity that is about a MIDAS scenario and contains population disease census data.
definition editor: Mathias Brochhausen
elucidation: An information content entity that is about a MIDAS scenario and contains population disease census data.
comment: need to change the text definition. need to change label to be more consistent with current Apollo terminology (possibly 'infectious disease scenario'.

recovered population
type: Class
subclass of: host population
definition editor: A population of organisms that have been infected, but are no longer able to transmit the disease and to acquire the infection again.
definition editor: Mathias Brochhausen

agent-level ecosystem data generation
type: Class
subclass of: dataset creating
editor preferred term: synthetic ecosystem constructing
definition: A planned process that has one or more synthetic ecosystem datasets as output.
definition editor: Mathias Brochhausen
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: creating a synthetic ecosystem dataset
alternative label: synthetic ecosystem generating
elucidation: A planned process that has one or more synthetic ecosystem datasets as output.

agent-level ecosystem census
type: Class
equivalent class: Class
  intersection of: census
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: agent-level ecosystem data generation
      intersection of: Restriction
        on property: has_specified_input
        some values from: population census
subclass of: census
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: agent-level ecosystem data generation
    intersection of: Restriction
      on property: has_specified_input
      some values from: population census
definition: A census that is the specified output of a agent-level ecosystem data generation that had census data as an input.
definition editor: Mathias Brochhausen
elucidation: A census that is the specified output of a agent-level ecosystem data generation that had census data as an input.

contaminated thing
type: Class
equivalent class: Class
  intersection of: independent continuant
  intersection of: Restriction
    on property: location of
    some values from: Class
      intersection of: pathogen
      intersection of: Class
        complement of: Restriction
subclass of: independent continuant
subclass of: Restriction
  on property: location of
  some values from: Class
    intersection of: pathogen
    intersection of: Class
      complement of: Restriction
        on property: participates in
        some values from: infection
definition: An independent continuant that is the localization of a pathogen, but is not undergoing an infection.
definition editor: Mathias Brochhausen
elucidation: An independent continuant that is the localization of a pathogen, but is not undergoing an infection.
Unique Apollo Label: ContaminatedThing
comment: A contaminated thing is an entity that contains a pathogen (either internal to itself or on its surface) that is not undergoing an infection.

contamination acquisition
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: has input
    some values from: pathogen
  intersection of: Restriction
    on property: has input
    some values from: Class
      complement of: contaminated thing
  intersection of: Restriction
    on property: has output
    some values from: contaminated thing
subclass of: contamination
subclass of: entry into host
subclass of: Restriction
  on property: has input
  some values from: pathogen
subclass of: Restriction
  on property: has input
  some values from: Class
    complement of: contaminated thing
subclass of: Restriction
  on property: has output
  some values from: contaminated thing
definition: A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan
elucidation: A biological process whereby an entity that is not in contact with a pathogen of a particular biological taxon begins to undergo contamination with that pathogen.
Unique Apollo Label: ContaminationAcquisition

nursery school student population census
type: Class
equivalent class: Class
  intersection of: school student population census
  intersection of: Restriction
    on property: is about
    some values from: nursery school student population
subclass of: school student population census
subclass of: Restriction
  on property: is about
  some values from: nursery school student population
comment: Motivating use case is Synthia synthetic population data.

primary school student population census
type: Class
equivalent class: Class
  intersection of: school student population census
  intersection of: Restriction
    on property: is about
    some values from: primary school student population
subclass of: school student population census
subclass of: Restriction
  on property: is about
  some values from: primary school student population
comment: Motivating use case is Synthia synthetic population data.

secondary school student population census
type: Class
equivalent class: Class
  intersection of: school student population census
  intersection of: Restriction
    on property: is about
    some values from: secondary school student population
subclass of: school student population census
subclass of: Restriction
  on property: is about
  some values from: secondary school student population
comment: Motivating use case is Synthia synthetic population data.

antiviral treatment
type: Class
equivalent class: Class
  intersection of: drug treatment
  intersection of: Restriction
    on property: has_specified_input
    some values from: antiviral drug
subclass of: drug treatment
subclass of: Restriction
  on property: has_specified_input
  some values from: antiviral drug
definition: A treatment with an antiviral drug.
elucidation: A treatment of a particular host with a particular antiviral drug with activity against a particular viral pathogen.
Unique Apollo Label: AntiviralTreatment

susceptibility
type: Class
equivalent class: Class
  intersection of: disposition
  intersection of: Restriction
    on property: is realized by
    all values from: infection acquisition
  intersection of: Restriction
    on property: characteristic of
    all values from: Class
      intersection of: organism
      intersection of: Class
        complement of: host organism
subclass of: disposition
definition: The ability to participate in infection acquisition as a host.
definition editor: Mathias Brochhausen
elucidation: The ability to participate in infection acquisition as a host.

census
type: Class
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: Class
definition: A data set of a specific entity in a specified region at a specified time.
definition editor: Mathias Brochhausen
elucidation: A data set of a specific entity in a specified region at a specified time.
Unique Apollo Label: CensusData

disease transmission model
type: Class
subclass of: algorithm
definition: An algorithm that models the progress of a transmissible disease in a population.
elucidation: An algorithm that models the progress of a transmissible disease in a population.
Unique Apollo Label: disease transmission model

obsolete school organization
type: Class
subclass of: Obsolete Class
definition: An organization created with the purpose of providing education to those of its members that are bearer of student role.
definition editor: Mathias Brochhausen
elucidation: An organization created with the purpose of providing education to those of its members that are bearer of student role.
deprecated: true

school student population census
type: Class
equivalent class: Class
  intersection of: population census
  intersection of: Restriction
    on property: is about
    some values from: school student population
subclass of: population census
subclass of: Restriction
  on property: is about
  some values from: school student population
definition editor: Mathias Brochhausen
comment: Motivating use case is Synthia synthetic population data.

school student population
type: Class
equivalent class: Class
  intersection of: collection of humans
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: Homo sapiens
      intersection of: Restriction
        on property: bearer of
        some values from: student role
      intersection of: Restriction
        on property: is enrolled in school
        qualified cardinality: 1
        on class: school organization
subclass of: collection of humans
definition: The collection of students administrated by exaclty one school organization.
definition editor: Mathias Brochhausen
elucidation: The collection of students administrated by exaclty one school organization.
comment: Key motivating use case was Synthia synthetic population data.

simulator configuration
type: Class
subclass of: epidemic simulator action specification
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is about
    some values from: ecosystem
definition: An information content entity that contains everything a simulator needs to run, including the representation of a scenario.
elucidation: An information content entity that contains everything a simulator needs to run, including the representation of a scenario.
Unique Apollo Label: simulatorConfiguration

obsolete student role
type: Class
subclass of: Obsolete Class
definition: A human social role that is realized by attending a school to receive formal education.
definition editor: Mathias Brochhausen
elucidation: A human social role that is realized by attending a school to receive formal education.
deprecated: true

antiviral control strategy
type: Class
subclass of: anti-infective individual treatment control strategy
definition: An anti-infective individual treatment control strategy that has as part an action specification that is realized in antiviral treatment.
definition editor: Mathias Brochhausen
elucidation: An anti-infective individual treatment control strategy that uses anti-viral medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period.

contagiousness
type: Class
subclass of: disposition

simulator time specification
type: Class
subclass of: epidemic simulator action specification
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: simulation run length
  intersection of: Restriction
    on property: has part
    some values from: simulation time step action specification
definition: An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).
elucidation: An information content entity that specifies the length in time of a single simulator step (e.g., 1 day) and the requested run length of the simulation (number of steps).
Unique Apollo Label: SimulatorTimeSpecification

infectious disease scenario
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: ecosystem
definition: A dataset that represents at least one pathogen population (of a particular biological taxon) in one host population (of a particular biological taxon) in an ecosystem in a particular location at a particular point in time.
definition editor: William R. Hogan
elucidation: Data about an infection in an ecosystem at a specific location and point in time.
Unique Apollo Label: InfectiousDiseaseScenario
comment: An infectious disease scenario contains counts of infections of a particular pathogen in a particular host in a particular ecosystem at a particular point in time, minimally. Agent-based ecosystems represent each host individually. The infectious disease scenario typically also includes a lot of additional data about the ecosystem, including data about things like transmission probabililites, control measures, the immunity or other resistance status of host individuals, and so on.

scenario date
type: Class
subclass of: identifier
definition: An identifier that denotes a real date corresponding to simulator time zero.
elucidation: A reference to the date that corresponds to simulator time zero.
Unique Apollo Label: scenarioDate

contamination
type: Class
equivalent class: Class
  union of: Class
    intersection of: reproduction
    intersection of: Restriction
      on property: has_participant
      some values from: pathogen
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: material entity
        intersection of: Class
  union of: Class
    intersection of: biological_process
    intersection of: Restriction
      on property: has_participant
      some values from: pathogen
    intersection of: Restriction
      on property: has_participant
      some values from: material entity
subclass of: biological_process
editor preferred term: biological contamination
definition: The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism.
definition editor: William R. Hogan
elucidation: The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism.
Unique Apollo Label: Contamination
comment: the preferred term is biological contamination to distinguish from things like radiological contamination, contamination of the Gulf of Mexico with oil, the contamination of air with pollution, etc.

population treatment census
type: Class
subclass of: census
definition: A census about a particular medical treatment of a population.
elucidation: A census of a population that determines for a particular treatment whether each organism in the population has undergone that treatment.
Unique Apollo Label: PopulationTreatmentCensus

population and environment census
type: Class
subclass of: census
definition: A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.
elucidation: A census that represents the biotic and abiotic elements of an ecosystem at simulator time zero.
comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.
comment: This census should exclude infection, immunity, treatment, or contamination.

control strategy inventory census
type: Class
subclass of: census
definition: A census that is the outcome of assessing control-strategy-related facilities and supply chains.
elucidation: A census that is the outcome of assessing control-strategy-related facilities and supply chains.

contagious organism
type: Class
equivalent class: Class
  intersection of: host organism
  intersection of: Restriction
    on property: bearer of
    some values from: contagiousness
subclass of: host organism
subclass of: Restriction
  on property: bearer of
  some values from: contagiousness
definition: A host who is able to transmit some infection to another organism.
elucidation: An infected organism of a particular species who is able to transmit the infection to a susceptible organism of a particular species. Note that the infected and susceptible organisms may be of different species.
Unique Apollo Label: infectious

transmission coefficient
type: Class
subclass of: rate measurement datum
definition: An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population.
elucidation: An information content entity that represents the rate that an infection moves from infected individuals to susceptible individuals in a population.
Unique Apollo Label: beta

obsolete vaccination efficacy measured
type: Class
definition: A data item specifying a measured vaccination efficacy.
elucidation: A data item specifying a measured vaccination efficacy.
deprecated: true

vaccination efficacy inferred
type: Class
subclass of: data item
definition: A data item inferring a vaccination efficacy based on epidemiological data.
elucidation: A data item inferring a vaccination efficacy based on epidemiological data.
Unique Apollo Label: VaccinationEfficacyInferred

individual treatment control strategy
type: Class
subclass of: Class
  intersection of: infectious disease control strategy
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: action specification
      intersection of: Restriction
        on property: is about
        some values from: Restriction
example of usage: vaccination control strategy, antiviral control strategy
definition: An infectious disease control strategy that immediately targets individuals.
definition editor: Mathias Brochhausen
elucidation: An infectious disease control strategy that immediately targets individuals.
Unique Apollo Label: IndividualTreatmentControlMeasure

target population
type: Class
subclass of: population
definition: An organism population that is the target for a disease control strategy.
elucidation: An organism population that is the target for a disease control strategy.
Unique Apollo Label: TargetPopulation

ring vaccination individual treatment control strategy
type: Class
subclass of: vaccination control strategy

agent level population and environment census
type: Class
subclass of: population and environment census
comment: An instance of the an AgentLevel PopulationAndEnvironmentCensus type comprises an AgentLevel PopulationAndEnvironmentCensus Description, which describes the biotic and abiotic ecosystems elements that are counted by the census, and a URL where the census (the counts) can be retrieved.

agent model ecosystem census description
type: Class
comment: At present, this class corresponds with an XSD type that contains authentication plus information needed to generate a Synthia synthetic population dataset including (1) geographical location and (2) a list of household characteristics.
deprecated: true

compartment model population and environment census
type: Class
comment: The Apollo XSD allows us to specify counts of certain subpopulations and abiotic ecosystem elements for a compartmental model (vs. specifying each individual in the population as in agent model population and environment census).
deprecated: true

population strata definition
type: Class
subclass of: information content entity
Unique Apollo Label: PopulationStrataDefinition

contaminated thing census
type: Class
subclass of: census
definition: A census about contaminated things of a given type in an area of interest.
elucidation: A census about contaminated things of a given type in an area of interest.
Unique Apollo Label: ContaminatedThingCensus

indexable Apollo item
type: Class
subclass of: information content entity
Unique Apollo Label: ApolloIndexableItem
comment: A class representing an abstract type. This class has no attributes and programmers should use it to determine whether an instance should be saved or can be retrieved.

NCBI taxon identifier
type: Class
subclass of: taxonomy identifier
definition: A taxonomy identifier curated by the NCBI Taxonomy that designates a biological taxon.
elucidation: An identifier curated by the National Center for Biotechnology Information (NCBI) that designates a particular biological taxon (e.g., Homo sapiens).
Unique Apollo Label: NcbiTaxonId

disease outcome
type: Class
subclass of: process
subclass of: Class
  union of: Restriction
    on property: part of
    some values from: disease course
  union of: Restriction
    on property: immediately_preceded_by
    some values from: disease course
definition: A processual entity that is either the outcome of a disease course or a part of a disease course and has etiological relevance.
definition editor: William R. Hogan
elucidation: An event that happens during the course of a disease and that results from pathological processes that happened earlier in the disease.
Unique Apollo Label: diseaseOutcome
comment: The infectious disease type in the XSD has a disease outcome element, which specifies whether someone became symptomatic, was hospitalized, etc. All of these outcomes require some process to occur. For sequalae of disease, it is that the realization of the disease is an etiological process that creates some other disorder. For example, fever is often occurs because of high levels of certain interleukins (which is a disorder). So I am comfortable with disease outcome as a process. It is also consistent with the probabilitistic information that will go with it, as a future probability is almost always (if not always) the probability of some event occurring (e.g., coin turning up heads, raining, developing a disease),

susceptible organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: bearer of
    some values from: susceptibility
subclass of: organism
subclass of: Restriction
  on property: bearer of
  some values from: susceptibility
definition: An organism that is the bearer of a susceptibility disposition.
definition editor: William R. Hogan
elucidation: An organism of a particular species that can undergo infection with a particular pathogen.
Unique Apollo Label: susceptible

immune organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: bearer of
    some values from: immune resistance to infection
subclass of: resistant organism
subclass of: Restriction
  on property: bearer of
  some values from: immune resistance to infection
definition: An organism that is the bearer of an immune resistance disposition.
definition editor: William R. Hogan
elucidation: An organism of a particular species that has developed immune resistance to infection with a pathogen of a particular species.
Unique Apollo Label: immune

resistant organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: bearer of
    some values from: resistance to infection
subclass of: organism
subclass of: Restriction
  on property: bearer of
  some values from: resistance to infection
definition: an organism that is the bearer of resistance to infection
definition editor: William R. Hogan
elucidation: An organism of a particular species that is unable to undergo infection with a particular pathogen.
Unique Apollo Label: resistant

control strategy start time information
type: Class
subclass of: information content entity
definition: An information content entity that specifies the start time of the implementation of a infectious disease control strategy.
elucidation: A specification of when an infectious disease control strategy starts.
Unique Apollo Label: controlMeasureStartTime

infected organism
type: Class
equivalent class: Class
  intersection of: host organism
  intersection of: Class
    complement of: Restriction
      on property: has disposition
      some values from: contagiousness
subclass of: host organism
editor preferred term: organism in latent period of infection
definition: An infectious agent host who is NOT able to transmit the infection to another organism of the same species.
definition editor: William R. Hogan
elucidation: An infected organism of a particular species that is not yet able to transmit the infection to a susceptible organism of a particular species. Note that the infected and sucseptible organisms may be of different species.
Unique Apollo Label: infected

apollo simulator configuration
type: Class
subclass of: simulator configuration
definition: A simulator configuration that start an Apollo simulator.
definition editor: Mathias Brochhausen
elucidation: A simulator configuration that start an Apollo simulator.
Unique Apollo Label: RunSimulationMessage

transmission probability
type: Class
subclass of: probability
definition: The probability of the occurence of an infection acquisition from one infected organism to another when in contact.
elucidation: The probability of the occurence of an infection acquisition from one infected organism to another when in contact.
Unique Apollo Label: TransmissionProbability

treatment administration capacity schedule
type: Class
subclass of: plan specification
definition: A plan specification that specifies the capacity to administer a particular treatment over a specific temporal interval in a specified geographical region.
elucidation: A specification of how many doses (of material) of an individual treatment can be administered per unit time in a particular geographical location.
Unique Apollo Label: capacitySchedule

treatment supply schedule
type: Class
subclass of: schedule
definition: A schedule that specifies the availability of a particular drug over a specific temporal interval in a specified geographical region.
definition editor: Mathias Brochhausen
elucidation: A specification of how many doses (of material such as drug or vaccine) of a treatment become available per unit time in a particular geographical location.
Unique Apollo Label: supplySchedulePerDay

vaccination efficacy for simulator configuration
type: Class
subclass of: information content entity
definition: An information content entity that specifies the vaccination efficacy that is part of a simulator configuration.
definition editor: Mathias Brochhausen
elucidation: An information content entity that specifies the vaccination efficacy that is part of a simulator configuration.
Unique Apollo Label: VaccinationEfficacyForSimulatorConfiguration

probability distribution
type: Class
subclass of: information content entity
definition: An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.
definition source: http://en.wikipedia.org/wiki/Probability_distribution
elucidation: An information content entity that assigns a probability to each measurable subset of the possible outcomes of a random experiment, survey, or procedure of statistical inference.
Unique Apollo Label: ProbabilityDistribution

discrete probability distribution
type: Class
subclass of: probability distribution
definition: a probability distribution over a discrete random variable
elucidation: a probability distribution over a discrete random variable

infection state data item
type: Class
subclass of: data item
definition: A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen.
definition editor: Mathias Brochhausen
elucidation: A data item that specifies the epidemiologically-relevant state of a host organism at a specific time with respect to infection with a particular pathogen.
Unique Apollo Label: infectionState

vaccination preventable outcome
type: Class
subclass of: objective specification
definition: An objective specification that specifies the disease outcome a vaccination seeks to prevent.
definition editor: Mathias Brochhausen
elucidation: An objective specification that specifies the disease outcome a vaccination seeks to prevent.
Unique Apollo Label: vaccinationPreventableOutcome

Apollo pathogen code
type: Class
subclass of: identifier
definition: An information content entity that designates a biological taxon and optionally a clade of pathogens.
definition editor: Mathias Brochhausen
elucidation: An identifier that represents the taxonomy of a pathogen by a required NCBI Taxonomy identifier AND an optional clade name. The clade name is a string in XSD version 2.0.1.
Unique Apollo Label: ApolloPathogenCode

abiotic ecosystem element
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: material entity
    intersection of: Class
      complement of: organism
  intersection of: Restriction
    on property: part of
    some values from: abiotic ecosystem
subclass of: material entity
subclass of: Restriction
  on property: part of
  some values from: abiotic ecosystem
definition: A material entity that is part of an abiotic ecosystem.
definition editor: Mathias Brochhausen
elucidation: A material entity that is part of an abiotic ecosystem.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

immune population acting like immune
type: Class
subclass of: immune population
definition: An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.).
definition editor: Mathias Brochhausen
elucidation: An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.).

immune population acting like not immune
type: Class
subclass of: immune population
definition: An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment).
definition editor: Mathias Brochhausen
elucidation: An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment).

becoming asymptomatic
type: Class
subclass of: disease outcome
definition: The process of an organism stopping to experience any symptoms caused by a disease.
definition editor: Mathias Brochhausen
elucidation: The process of an organism stopping to experience any symptoms caused by a disease.
Unique Apollo Label: asymptomatic

becoming symptomatic
type: Class
subclass of: disease outcome
definition: The process of an organism beginning to experience symptoms caused by a disease.
definition editor: Mathias Brochhausen
elucidation: The process of an organism beginning to experience symptoms caused by a disease.
Unique Apollo Label: symptomatic

becoming severely symptomatic
type: Class
subclass of: disease outcome
definition: The process of an organism beginning to experience severe symptoms caused by a disease.
definition editor: Mathias Brochhausen
elucidation: The process of an organism beginning to experience severe symptoms caused by a disease.
Unique Apollo Label: severely symptomatic

infectiousness profile
type: Class
subclass of: process profile
definition: A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism.
definition editor: Mathias Brochhausen
elucidation: A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism.
Unique Apollo Label: infectiousnessProfile
comment: This is probably a 'process profile' according to BFO2

infectious disease treatment efficacy
type: Class
subclass of: disposition
definition: The disposition of one or more portions of material entity, when administered to a susceptible organism by a certain route and according to a certain schedule, to produce a structural change in an organism of a specific species, whereby this structural change serves as the physical basis of a protective resistance disposition.
definition editor: William R. Hogan
elucidation: The disposition of one or more portions of material entity, when administered to a susceptible organism by a certain route and according to a certain schedule, to produce a structural change in an organism of a specific species, whereby this structural change serves as the physical basis of a protective resistance disposition.
Unique Apollo Label: TreatmentEfficacy
comment: need to generate class restriction. Something like: 'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance')) we'd also like to say that the protective resistance disposition began to exist during the process. can't recall whether we should use process or processual_entity for future BFO compatibility.

border control strategy
type: Class
subclass of: travel-related infectious disease control strategy
definition: A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders.
definition editor: William R. Hogan
elucidation: A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders.
Unique Apollo Label: BorderControlMeasure

place closure control strategy
type: Class
subclass of: infectious disease control strategy
definition: an infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open.
definition editor: William R. Hogan
elucidation: An infectious disease control strategy that attempts to prevent infection of susceptible host organisms in a population by preventing potentially infectious contacts (for a particular pathogen) among the organisms in the population.
Unique Apollo Label: PlaceClosureControlMeasure

case isolation control strategy
type: Class
subclass of: infectious disease control strategy
definition: an infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious.
definition editor: William R. Hogan
elucidation: An infectious disease control strategy that isolates infected and/or infectious individuals in a population from most or all potentially infectious contacts with susceptible individuals.
Unique Apollo Label: CaseQuarantineControlMeasure

travel restriction control strategy
type: Class
subclass of: travel-related infectious disease control strategy
definition: A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem
definition editor: William R. Hogan
elucidation: A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one geographical region to another
Unique Apollo Label: TravelRestrictionControlMeasure

clade name
type: Class
subclass of: taxonomy identifier
definition: A taxonomy identifier that denotes a group of organisms or groups of organisms based on common ancestors.
definition editor: Mathias Brochhausen
elucidation: A reference to a group or groups of organisms that are based on common ancestry.
Unique Apollo Label: cladeName
comment: Some regard a clade to be a single branch on the tree of life. [http://en.wikipedia.org/wiki/Clade]

infected population
type: Class
equivalent class: Class
  intersection of: host population
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: contains process
        some values from: infection
subclass of: host population
definition: A population of only infected members of one species.
elucidation: A population of only infected members of one species.

susceptible population
type: Class
equivalent class: Class
  intersection of: host population
  intersection of: Restriction
    on property: has member
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: susceptibility
subclass of: host population
definition: A population of organisms that are all susceptible.
elucidation: A population of organisms that are all susceptible.

immune population
type: Class
subclass of: host population
definition: A population of organisms that are all immune.
elucidation: A population of organisms that are all immune.

asymptomatic host
type: Class
subclass of: host organism

pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: bearer of
    some values from: infectiousness
subclass of: organism
subclass of: Restriction
  on property: bearer of
  some values from: infectiousness
definition: An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.
elucidation: An organism, virus, or prion that can infect another organism.
Unique Apollo Label: pathogen

host organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: contains process
    some values from: reproduction
subclass of: organism
subclass of: Restriction
  on property: contains process
  some values from: reproduction
definition: An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
elucidation: An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
Unique Apollo Label: host

infectious disease
type: Class
equivalent class: Class
  intersection of: disease
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: disease course
      intersection of: Restriction
        on property: causally downstream of
        some values from: infection
  intersection of: Restriction
    on property: characteristic of
    all values from: host organism
subclass of: disease
definition: A disease that inheres in a host and, when realized, is realized as a disease course that is causally preceded by an infection.
elucidation: A disease that is caused by an infection.
Unique Apollo Label: InfectiousDisease
comment: Infection is the etiological process, as defined by OGMS, for infectious disease. However, OGMS does not relate its etiological process class to its disorder class as of this writing. So it is not clear how to connect infectious disease to its infection etiological process.

census reference date
type: Class
subclass of: information content entity
definition: A information content entity that specifies the date of a census.
definition editor: Mathias Brochhausen
elucidation: A information content entity that specifies the date of a census.
Unique Apollo Label: referenceDate

age range category
type: Class
subclass of: scalar value specification
definition: An information content entity specifying the upper and lower limit of a range of ages of continuants.
definition editor: Mathias Brochhausen
elucidation: An information content entity specifying the upper and lower limit of a range of ages of continuants.
Unique Apollo Label: AgeRangeCategoryDefinition

name of temporal interval
type: Class
subclass of: name of temporal region
subclass of: Restriction
  on property: has part
  some values from: time unit
definition: A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration.
definition editor: Mathias Brochhausen
elucidation: An information content entity that specifies a time span on a specified time scale by giving a start time and a duration.
Unique Apollo Label: TimeSpanCategoryDefinition

duration
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: one-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: process
definition: A measurement datum that quantifies a temporal region that is occupied by a processual entity.
definition editor: Mathias Brochhausen
elucidation: A measurement datum that quantifies a temporal region that is occupied by a processual entity.
Unique Apollo Label: Duration

disease unique identifier
type: Class
subclass of: disease identifier
definition: a unique identifier that refers to a disease.
definition editor: Mathias Brochhausen
elucidation: A unique identifier that refers to a particular type of disease.
comment: This class is different from its superclass, in that the identifier is non-redundant with other identifiers in its context (such as a coding system or terminology or ontology). The superclass admits of natural langugage names of diseases, whereas this one typically does not.
comment: We still need to decide which coding schema to adopt.-MB

conditional probability distribution
type: Class
subclass of: probability distribution
definition: A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value.
definition editor: Mathias Brochhausen
elucidation: A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value.
Unique Apollo Label: ConditionalProbabilityDistribution

joint probability distribution
type: Class
subclass of: probability distribution
definition: In the study of probability, given at least two random variables X, Y, ..., that are defined on a probability space, the joint probability distribution for X, Y, ... is a probability distribution that gives the probability that each of X, Y, ... falls in any particular range or discrete set of values specified for that variable.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/w/index.php
elucidation: In the study of probability, given at least two random variables X, Y, ..., that are defined on a probability space, the joint probability distribution for X, Y, ... is a probability distribution that gives the probability that each of X, Y, ... falls in any particular range or discrete set of values specified for that variable.

unconditional probability distribution
type: Class
subclass of: probability distribution
definition: An unconditional probability distribution is the probability distribution of an uncertain variable, U, implicitly incorporating the uncertainty introduced by any other relevant variables. Mathematically, U’s unconditional probability distribution is written {U | E}, where E represents the background state of information under which the distribution is assessed.
definition editor: Mathias Brochhausen
definition source: http://grahamjeffery.com/glossary/213-unconditional-probability-distribution
elucidation: An unconditional probability distribution is the probability distribution of an uncertain variable, U, implicitly incorporating the uncertainty introduced by any other relevant variables. Mathematically, U’s unconditional probability distribution is written {U | E}, where E represents the background state of information under which the distribution is assessed.
Unique Apollo Label: UnconditionalProbabilityDistribution

obsolete parametric probability distribution
type: Class
definition editor: Mathias Brochhausen
Unique Apollo Label: ParametricProbabilityDistribution
deprecated: true

nonparametric probability distribution
type: Class
definition editor: Mathias Brochhausen
term replaced by: non-parametric distribution
Unique Apollo Label: NonparametricProbabilityDistribution
deprecated: true

discrete parametric probability distribution
type: Class
subclass of: parametric probability distribution
definition editor: Mathias Brochhausen
Unique Apollo Label: DiscreteParametricProbabilityDistribution

continuous parametric probability distribution
type: Class
subclass of: parametric probability distribution
definition editor: Mathias Brochhausen
Unique Apollo Label: ContinuousParametricProbabilityDistribution

discrete nonparametric probability distribution
type: Class
subclass of: non-parametric distribution
definition editor: Mathias Brochhausen
Unique Apollo Label: DiscreteNonparametricProbabilityDistribution

continuous nonparametric probability distribution
type: Class
subclass of: non-parametric distribution
definition editor: Mathias Brochhausen

log normal distribution
type: Class
subclass of: continuous parametric probability distribution
definition: A continuous parametric probability distribution that takes as its input a normally-distributed logarithmic function with mean μ and standard deviation σ.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/w/index.php
elucidation: a log-normal (or lognormal) distribution is a continuous probability distribution of a random variable whose logarithm is normally distributed.
Unique Apollo Label: LogNormalDistribution

gamma distribution
type: Class
subclass of: continuous parametric probability distribution
definition: the gamma distribution is a two-parameter family of continuous probability distributions
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/w/index.php
elucidation: the gamma distribution is a two-parameter family of continuous probability distributions
Unique Apollo Label: GammaDistribution

Weibull Distribution
type: Class
subclass of: continuous parametric probability distribution
definition: A continuous parametric probability distribution that gives the distribution of lifetimes of objects. It was originally proposed to quantify fatigue data, but it is also used in analysis of systems involving a "weakest link."
definition editor: Mathias Brochhausen
elucidation: A continuous parametric probability distribution that gives the distribution of lifetimes of objects. It was originally proposed to quantify fatigue data, but it is also used in analysis of systems involving a "weakest link."
Unique Apollo Label: WeibullDistribution

continuous uniform distribution
type: Class
subclass of: continuous parametric probability distribution
definition: the continuous uniform distribution or rectangular distribution is a family of symmetric probability distributions such that for each member of the family, all intervals of the same length on the distribution's support are equally probable.
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/w/index.php
elucidation: the continuous uniform distribution or rectangular distribution is a family of symmetric probability distributions such that for each member of the family, all intervals of the same length on the distribution's support are equally probable.
Unique Apollo Label: ContinuousUniformDistribution

delay from symptoms to treatment
type: Class
subclass of: duration
definition: The duration between the appearance of symptoms of a disease and the start of a treatment.
definition editor: Mathias Brochhausen
elucidation: The duration between the appearance of symptoms of a disease and the start of a treatment.
Unique Apollo Label: delayFromSymptomsToTreatment

apollo location code
type: Class
subclass of: identifier
definition: An identifier that refers to a particular geographical region and that is constructed per guidelines of the Apollo project.
elucidation: A hierarchical identifier beginning with an ISO 2-letter nation code (e.g., US) and that represents one partition of an exclusive and exhaustive partitioning of that nation (including the trivial case of just representing the entire region of the nation).
Unique Apollo Label: ApolloLocationCode
creator: William R. Hogan

control strategy stop time information
type: Class
subclass of: information content entity
definition: An information content entity that specifies the time at which an infectious disease control strategy ends.
elucidation: An information content entity that specifies the time at which an infectious disease control strategy ends.
Unique Apollo Label: controlMeasureStopTime
creator: William R. Hogan

infectious disease control strategy trigger definition
type: Class
subclass of: rule
definition: A rule that specifies the event that, when it occurs, is the trigger to either start or stop an infectious disease control strategy.
elucidation: A rule that says when to start or stop a control strategy. It can be either the passage of time, a disease surveillance result (exceeding the threshold of a certain fraction of the population that is infected), or a treatment surveillance result (reaching a certain fraction of the population that has received an antiviral or vaccination).
Unique Apollo Label: TriggerDefinition
creator: William R. Hogan

contamination probability
type: Class
subclass of: probability
definition: The probability of the occurence of a contamination acquisition from either an infected organism or another contaminated thing.
elucidation: The probability of the occurence of a contamination acquisition from either an infected organism or another contaminated thing.
creator: William R. Hogan

control strategy stand-down delay
type: Class
subclass of: measurement datum
definition: A measurement datum of the time interval from the decision to cease an infectious disease control strategy to the time the control strategy ends expressed in number of time intervals.
elucidation: A period from the conclusion of a control strategy until its disease-controlling activities actually end. For example, it may take time to communicate to workers to stop vaccinating and thus they keep vaccinating for some time after the control strategy is concluded.
Unique Apollo Label: controlMeasureStandDownDelay
creator: William R. Hogan

infection acquisition from contaminated thing
type: Class
equivalent class: Class
  intersection of: entry into host
  intersection of: Restriction
    on property: occurs in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: susceptibility
  intersection of: Restriction
    on property: has_participant
    some values from: contaminated thing
  intersection of: Restriction
    on property: causally upstream of
    some values from: infection
subclass of: infection acquisition
subclass of: Restriction
  on property: has_participant
  some values from: contaminated thing
definition: An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing.
definition editor: William R. Hogan
elucidation: An infection acquisition from a contaminated thing.
Unique Apollo Label: InfectionAcquisitionFromContaminatedAbioticThing

infection acquisition from infectious host
type: Class
equivalent class: Class
  intersection of: entry into host
  intersection of: Restriction
    on property: occurs in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: susceptibility
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: host organism
      intersection of: Restriction
        on property: bearer of
        some values from: contagiousness
  intersection of: Restriction
    on property: causally upstream of
    some values from: infection
subclass of: infection acquisition
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: host organism
    intersection of: Restriction
      on property: bearer of
      some values from: contagiousness
definition: An infection acquisition whereby a susceptible host acquires an infection from an infectious host.
definition editor: William R. Hogan
elucidation: An infection acquisition from an individual who is infectious. The individual acquiring the infection can be of a different species than the one who is infectious.
Unique Apollo Label: InfectionAcquisitionFromInfectedHost

disease surveillance capability
type: Class
subclass of: disposition
definition: A disposition of a disease surveillance infrastructure to detect the outbreak of one particular disease in the geographical region the infrastructure aims to cover.
definition editor: Mathias Brochhausen
elucidation: A capability associated with a location to detect individuals in a population with a particular type of disease.
Unique Apollo Label: DiseaseSurveillanceCapability
comment: Specifies location, pathogen, host taxon, caseDefinition, sensitivity, specificity, and time delay of case detection

time delay to case detection
type: Class
subclass of: duration
definition: The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition
definition editor: Mathias Brochhausen
elucidation: The period from the time an organism satisfies the criteria of a case definition until a process or system detects the organism as satisfying those criteria.
Unique Apollo Label: timeDelayToCaseDetection

time scale name
type: Class
subclass of: identifier
definition: An identifier that designates a scale according to which time is measured (e.g., Gregorian Calendar).
definition editor: William R. Hogan
elucidation: A system of measurement of time with respect to an arbitrary reference point or event, which typically has a measured value of zero elapsed time. In epidemic simulation, it can be 'simulator time' where time zero is the starting point of an infectious disease scenario, or it can be 'control strategy time' where time zero is the time at which the control strategy is initiated.
Unique Apollo Label: timeScale

disease surveillance trigger definition
type: Class
subclass of: infectious disease control strategy trigger definition
definition: An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance.
definition editor: Mathias Brochhausen
elucidation: A control strategy trigger that occurs once a particular disease surveillance event occurs. For example, the trigger could occur once the incidence or prevalence of the infectious disease exceeds a fixed threshold.
Unique Apollo Label: DiseaseSurveillanceTriggerDefinition

treatment surveillance trigger definition
type: Class
subclass of: infectious disease control strategy trigger definition
definition: An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance.
definition editor: Mathias Brochhausen
elucidation: An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance.
Unique Apollo Label: TreatmentSurveillanceTriggerDefinition

temporal trigger definition
type: Class
subclass of: infectious disease control strategy trigger definition
definition: An infectious disease control trigger definition that is based on the passage of a specified interval of time.
elucidation: A control strategy trigger that occurs once a constant duration of time has elapsed.
Unique Apollo Label: TemporalTriggerDefinition

time since time scale zero
type: Class
subclass of: duration
definition: the duration of time that has elapsed from the zero reference point to a later time on the time scale
definition editor: William R. Hogan
elucidation: A duration of time that has elapsed since the zero reference point of a time scale.
Unique Apollo Label: timeSinceTimeScaleZero

seasonal function parameter
type: Class
subclass of: information content entity
Unique Apollo Label: SeasonalityFunctionParameters

maximum seasonal latitude
type: Class
subclass of: seasonal function parameter
Unique Apollo Label: maximumSeasonalLatitude

minimum seasonal latitude
type: Class
subclass of: seasonal function parameter
Unique Apollo Label: minimumSeasonalLatitude

seasonal temporal offset
type: Class
subclass of: seasonal function parameter
Unique Apollo Label: seasonalTemporalOffset

sensitivity of case detection
type: Class
subclass of: true positive rate
definition: The sensitivity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X.
elucidation: The sensitivity of a process or system that detects organisms who satisfy a case definition.
Unique Apollo Label: sensitivityOfCaseDetection

probability of entry into a country is denied
type: Class
subclass of: probability
definition: The probability that entry is denied as part of a border control strategy.
definition editor: Mathias Brochhausen
elucidation: The probability that entry is denied as part of a border control strategy.
Unique Apollo Label: probabilityEntryDenied

probability of exit from a country is denied
type: Class
subclass of: probability
definition: The probability that exit is denied as part of a border control strategy.
definition editor: Mathias Brochhausen
elucidation: The probability that exit is denied as part of a border control strategy.
Unique Apollo Label: probabilityExitDenied

duration of treatment course
type: Class
subclass of: duration
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: one-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: treatment
definition: A duration that measures the temporal interval occupied by a treatment course.
definition editor: Mathias Brochhausen
elucidation: A period from the start to the end of a treatment course.
Unique Apollo Label: durationOfTreatmentCourse

number of doses in a treatment course
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: treatment
definition: The count of the number of doses that are part of a treatment course.
definition editor: Mathias Brochhausen
elucidation: The number of doses (of material such as antiviral drug or vaccine) that constitutes a particular course of treatment
Unique Apollo Label: numDosesInTreatmentCourse

target populations and prioritizations information
type: Class
subclass of: information content entity
elucidation: A specification of the target populations of a control strategy and the priority of each population in the strategy.
Unique Apollo Label: targetPopulationsAndPrioritizations

school transmission multiplier
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a school.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A factor by which to multiply the transmission coefficient for contacts that occur in in a school.
Unique Apollo Label: schoolTransmissionMultiplier

household transmission multiplier
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a household.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A factor by which to multiply the transmission coefficient for contacts that occur in a household.
Unique Apollo Label: householdTransmissionMultiplier

workplace transmission multiplier
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a workplace.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A factor by which to multiply the transmission coefficient for contacts that occur in a workplace.
Unique Apollo Label: workplaceTransmissionMultiplier

close individual places independently strategy
type: Class
subclass of: place closure control strategy
definition: A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time.
elucidation: A place-closure control strategy that decides on a case-by-case basis whether to close places of a certain type, as opposed to blanket policy that closes all places of a certain type at the same time.
Unique Apollo Label: closeIndividualPlacesIndependently

place closure period
type: Class
subclass of: duration
definition: The duration from the closure of a place until the time when it is reopened.
definition editor: William R. Hogan
Unique Apollo Label: closurePeriod

community transmission multiplier
type: Class
subclass of: epidemic simulator action specification
Unique Apollo Label: communityTransmissionMultiplier

maximum travel distance in km information
type: Class
subclass of: information content entity
Unique Apollo Label: maximumTravelDistanceInKm

treatment preventable outcome
type: Class
subclass of: objective specification
definition: An objective specification that specifies the disease outcome that a treatment seeks to prevent.
definition editor: William Hogan
elucidation: An objective specification that specifies the disease outcome that a treatment seeks to prevent.
Unique Apollo Label: TreatmentPreventableOutcome

time delay of treatment detection
type: Class
subclass of: duration
definition: The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population
definition editor: William R. Hogan
elucidation: The duration from treatment until a treatment surveillance system detects it in a population
Unique Apollo Label: timeDelayOfTreatmentDetection

individual treatment strategy supply schedule unit of measure
type: Class
subclass of: unit
definition: The unit of measure for the supply schedule of an individual treatment.
definition editor: William R. Hogan
elucidation: The unit of measure for the supply schedule of an individual treatment. For example, 'daily dose'.
Unique Apollo Label: supplyScheduleUnits

individual treatment strategy administration capacity unit of measure
type: Class
subclass of: unit
definition editor: William R. Hogan
elucidation: The unit of measure for the administration capacity of an individual treatment. For example, 'daily dose'.
Unique Apollo Label: administrationCapacityUnits

agent-based disease transmission model
type: Class
subclass of: disease transmission model
definition editor: William R. Hogan
elucidation: A disease transmission model that explicitly represents each individual in the population and simulates the acquisition of disease by individuals who do not already have it at simulator time zero.

reactive control strategy threshold unit of measure
type: Class
subclass of: unit
definition: A unit of measure for a threshold in a reactive infectious disease control strategy.
definition editor: William R. Hogan
elucidation: A unit of measure for a threshold in a reactive infectious disease control strategy.
Unique Apollo Label: unitOfMeasureForThreshold

case definition
type: Class
subclass of: information content entity
definition: An information content entity that specifies the criteria that an organism must meet to be considered to be in some abnormal state.
definition editor: William R. Hogan
elucidation: A specification of the criteria an organism must meet to be considered to be in some abnormal state. The abnormal state could be having a disease, carrier status, a syndrome, a structural abnormality (e.g., congenital heart defect), and so on.
Unique Apollo Label: CaseDefinition

obsolete quarantine period
type: Class
definition editor: William R. Hogan
elucidation: A period during which an infectious host organism is isolated from contact with other organisms in the ecosystem as part of a quarantine control strategy.
deprecated: true

epidemic
type: Class
subclass of: infection in ecosystem
definition: A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of infection acquisition becomes constant.
definition editor: William R. Hogan
alternative label: epidemic of infection
elucidation: A process whose beginning is demarcated by accelerating infection acquisition by one or more host species of a particular pathogen in a particular location and whose end is demarcated by the time when the rate of of infection acquisition becomes constant. The constant rate may be zero. The period of an epidemic may be defined using statistical criteria based on incidence rates or causal models based on their fit to incidence data.
Unique Apollo Label: Epidemic
comment: An example of multiple host species is foot and mouth disease (such as the 2001 epidemic in the UK, see: http://www.sciencemag.org/content/292/5519/1155.long) and swine flu. The foot and mouth disease epidemic affected sheep, pigs, and cattle.

immune organism that acts like it is immune
type: Class
subclass of: immune organism
definition: An immune organism that acts as if it is immune (i.e., it does not seek vaccination or avoid contact with infectious organisms).
definition editor: William R. Hogan
elucidation: An organism of a particular species who is immune to infection with a pathogen of a particular species, and that acts as if it is immune (that is, it does not seek vaccination, avoid contact with infectious organisms, etc.)
Unique Apollo Label: immuneAndActsLikeImmune

immune organism that acts like it is not immune
type: Class
subclass of: immune organism
definition: An immune organism that acts as if it is NOT immune (i.e., it seeks vaccination and/or avoids contact with infectious organisms).
definition editor: William R. Hogan
elucidation: An organism of a particular species who is immune to infection with a pathogen of a particular species, and that acts as if it is NOT immune (that is, it does seeks vaccination, avoids contact with infectious organisms, etc.)
Unique Apollo Label: immuneButActsLikeNotImmune

naturally-acquired active immune resistance
type: Class
subclass of: immune resistance to infection
definition: An immune resistance to infection that is causally preceded by an infection and an immune response to that infection with the production of antibodies to antigens from the pathogen population participating in the infection.
definition editor: William R. Hogan
elucidation: An immune resistance to infection that is causally preceded by an infection and an immune response to that infection with the production of antibodies to antigens from the pathogen population participating in the infection.

recovered organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: bearer of
    some values from: naturally-acquired active immune resistance
subclass of: immune organism
subclass of: Restriction
  on property: bearer of
  some values from: naturally-acquired active immune resistance
definition: An organism that is the bearer of a naturally-acquired, active immune resistance to infection.
definition editor: William R. Hogan
elucidation: An organism that has recovered from infection with a particular pathogen, is no longer infectious to other organisms of any species, and is not able to be infected again with that pathogen.
Unique Apollo Label: recovered

compartmental disease transmission model
type: Class
subclass of: disease transmission model
elucidation: A disease transmission model that represents populations of susceptible and infected individuals (but not these individuals directly themselves) and simulates movement of individuals from one such population (a.k.a. compartment) to another.

anti-infective individual treatment control strategy
type: Class
subclass of: individual treatment control strategy
definition: An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment.
definition editor: William R. Hogan
elucidation: An anti-infective individual treatment control strategy that uses anti-infective medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period.
Unique Apollo Label: DrugTreatmentControlStrategy
Unique Apollo Label: anti-infective control strategy

anti-bacterial control strategy
type: Class
subclass of: anti-infective individual treatment control strategy
definition: An anti-infective individual treatment control strategy that has as part an action specification that is realized in antibacterial treatment.
definition editor: William R. Hogan
elucidation: An anti-infective individual treatment control strategy that uses anti-bacterial medications to treat infected hosts in an attempt to limit their infectiousness and/or infectious period.

infection in ecosystem
type: Class
subclass of: process
subclass of: Restriction
  on property: has proper occurrent part
  some values from: infection
subclass of: Restriction
  on property: has proper occurrent part
  some values from: infection acquisition
editor preferred term: infection in an ecosystem
definition: A process comprised of numerous infections and infection acquisitions with a particular pathogen in one or more populations of hosts.
definition editor: William R. Hogan
elucidation: A process of ongoing infection and infection acquisition in individuals in one or more populations in an ecosystem.

endemic
type: Class
subclass of: infection in ecosystem

vector control strategy
type: Class
equivalent class: Class
  intersection of: infectious disease control strategy
  intersection of: Restriction
    on property: has part
    some values from: vector control action specification
subclass of: infectious disease control strategy
subclass of: Restriction
  on property: has part
  some values from: vector control action specification
definition: An infectious disease control strategy that has a vector control action specification as part.
definition editor: William R. Hogan
elucidation: An infectious disease control strategy that attempts to reduce infections in a population of a particular host species by limiting infection acquisitions from a second host species, called the 'vector'.
Unique Apollo Label: VectorControlMeasure
comment: Typically, the strategy is to limit the population of the second host species, which is called the "vector" for the infection.

abiotic ecosystem census
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: Class
subclass of: census
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: entity
        intersection of: Restriction
definition: A census of entities of a certain type or types in the abiotic ecosystem.
definition editor: William R. Hogan
elucidation: A census of things in the abiotic ecosystem.
Unique Apollo Label: AbioticThingCensus

vector control action specification
type: Class
subclass of: infectious disease control strategy action specification
definition: An action specification that is realized in reducing the number of infection acquistions in one population of a particular species from infectious hosts in a population of another particular species, called the "vector".
definition editor: William R. Hogan
elucidation: An action specification that is realized in reducing the number of infection acquistions in one population of a particular species from infectious hosts in a population of another particular species, called the "vector".

Breteau Index
type: Class
subclass of: average value
definition: The average number of water containers testing positive for the presence of a particular mosquito species, typically Aedes aegyptii, per 100 households in the geographical region under surveillance.
definition editor: William R. Hogan
elucidation: The average number of containers positive (for presence of mosquito) per 100 households.
Unique Apollo Label: breteauIndex

individual mosquito reproduction
type: Class
equivalent class: Class
  intersection of: reproduction
  intersection of: Restriction
    on property: obsolete has active participant
    some values from: Culicidae
subclass of: reproduction
subclass of: obsolete multicellular organism reproduction
subclass of: Restriction
  on property: obsolete has active participant
  some values from: Culicidae
definition: A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)
definition editor: William R. Hogan
elucidation: Reproduction of a single mosquito
Unique Apollo Label: MosquitoReproduction

gonotrophic cycle duration
type: Class
equivalent class: Restriction
  on property: is about
  some values from: Class
    intersection of: one-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: gonotrophic cycle
subclass of: duration
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: one-dimensional temporal region
    intersection of: Restriction
      on property: has temporal occupant
      some values from: gonotrophic cycle
definition: The duration of the temporal interval occupied by a gonotropic period.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The duration of the gonotrophic cycle in a female mosquito.
Unique Apollo Label: gonotrophicPeriodDuration

gonotrophic cycle
type: Class
subclass of: biological_process
definition: The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition).
definition editor: William R. Hogan
elucidation: The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition).

oviposition site census
type: Class
subclass of: abiotic ecosystem census
definition: An abiotic ecosystem census of the locations where pregnant female mosquitos lay their eggs.
definition editor: William R. Hogan
elucidation: A census of sites where mosquitoes have laid their eggs.
Unique Apollo Label: OvipositionSiteCensus

obsolete carrying capacity per house
type: Class
definition editor: William R. Hogan
elucidation: The maximum number of ovisites in/around a single house or other dwelling structure.
Unique Apollo Label: carryingCapacityPerHouse
deprecated: true

incubation period
type: Class
subclass of: process
subclass of: Restriction
  on property: temporal part of
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: realizes
      some values from: infectious disease
definition: A process that is part of an infectious disease course, has the same beginning temporal boundary as the disease course, and has an ending temporal boundary at the onset of symptoms due to the infectious disease.
definition editor: William R. Hogan
elucidation: The period from onset of infection to onset of symptoms.
Unique Apollo Label: incubationPeriod

drug treatment
type: Class
equivalent class: Class
  intersection of: treatment
  intersection of: Restriction
    on property: has_specified_input
    some values from: drug product
subclass of: treatment
subclass of: Restriction
  on property: has_specified_input
  some values from: drug product
definition: A treatment with a drug product.
definition editor: William R. Hogan
elucidation: Treatment with a drug.
Unique Apollo Label: DrugTreatment

voluntary household quarantine control strategy
type: Class
subclass of: infectious disease control strategy
definition: An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts.
definition editor: William R. Hogan
elucidation: An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts.
Unique Apollo Label: VoluntaryHouseholdQuarantineControlMeasure

liberal sick leave control strategy
type: Class
subclass of: infectious disease control strategy
definition: An infectious disease conrol straegy that seeks to reduce disease transmission by offering employees extra paid time off to stay home, in an attempt to reduce contacts that transmit disease in the workplace.
definition editor: William R. Hogan
elucidation: An infectious disease conrol straegy that seeks to reduce disease transmission by offering employees extra paid time off to stay home, in an attempt to reduce contacts that transmit disease in the workplace.
Unique Apollo Label: LiberalSickLeaveControlMeasure

epidemic investigation design
type: Class
subclass of: study design
editor preferred term: epidemic investigation study design
definition editor: William R. Hogan
elucidation: A study design that specifies which epidemic(s) to investigate, how, and what information to output.

quarantine control strategy
type: Class
subclass of: infectious disease control strategy
editor preferred term: quarantine control strategy
definition editor: William R. Hogan
elucidation: An infectious disease control strategy whereby organisms who have had contact with infectious organisms but are not symptomatic or otherwise known to be infectious are prevented from having contact with other susceptible organisms.

larvicide control strategy
type: Class
subclass of: vector control strategy
definition: A vector control strategy that has an action specification that is realized by reducing the number of larval-stage organisms of a vector population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control strategy that kills larval-stage vector organisms
Unique Apollo Label: LarvicideControlMeasure

colonization
type: Class
equivalent class: Class
  intersection of: reproduction
  intersection of: Restriction
    on property: occurs in
    some values from: Class
      intersection of: Class
        complement of: tissue
      intersection of: Restriction
        on property: part of
        some values from: organism
subclass of: reproduction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: Class
      complement of: tissue
    intersection of: Restriction
      on property: part of
      some values from: organism
editor preferred term: biological colonization
definition: a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host.
definition editor: William R. Hogan
elucidation: a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host.
Unique Apollo Label: Colonization
comment: Primary use case is colonization of humans, animals with Staph aureus, but it also covers bacteriuria, transient bactermia, and normal gut flora.

infection in population
type: Class
subclass of: infection in ecosystem
editor preferred term: infection in a population
definition: an infection in an ecosystem occurring in one population of organisms
definition editor: William R. Hogan
elucidation: an infection in an ecosystem occurring in one population of organisms
Unique Apollo Label: Infection

colonization acquisition
type: Class
subclass of: entry into host
editor preferred term: colonization acquisition
definition: a biological process where a pathogen organism of a particular biological taxon enters into a host organism of a particular taxon and begins to undergo reproduction in a location external to tissues of the host
definition editor: William R. Hogan
elucidation: a biological process where a pathogen organism of a particular biological taxon enters into a host organism of a particular taxon and begins to undergo reproduction in a location external to tissues of the host
Unique Apollo Label: ColonizationAcquisition
comment: the host organism was not colonized wtih the pathogen prior to the colonization acquisition

decolonization control strategy
type: Class
subclass of: individual treatment control strategy
editor preferred term: decolonization control strategy
definition: an indivdiual treatment control strategy that prevents infectious disease by treating indivdiuals colonized with a pathogen of a particular species to limit or end the colonization
definition editor: William R. Hogan
elucidation: an indivdiual treatment control strategy that prevents infectious disease by treating indivdiuals colonized with a pathogen of a particular species to limit or end the colonization
Unique Apollo Label: DecolonizationControlMeasure
comment: typically the pathogen is a bacterium

infection acquistion from self colonization
type: Class
equivalent class: Class
  intersection of: biological_process
  intersection of: Restriction
    on property: immediately_preceded_by
    some values from: Class
      intersection of: colonization
      intersection of: Restriction
        on property: has_participant
        some values from: pathogen
      intersection of: Restriction
        on property: has_participant
        some values from: Class
subclass of: entry into host
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: Class
    intersection of: colonization
    intersection of: Restriction
      on property: has_participant
      some values from: pathogen
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: host organism
        intersection of: Restriction
editor preferred term: establishment of infection from self colonization
definition: An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there.
definition editor: William R. Hogan
elucidation: An infection acquisition by which a pathogen organism from a particular biological taxon, which previously was participating in a colonization process in a host organism from another taxon, begins to invade the tissues of the same host organism and reproduce there.

chemical resistance to infection
type: Class
subclass of: Class
  intersection of: resistance to infection
  intersection of: Restriction
    on property: has material basis at all times
    some values from: scattered molecular aggregate
editor preferred term: chemical resistance to infection
definition: A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism.
definition editor: William R. Hogan
alternative label: chemoprotection
alternative label: chemoprotective resistance
alternative label: chemotherapeutic resistance to infection
elucidation: A resistance to infection that is conferred by the presence, in sufficient quantity, of a particular molecular entity that is not normally present in the organism.
comment: As with all dispositions, chemical resistance need not be realized to exist. The presence of cholorquine confers this disposition even if the person is never bitten by a mosquito, let alone a malaria-laden mosquito.
comment: Examples: chemoprophylaxis of malaria with chloroquine, treatment of infections with antibiotics, antiviral treatment

resistance to malaria infection
type: Class
subclass of: resistance to infection
editor preferred term: resistance to malaria infection
definition: A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum.
definition editor: William R. Hogan
alternative label: malaria resistance
alternative label: resistance to malaria
elucidation: A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum.

ectosymbiosis
type: Class
equivalent class: Class
  intersection of: symbiosis
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: spatially disjoint from
        some values from: organism
subclass of: symbiosis
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: spatially disjoint from
      some values from: organism
definition: A symbiosis where the organisms that are interacting remain physically external to one another.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A symbiosis where the organisms that are interacting remain physically external to one another.
comment: It includes situations where one organism lives on the surface of the other organism.

antagonism
type: Class
subclass of: ectosymbiosis
definition: An ectosymbiosis that results in harm to all participating organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An ectosymbiosis that results in harm to all participating organisms.
comment: Example: competition between lions and hyenas for food

amensalism
type: Class
equivalent class: Class
  intersection of: ectosymbiosis
  intersection of: Class
    complement of: Restriction
      on property: realizes
      some values from: Class
        intersection of: homeostasis
        intersection of: Restriction
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: bodily harm
subclass of: ectosymbiosis
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: bodily harm
definition: An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms.
comment: Example: Spanish ibex and weevils of the genus Timarcha

agonism
type: Class
equivalent class: Class
  intersection of: ectosymbiosis
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: bodily harm
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: bodily benefit
subclass of: ectosymbiosis
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: bodily harm
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: bodily benefit
definition: An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism.

intimate agonism
type: Class
subclass of: agonism
definition: An agonism where the participating organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An agonism where the participating organisms, although physically external to one another, nevertheless have close and persistent physical contact for most or all of the interaction.

ectosymbiotic parasitism
type: Class
equivalent class: Class
  intersection of: intimate agonism
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: bodily harm
      intersection of: Class
        complement of: Restriction
subclass of: intimate agonism
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: bodily harm
    intersection of: Class
      complement of: Restriction
        on property: has part
        some values from: life-death temporal boundary
definition: An intimate agonism in which the harm is not fatal to the host.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: ectoparasitism
elucidation: An intimate agonism in which the harm is not fatal to the host.
comment: Example: Temnocephala chilensis and various marine wildlife

facultative ectosymbiotic parasitism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic parasitism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: ectosymbiotic parasitism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An ectosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative ectoparasitism
elucidation: An ectosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions.
comment: Example: Armillaria (type of wood fungus) and trees

obligatory ectosymbiotic parasitism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic parasitism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic parasitism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: parasite
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory ectoparasitism
elucidation: An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
comment: Example: European common cuckoo and other bird species (brood parasitism)

ectosymbiotic parasitoidism
type: Class
subclass of: intimate agonism
definition: An intimate agonism in which the harm is fatal to the host.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: ectoparasitoidism
elucidation: An intimate agonism in which the harm is fatal to the host.

facultative ectosymbiotic parasitoidism
type: Class
subclass of: ectosymbiotic parasitoidism
definition: An ectosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative ectoparasitoidism
elucidation: An ectosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions.
comment: Example: Pachycrepoideus dubius and Ceratitis capitata

obligatory ectosymbiotic parasitoidism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic parasitoidism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic parasitoidism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: parasitoid
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory ectoparasitoidism
elucidation: An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
comment: Example: Mutillidae (family of wasps) and other wasps/ants

ectosymbiotic commensalism
type: Class
equivalent class: Class
  intersection of: ectosymbiosis
  intersection of: Class
    complement of: Restriction
      on property: realizes
      some values from: Class
        intersection of: homeostasis
        intersection of: Restriction
  intersection of: Restriction
    on property: has part
    some values from: bodily benefit
subclass of: ectosymbiosis
subclass of: Restriction
  on property: has part
  some values from: bodily benefit
definition: An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: ectocommensalism
elucidation: An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.

facultative ectosymbiotic commensalism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic commensalism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: ectosymbiotic commensalism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An ectosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative ectocommensalism
elucidation: An ectosymbiotic commensalism that realizes a dispostion of the organism that benefits that is not one of its biological functions.
comment: Example: Ophiodromus pugettensis and Patiria miniata

obligatory ectosymbiotic commensalism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic commensalism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic commensalism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: organism
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory ectocommensalism
elucidation: An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
comment: Example: Basicladia algae and sea turtles

ectosymbiotic mutualism
type: Class
equivalent class: Class
  intersection of: ectosymbiosis
  intersection of: Restriction
    on property: has part
    some values from: bodily benefit
  intersection of: Restriction
    on property: has part
    all values from: bodily benefit
subclass of: ectosymbiosis
subclass of: Restriction
  on property: has part
  some values from: bodily benefit
definition: An ectosymbiosis that results in benefit to all participating organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: ectomutualism
elucidation: An ectosymbiosis that results in benefit to all participating organisms.

facultative ectosymbiotic mutualism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic mutualism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: ectosymbiotic mutualism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An ectosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative ectomutualism
elucidation: An ectosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism.
comment: Example: ants that feed off of honeydew from aphids, and in turn protect the aphids

obligatory ectosymbiotic mutualism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic mutualism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic mutualism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: organism
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory ectomutualism
elucidation: An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
comment: Example: bees and flowers

endosymbiosis
type: Class
equivalent class: Class
  intersection of: symbiosis
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: located in
        some values from: organism
subclass of: symbiosis
subclass of: Restriction
  on property: has_participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: located in
      some values from: organism
definition: A symbiosis where one organism is physically contained within another organism (called the 'host').
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A symbiosis where one organism is physically contained within another organism (called the 'host').

endosymbiotic parasitism
type: Class
equivalent class: Class
  intersection of: endosymbiosis
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: bodily harm
      intersection of: Class
        complement of: Restriction
subclass of: endosymbiosis
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: bodily harm
    intersection of: Class
      complement of: Restriction
        on property: has part
        some values from: life-death temporal boundary
definition: An endosymbiosis that results in benefit to the parasite and harm to the host.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: endoparasitism
elucidation: An endosymbiosis that results in benefit to the parasite and harm to the host.

transient agonism
type: Class
subclass of: agonism
definition: An agonism where the participating organisms maintain significant physical separation from one another through most or all of the interaction.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An agonism where the participating organisms maintain significant physical separation from one another through most or all of the interaction

predation
type: Class
equivalent class: Class
  intersection of: transient agonism
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: bodily harm
      intersection of: Restriction
        on property: has part
        some values from: Class
subclass of: transient agonism
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: bodily harm
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: life-death temporal boundary
        intersection of: Restriction
definition: A non-intimate agonism in which the harm is fatal.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A non-intimate agonism in which the harm is fatal.
comment: Example: lion and gazel

grazing
type: Class
equivalent class: Class
  intersection of: transient agonism
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: bodily harm
      intersection of: Class
        complement of: Restriction
subclass of: transient agonism
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: bodily harm
    intersection of: Class
      complement of: Restriction
        on property: has part
        some values from: life-death temporal boundary
definition: A non-intimate agonism in which the harm is not fatal.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A non-intimate agonism in which the harm is not fatal.
comment: Example: Giant panda and bamboo

facultative endosymbiotic parasitism
type: Class
equivalent class: Class
  intersection of: endosymbiotic parasitism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: endosymbiotic parasitism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An endosymbiotic parasitism that realizes some facultative parasite role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative endoparasitism
elucidation: An endosymbiotic parasitism that realizes a disposition of the parasite that is not one of its biological functions.
comment: Example: Strongyloides stercoralis (roundworm) and humans

obligatory endosymbiotic parasitism
type: Class
equivalent class: Class
  intersection of: endosymbiotic parasitism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic parasitism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: parasite
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory endoparasitism
elucidation: An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
comment: Example: Necator americanus (hookworm) and humans

endosymbiotic parasitoidism
type: Class
equivalent class: Class
  intersection of: endosymbiosis
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: bodily harm
      intersection of: Restriction
        on property: has part
        some values from: life-death temporal boundary
subclass of: endosymbiosis
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: bodily harm
    intersection of: Restriction
      on property: has part
      some values from: life-death temporal boundary
definition: An endosymbiosis that results in benefit to the parasitoid and is fatal to the host.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: endoparasitoidism
elucidation: An endosymbiosis that results in benefit to the parasitoid and is fatal to the host.

facultative endosymbiotic parasitoidism
type: Class
equivalent class: Class
  intersection of: endosymbiotic parasitoidism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: endosymbiotic parasitoidism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An endosymbiotic parasitoidism that realizes some facultative parasitoid role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative endoparasitoidism
elucidation: An endosymbiotic parasitoidism that realizes a disposition of the parasitoid that is not one of its biological functions.
comment: Example: Naegleria fowleri (brain-eating amoeba) and humans

obligatory endosymbiotic parasitoidism
type: Class
equivalent class: Class
  intersection of: endosymbiotic parasitoidism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic parasitoidism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: parasitoid
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory endoparasitoidism
elucidation: An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
comment: Example: Ichneumon eumerus (wasp) and Phengaris rebeli (butterfly caterpillar)

endosymbiotic commensalism
type: Class
equivalent class: Class
  intersection of: endosymbiosis
  intersection of: Class
    complement of: Restriction
      on property: realizes
      some values from: Class
        intersection of: homeostasis
        intersection of: Restriction
  intersection of: Restriction
    on property: has part
    some values from: bodily benefit
subclass of: endosymbiosis
subclass of: Restriction
  on property: has part
  some values from: bodily benefit
definition: An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: endocommensalism
elucidation: An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.

facultative endosymbiotic commensalism
type: Class
equivalent class: Class
  intersection of: endosymbiotic commensalism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: endosymbiotic commensalism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An endosymbiotic commensalism that realizes some facultative commensal role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative endocommensalism
elucidation: An endosymbiotic commensalism that realizes a dispostion of the non-host organism that benefits that is not one of its biological functions.
comment: Example: Malaria and mosquito vector

obligatory endosymbiotic commensalism
type: Class
equivalent class: Class
  intersection of: endosymbiotic commensalism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic commensalism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: organism
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory endocommensalism
elucidation: An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
comment: Example: Passalurus ambiguus (nematode) and rabbits

endosymbiotic mutualism
type: Class
equivalent class: Class
  intersection of: endosymbiosis
  intersection of: Restriction
    on property: has part
    some values from: bodily benefit
  intersection of: Restriction
    on property: has part
    all values from: bodily benefit
subclass of: endosymbiosis
subclass of: Restriction
  on property: has part
  some values from: bodily benefit
definition: An endosymbiosis that results in benefit to all participating organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: endomutualism
elucidation: An endosymbiosis that results in benefit to all participating organisms.

facultative endosymbiotic mutualism
type: Class
equivalent class: Class
  intersection of: endosymbiotic mutualism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: facultative role
      intersection of: Restriction
        on property: is realized by
        some values from: bodily benefit
      intersection of: Restriction
        on property: characteristic of
        some values from: organism
subclass of: endosymbiotic mutualism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: facultative role
    intersection of: Restriction
      on property: is realized by
      some values from: bodily benefit
    intersection of: Restriction
      on property: characteristic of
      some values from: organism
definition: An endosymbiotic mutualism that realizes some facultative mutualist role inhering in an organism that is also realized by a bodily benefit to that organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: facultative endomutualism
elucidation: An endosymbiotic mutualism that realizes one or more dispositions of one or both organisms and these dispostions are not biological functions of either organism.
comment: Example: Hamiltonella defensa and aphids

obligatory endosymbiotic mutualism
type: Class
equivalent class: Class
  intersection of: endosymbiotic mutualism
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic mutualism
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Class
      intersection of: Restriction
        on property: proper part of continuant at all times
        some values from: organism
      intersection of: Restriction
        on property: characteristic of
        some values from: anatomical structure
definition: An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: obligatory endomutualism
elucidation: An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
comment: Example: marine worms of genus Riftia and their endosymbiotic bacteria

deprecated homeostasis
type: Class
definition: A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.
deprecated: true

bodily harm
type: Class
subclass of: process
definition: A process that has as output a material entity that is the material basis for an abnormal homeostasis dispostion.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A process that has as output a material entity that is the material basis for an abnormal homeostasis dispostion.

bodily benefit
type: Class
subclass of: process
definition: A process that facilitates the realization of one or more normal homeostasis dispositions borne by an organism and/or one or more causally relatively isolated parts of the organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A process that facilitates the realization of one or more normal homeostasis dispositions borne by an organism and/or one or more causally relatively isolated parts of the organism.

parasite
type: Class
subclass of: organism
definition: An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits.

parasitoid
type: Class
subclass of: organism
definition: An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits.

target population definition
type: Class
subclass of: information content entity
definition: An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied.
elucidation: An information content entity that is part of an infectious disease control strategy and that specifies the intended population to which one or more interventions in the control strategy will be applied.
Unique Apollo Label: TargetPopulationDefinition

name of a temporal boundary
type: Class
subclass of: name of temporal region
definition: A name of temporal region that designates a temporal boundary
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that designates a temporal boundary
Unique Apollo Label: RealTimePointCategoryDefinition

location definition
type: Class
subclass of: information content entity
definition: An information content entity that specifies a geographical region by (1) listing the names of other geographical regions whose mereological sum constitutes it and optionally (2) listing the names of other geographical regions that are subsequently subtracted from the mereological sum.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that specifies a geographical region by (1) listing the names of other geographical regions whose mereological sum constitutes it and optionally (2) listing the names of other geographical regions that are subsequently subtracted from the mereological sum.
Unique Apollo Label: LocationDefinition

treatment contraindication
type: Class
subclass of: contraindication
definition: A contraindication that increases the risk of a treatment.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A contraindication that increases the risk of a treatment.
Unique Apollo Label: TreatmentContraindication

uncertain duration
type: Class
subclass of: duration
definition: A duration that is specified as a probability distribution over a range of numbers.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A duration that is specified as a probability distribution over a range of numbers.
Unique Apollo Label: UncertainDuration

fraction of contaminated thing
type: Class
subclass of: measurement datum
definition: A measurement datum that is the fraction of things of a particular type in a particular geographical region or site that are contaminated with a pathogen.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A measurement datum that is the fraction of things of a particular type in a particular geographical region or site that are contaminated with a pathogen.
Unique Apollo Label: fractionContaminated

specificity of case detection
type: Class
subclass of: true negative rate
editor preferred term: specificity of case detection
definition: The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X.
definition editor: William R. Hogan
elucidation: The specificity of a process or system that detects organisms who satisfy a case definition.
Unique Apollo Label: specificityOfCaseDetection

specificity of treatment detection
type: Class
subclass of: true negative rate
definition: The specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment.
definition editor: William R. Hogan
elucidation: The specificity of the process or system that detects organisms that have undergone a particular treatment.
Unique Apollo Label: specificityOfTreatmentDetection

sensitivity of treatment detection
type: Class
subclass of: true positive rate
definition: The sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment.
definition editor: William R. Hogan
elucidation: The sensitivity of the process or system that detects organisms that have undergone a particular treatment.
Unique Apollo Label: sensitivityOfTreatmentDetection

fixed duration
type: Class
subclass of: duration
definition: A duration that is specified as a single number.
elucidation: A duration that is specified as a single number.
Unique Apollo Label: FixedDuration

real time span category definition
type: Class
subclass of: name of temporal interval
Unique Apollo Label: RealTimeSpanCategoryDefinition

real date span category definition
type: Class
subclass of: name of temporal interval
Unique Apollo Label: RealDateSpanCategoryDefinition

census objective specification
type: Class
subclass of: objective specification
definition: An objective specification to observe and/or estimate all the organisms of a particular taxon in a particular geographical region or place and create a data set about them.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An objective specification to observe all the organisms of a particular taxon in a particular geographical region or place and create a data set about them.
comment: Today, census taking typically consist of some mixture of counting the number of individuals in a population and estimating the numbers of subpopulations that are prone to overcounting or undercounting.

census plan specification
type: Class
subclass of: plan specification
definition: A plan specification with a census objective specification.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A plan specification with a census objective specification.

census taking
type: Class
subclass of: planned process
definition: A planned process that realizes a census plan specification.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A planned process that realizes a census plan specification.
Unique Apollo Label: Census

Wolbachia vector control strategy
type: Class
subclass of: vector control strategy
definition: A vector control strategy that is realized by releasing individuals of the vector population infected with bacteria of the taxon Wolbachia to inhibit reproduction of individuals in the vector population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control strategy that is realized by releasing individuals of the vector population infected with bacteria of the taxon Wolbachia to inhibit reproduction of individuals in the vector population.
Unique Apollo Label: WolbachiaControlStrategy

indoor residual spraying vector control strategy
type: Class
subclass of: vector control strategy
definition: A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population.
Unique Apollo Label: IndoorResidualSprayingVectorControlMeasure

container reduction vector control strategy
type: Class
subclass of: vector control strategy
definition: A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs.
Unique Apollo Label: ContainerReductionControlMeasure

treatment system logistics
type: Class
subclass of: information content entity
definition: An information content entity that specifies how many doses or courses of treatment, per a particular unit of time (typically one day), can be supplied for a given geographical region and/or how many of those doses or courses can subsequently be administered.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that specifies how many doses or courses of treatment, per a particular unit of time (typically one day), can be supplied for a given geographical region and/or how many of those doses or courses can subsequently be administered.
Unique Apollo Label: TreatmentSystemLogistics

treatment surveillance capability
type: Class
subclass of: disposition
definition: A disposition of a treatment surveillance infrastructure to detect individuals who have received treatment in the geographical region the infrastructure aims to cover.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A disposition of a treatment surveillance infrastructure to detect individuals who have received treatment in the geographical region the infrastructure aims to cover.
Unique Apollo Label: TreatmentSurveillanceCapability

name of temporal region
type: Class
subclass of: identifier

population serology survey
type: Class
subclass of: population survey
definition: A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population.
Unique Apollo Label: PopulationSerologySurvey

infection case list
type: Class
subclass of: data set
definition: A data set that is a collection of case records.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set that is a collection of case records.
Unique Apollo Label: CaseList

infection case record
type: Class
equivalent class: Restriction
  on property: is about
  qualified cardinality: 1
  on class: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: infection
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: infection
definition: A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set whose data items are about a host and its participation in an infection and potentially other activities occuring in the same time interval as the infection.
Unique Apollo Label: CaseRecord

deprecated infection case count
type: Class
definition: A count of individuals in a population who meet an infection case definition during a particular time interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A count of individuals in a population who meet an infection case definition during a particular time interval.
deprecated: true

epidemic interval
type: Class
subclass of: one-dimensional temporal region
definition: The temporal interval occupied by an epidemic.
definition editor: Matthew Diller
alternative label: epidemic period
elucidation: The temporal interval occupied by an epidemic.
Unique Apollo Label: EpidemicPeriod

individual mosquito behavior
type: Class
subclass of: behavior
definition: An individual behavior of a mosquito (organism of family Culicidae).
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An individual behavior of a mosquito (organism of family Culicidae).
Unique Apollo Label: MosquitoBehavior

individual human behavior
type: Class
subclass of: behavior
definition: An individual behavior of a human being.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An individual behavior of a human being.
Unique Apollo Label: HumanBehavior

transmission tree
type: Class
subclass of: data representational model
definition: A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data structure that represents, for a particular infection in ecosystem, a subset of infected organisms and for each infected organism in the subset except the first one infected temporally, its infection acquisition from an infected host as a machine-readable link to that infected host.
Unique Apollo Label: TransmissionTree
comment: Because a set A is a subset of itself, we capture the possibility that all infected organisms in the epidemic are represented in the tree.
comment: This definition allows for multiple trees in an epidemic because we did not require that the first case infected temporally be the index case, although the ideal situation is that there is one tree for the epidemic that includes the index case.

infectiousness
type: Class
equivalent class: Class
  intersection of: disposition
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
  intersection of: Restriction
    on property: is realized by
    all values from: infection
subclass of: disposition
subclass of: Restriction
  on property: characteristic of
  some values from: organism
editor preferred term: infectious disposition
definition: A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon.
definition editor: William R. Hogan
elucidation: A disposition inhering in an organism of a particular biological taxon that is realized only by the organism participating in an infection as the reproducing organism inside another organism of a different particular biological taxon.
comment: The disposition of Influenza A virus H3N2 subtype to infect human beings, the disposition of Plasmodium vivax to infect mosquitos and humans, the disposition of foot and mouth disease virus to infect cloven-hooved animals (sheep, cows, pigs, etc.).

potentially infectious contacting
type: Class
subclass of: biological_process
editor preferred term: potentially infectious contact process
definition: A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen.
definition editor: William R. Hogan
alternative label: potentially infectious contact
elucidation: A biological process that brings the organism into sufficiently close physical proximity to a pathogen population, either in or on a contaminated thing or an infectious host, such that the organism is likely but not certain to acquire an infection with the pathogen.

potentially infectious contact role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: is realized by
    some values from: potentially infectious contacting
subclass of: role
subclass of: Restriction
  on property: is realized by
  some values from: potentially infectious contacting
editor preferred term: potentially infectous contact role
definition: A role borne by an organism that is realized in a potentially infectious contact process.
definition editor: William R. Hogan
alternative label: contact role
alternative label: infectious contact role
elucidation: A role borne by an organism that is realized in a potentially infectious contact process.
comment: The organism bearing this role is the organism at risk for acquiring an infection when the role is realized. Also, this role differentiates participants in a process when there are two organisms participating, so it only begins to exist during its realization, justifying its existential restriction.

contacted organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: bearer of
    some values from: potentially infectious contact role
subclass of: organism
subclass of: Restriction
  on property: bearer of
  some values from: potentially infectious contact role
editor preferred term: potentially infectious contact organism
definition: An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process.
definition editor: William R. Hogan
elucidation: An organism that has been exposed to a pathogen by coming into close physical proximity with either an infectious host or a contaminated thing.

contact definition
type: Class
subclass of: information content entity
editor preferred term: potentially infectious contact definition
definition: An information content entity that specifies which kinds of processes involving an interaction between a given organism and either (1) another, potentially infectious organism or (2) a contaminated environment have a sufficiently high probability of resultling in an infection acquisition by the organism to be of interest to an outbreak investigation.
definition editor: William R. Hogan
elucidation: An information content entity that specifies which kinds of processes involving an interaction between a given organism and either (1) another, potentially infectious organism or (2) a contaminated environment have a sufficiently high probability of resultling in an infection acquisition by the organism to be of interest to an outbreak investigation.
Unique Apollo Label: ContactDefinition

ring individual treatment control strategy
type: Class
subclass of: individual treatment control strategy
definition: An individual treatment control strategy that immediately targets individuals in the population who are at the perimeter of an epidemic.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An individual treatment control strategy that immediately targets individuals in the population who are at the perimeter of an epidemic.
Unique Apollo Label: RingIndividualTreatmentControlMeasure

Wolbachia release site
type: Class
subclass of: seed site
definition: A seed site for a Wolbachia control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A site that is the bearer of a role which is realized by the release of Wolbachia-infected mosquitos.
Unique Apollo Label: wolbachiaReleaseSites

Wolbachia every nth site release action specification
type: Class
subclass of: vector release site action specification
definition: A vector release site action specification for a Wolbachia control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control action specification that specifies the location of Wolbachia release sites according to some predetermined spatial interval.
Unique Apollo Label: wolbachiaSitesEveryNth

leakage rate of Wolbachia infection in mosquito population infected with Wolbachia
type: Class
subclass of: rate measurement datum
definition: The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia.
Unique Apollo Label: wolbachiaEffectOnLeakageRate

transmission rate of pathogen to human from Wolbachia-infected mosquito bites
type: Class
subclass of: rate measurement datum
definition: The rate at which bites of mosquitoes infected with both Wolbachia and a particular pathogen such as dengue result in an infection in a susceptible human host.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The rate at which bites of mosquitoes infected with both Wolbachia and a particular pathogen such as dengue result in an infection in a susceptible human host.
Unique Apollo Label: wolbachiaEffectOnVectorialCapacity

adult vector control strategy
type: Class
subclass of: vector control strategy
definition: A vector control strategy that is realized by reducing the number of adults in a vector population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control strategy that is realized by reducing the number of adults in a vector population.

Wolbachia prerelease adult vector control strategy
type: Class
subclass of: adult vector control strategy
definition: An adult vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the adult population that gets infected with Wolbachia.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An adult vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the adult population that gets infected with Wolbachia.
Unique Apollo Label: wolbachiaPreReleaseAdultSuppressionEfficacy

Wolbachia prerelease larvicide vector control strategy
type: Class
subclass of: larvicide control strategy
definition: An larvicide vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the population that gets infected with Wolbachia.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An larvicide vector control strategy that is used prior to a Wolbachia vector control strategy to increase the percentage of the population that gets infected with Wolbachia.
Unique Apollo Label: wolbachiaPreReleaseLarvalSuppressionEfficacy

life stages with duration and mortality
type: Class
subclass of: data representational model
definition: A data structure that refers to (1) a subpopulation of a population based on life stage, (2) the rate of mortality of that subpopulation, and (3) the average duration of time that the individuals in the subpopulation spend in that life stage.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data structure that refers to (1) a subpopulation of a population based on life stage, (2) the rate of mortality of that subpopulation, and (3) the average duration of time that the individuals in the subpopulation spend in that life stage.
Unique Apollo Label: LifeStageWithDurationAndMortality

Wolbachia effect on egg mortality rate in mosquito population
type: Class
subclass of: biological process involved in interaction with host
definition: A process of change in the egg mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A process of change in the egg mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
Unique Apollo Label: wolbachiaEffectOnEggMortalityRate

Wolbachia effect on adult mortality rate in mosquito population
type: Class
subclass of: biological process involved in interaction with host
definition: A process of change in the adult mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A process of change in the adult mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
Unique Apollo Label: wolbachiaEffectOnAdultMortalityRate

Wolbachia effect on larval mortality rate in mosquito population
type: Class
subclass of: biological process involved in interaction with host
definition: A process of change in the larval mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A process of change in the larval mortality rate of a mosquito population that is the outcome of an infection in that population by a Wolbachia bacteria population.
Unique Apollo Label: wolbachiaEffectOnLarvalMortalityRate

Wolbachia effect on female fecundity in mosquito population
type: Class
subclass of: biological process involved in interaction with host
definition: A process of change in fecundity of females in a mosquito population that is the outcome of an infection in that population with a Wolbachia bacteria population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A process of change in fecundity of females in a mosquito population that is the outcome of an infection in that population with a Wolbachia bacteria population.
Unique Apollo Label: wolbachiaEffectOnFecundity

confidence interval
type: Class
subclass of: data item
definition: A data item that specifies both an interval estimate centered around some sample statistic, and the probability that the process/method of obtaining the interval estimate's range of values will generate an interval that contains some unobserved population parameter of interest.
definition editor: Matthew Diller
definition editor: William R. Hogan

Wolbachia release interval
type: Class
subclass of: seed release interval
definition: A seed release interval for a Wolbachia control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A seed release interval for a Wolbachia control measure.
Unique Apollo Label: wolbachiaReleaseInterval

mean with confidence interval
type: Class
subclass of: data representational model
definition: A data structure that specifies both the sample mean and the confidence interval generated by the measurement process.
definition editor: Matthew Diller
definition editor: William R. Hogan
Unique Apollo Label: MeanWithConfidenceInterval

mean with standard deviation
type: Class
subclass of: data representational model
definition: A data structure that specifies both the sample mean and the standard deviation generated by the measurement process.
definition editor: Matthew Diller
definition editor: William R. Hogan
Unique Apollo Label: MeanWithStandardDeviation

number of Wolbachia-infected mosquitoes released per house
type: Class
subclass of: vector control action specification
definition: A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household for some Wolbachia control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control action specification that specifies the number of Wolbachia-infected adult mosquitoes to be released at each household.
Unique Apollo Label: wolbachiaSeedAdultsPerHouse

clear Wolbachia upon vector migration
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that when set to true, results in the simuator clearing each simulated Wolbachia-infected mosquito of its simulated Wolbachia infection whenever it migrates out of the simulated population location.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator action specification that when set to true, results in the simulator clearing each simulated Wolbachia-infected mosquito of its simulated Wolbachia infection whenever it migrates out of the simulated population location.
Unique Apollo Label: clearWolbachiaOnMigration

disease outcome with probability
type: Class
subclass of: calculated datum
definition: A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism.
Unique Apollo Label: DiseaseOutcomeWithProbability

date
type: Class
subclass of: name of temporal region
definition: A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
Unique Apollo Label: date

ring diameter in meters
type: Class
subclass of: scalar value specification
definition: A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A scalar value specification that gives the diameter in meters of the circular area around which all organisms in a population are living will receive a vaccination as part of a ring vaccination control measure.
Unique Apollo Label: ringDiameterInMeters

Wolbachia effect on mating probability
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator actions specification that specifies the factor by which to multiply the mating probability of a male mosquito if it is infected with a Wolbachia bacterium.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator actions specification that specifies the factor by which to multiply the mating probability of a male mosquito if it is infected with a Wolbachia bacterium.
Unique Apollo Label: wolbachiaEffectOnMatingProbability

minimum value
type: Class
subclass of: data item
definition: A data item that specifies the smallest numerical value in a data set of scalar measurement data items.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that specifies the smallest numerical value in a data set of scalar measurement data items.
Unique Apollo Label: minimumValue

maximum value
type: Class
subclass of: data item
definition: A data item that specifies the largest numerical value in a data set of scalar measurement data itmes.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that specifies the largest numerical value in a data set of scalar measurement data itmes.
Unique Apollo Label: maximumValue

statistical confidence
type: Class
subclass of: calculated datum
definition: A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest.
Unique Apollo Label: confidence

closure period
type: Class
definition: A one-dimensional temporal region occupied by a place closure control strategy.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A one-dimensional temporal region occupied by a place closure control strategy.
deprecated: true

lower bound
type: Class
subclass of: information content entity
definition: An information content entity that delimits an interval data structure based on some value that is less than or equal to all other values within that data structure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that delimits an interval data structure based on some value that is less than or equal to all other values within that data structure.
Unique Apollo Label: lowerBound

fraction of vector adults affected
type: Class
subclass of: measurement datum
definition: A measurement datum that is the fraction of a particular adult vector population that have undergone 1) infection acquisition with a pathogen, and 2) have experienced some outcome of the resulting infection.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A measurement datum that is the fraction of a particular adult vector population that have undergone 1) infection acquisition with a pathogen, and 2) have experienced some outcome of the resulting infection.
Unique Apollo Label: fractionOfVectorIndividualsAffected

fraction reduction of eggs
type: Class
subclass of: measurement datum
definition: A measurement datum that is the fraction of eggs laid by a particular host population that has been destroyed and thus will not develop into a new member of the population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A measurement datum that is the fraction of eggs laid by a particular host population that has been destroyed and thus will not develop into a new member of the population.
Unique Apollo Label: fractionReductionOfEggs

fraction reduction of larvae
type: Class
subclass of: measurement datum
definition: A measurement datum that is the fraction of the larval subpopulation of a particular host population that has died due to some event in the population (e.g, due to a particular control measure).
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A measurement datum that is the fraction of the larval subpopulation of a particular host population that has died due to some event in the population (e.g, due to a particular control measure).
Unique Apollo Label: fractionReductionOfLarvae

vector bite radius
type: Class
subclass of: length measurement datum
definition: A length measurement datum that specifies the radius of a circle, which is centered at a vector organism, for which there is a certain probability that the vector organism will bite a susceptible host.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A length measurement datum that specifies the radius of a circle, which is centered at a vector organism, for which there is a certain probability that the vector organism will bite a susceptible host.
Unique Apollo Label: biteRadius

time between vector bites
type: Class
subclass of: duration
definition: A duration that measures the temporal interval between some vector bite n and some vector bite n+1.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A duration that measures the temporal interval between some vector bite n and some vector bite n+1.
Unique Apollo Label: timeBetweenBites

migration speed
type: Class
subclass of: rate measurement datum
definition: A rate measurement datum of that divides the total distance traveled during some migration process by the duration of the temporal interval occupied by that process.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A rate measurement datum of that divides the total distance traveled during some migration process by the duration of the temporal interval occupied by that process.
Unique Apollo Label: migrationSpeed

shade affinity
type: Class
subclass of: probability
definition: An information content entity that specifies the probability that a given mosquito will realize a disposition to seek out a shaded environment when it isn't seeking a host or ovisite.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that specifies the probability that a given mosquito will realize a disposition to seek out a shaded environment when it isn't seeking a host or ovisite.
Unique Apollo Label: shadeAffinity

movement speed
type: Class
subclass of: rate measurement datum
definition: A rate measurement datum that specifies the ratio of distance travelled during a movement process to the duration of the time interval occupied by the process.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A rate measurement datum that specifies the ratio of distance travelled during a movement process to the duration of the time interval occupied by the process.
Unique Apollo Label: speedOfMovement

mortality rate
type: Class
subclass of: rate measurement datum
definition: A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval.
Unique Apollo Label: mortalityRate

ratio of outdoor to indoor ovisites
type: Class
subclass of: data item
definition: A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that specifies, as a ratio, the total count of oviposition sites located externally to all places in a geographic region relative to the total count of oviposition sites located internally to some place in that geographic region.
Unique Apollo Label: ratioOfOutdoorToIndoorOvisites

upper bound
type: Class
subclass of: information content entity
definition: An information content entity that delimits an interval data structure based on some value that is greater than or equal to all other values within that data structure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that delimits an interval data structure based on some value that is greater than or equal to all other values within that data structure.
Unique Apollo Label: upperBound

standard deviation
type: Class
subclass of: data item
definition: A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: σ
elucidation: A data item that specifies the dispersion of values around some parameter in a set of data, and whose values are standardized to express the same unit of measure as the parameter of interest.
Unique Apollo Label: standardDeviation

quarantine period
type: Class
subclass of: duration
definition: The duration of some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The duration of some process wherein one or more potentially infectious contact organisms (i.e., contacted organisms) are under physical isolation from other organisms within a population.
Unique Apollo Label: quarantinePeriod

mosquito mating probability
type: Class
subclass of: probability
definition: The probability that some male mosquito and some female mosquito within a certain distance of each other realize some disposition to reproduce with one another.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The probability that some male mosquito and some female mosquito within a certain distance of each other realize some disposition to reproduce with one another.
Unique Apollo Label: matingProbability

affinity for buildings
type: Class
subclass of: probability
definition: An information content entity that specifies the probability that a given mosquito realizes some disposition to seek out a building if it isn't seeking a host or ovisite.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An information content entity that specifies the probability that a given mosquito realizes some disposition to seek out a building if it isn't seeking a host or ovisite.
Unique Apollo Label: buildingAffinity

linear distance travelled between oviposits
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the linear distance a female mosquito will travel to find the next oviposition site after depositing some of its eggs at the previous one.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator action specification that specifies the linear distance a female mosquito will travel to find the next oviposition site after depositing some of its eggs at the previous one.
Unique Apollo Label: straightTravelAfterOviposit

eggs per brood
type: Class
subclass of: average value
definition: An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population.
Unique Apollo Label: eggsPerBrood

efficacy
type: Class
subclass of: disposition
definition: A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process.
Unique Apollo Label: efficacy
comment: We often say in natural language it is the efficacy of the triggering planned process such as vaccination. However, processes do not have properties such as roles, dispositions, functions, qualities in BFO. And this is also not a process profile, because it is not the process of a quality changing values (determinates) over time. Nevertheless, it is natural to classify efficacies based on the type of triggering process because that is what differentiates what happens when they are realized. For example, a vaccination efficacy will be realized through different processes than a quarantine efficacy. For individual treatments, the triggering process is a treatment (as defined by OGMS).

prodromal period
type: Class
subclass of: process
definition: A temporal part of a disease course that itself has a temporal part of becoming symptomatic, followed by another temporal part that is characterized by the organism experiencing mild, non-disease-specific symptoms.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A temporal part of a disease course that itself has a temporal part of becoming symptomatic, followed by another temporal part that is characterized by the organism experiencing mild, non-disease-specific symptoms.

fulminant period
type: Class
subclass of: process
definition: A temporal part of a disease course that 1) itself has a temporal part of becoming severely symptomatic, 2) terminates in either death or some bodily harm, and 3) has a sudden onset and short duration.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A temporal part of a disease course that 1) itself has a temporal part of becoming severely symptomatic, 2) terminates in either death or some bodily harm, and 3) has a sudden onset and short duration.
comment: Although it is often or even typically preceded by a prodromal period, it is not always the case. Therefore "immediately preceded by some prodromal period" cannot be a necessary condition.

vector bite probability
type: Class
subclass of: probability
definition: The probablity that a female mosquito feeds on or probes the host given an interaction between the mosquito and the host that brings them within a certain proximity (the bite radius).
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The probability that a female mosquito feeds on or probes the host given an interaction between the mosquito and the host that brings them within a certain proximity (the bite radius).
Unique Apollo Label: biteProbability

male mosquito mating radius
type: Class
subclass of: length measurement datum
definition: A length measurement datum that specifies the radius of a circle, which is centered at a male vector organism, for which there is some probability that it will mate with a female mosquito.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A length measurement datum that specifies the radius of a circle, which is centered at a male vector organism, for which there is some probability that it will mate with a female mosquito.
Unique Apollo Label: maleMatingRadius

infectious disease control strategy cover radius
type: Class
subclass of: length measurement datum
definition: A length measurement datum that specifies the radius of a circle that defines the geographical region in which some infectious disease control strategy will be implemented.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A length measurement datum that specifies the radius of a circle that defines the geographical region in which some infectious disease control strategy will be implemented.
Unique Apollo Label: coverRadius

species of treated organism
type: Class
subclass of: taxonomy identifier
definition: A taxonomy identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the NCBI taxonomy database that specifies the taxonomic classification of some organism that is the recipient of some treatment.
Unique Apollo Label: speciesOfTreatedOrganism

drug identifier
type: Class
subclass of: identifier
definition: An identifier that denotes a drug product.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that denotes a drug product.
Unique Apollo Label: drugId

mean median minimum maximum summary statistics data structure
type: Class
subclass of: data representational model
definition: A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data.
Unique Apollo Label: MeanMedianMinimumMaximum

heterogenous carrying capacity
type: Class
subclass of: conditional specification
definition: A conditional specification for some epidemic simulator that is triggered by a Boolean value that, if true, specifies that there is a non-uniform distribution of oviposition site carrying capacities in a simulated vector population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A conditional specification for some epidemic simulator that is triggered by a Boolean value that, if true, specifies that there is a non-uniform distribution of oviposition site carrying capacities in a simulated vector population.
Unique Apollo Label: heterogenousCarryingCapacity

seed site
type: Class
subclass of: site
definition: A site that is the bearer of a role that is realized by the release of artificially-infected vectors for the purpose of infecting the local vector population with a certain pathogen.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A site that is the bearer of a role that is realized by the release of artificially-infected vectors for the purpose of infecting the local vector population with a certain pathogen.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

seed release interval
type: Class
subclass of: vector control action specification
definition: A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

vector release site action specification
type: Class
subclass of: vector control action specification
definition: A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

number of artificially-infected vectors released per house
type: Class
subclass of: vector control action specification
definition: A vector control action specification that specifies the number of artificially-infected vectors to be released at each household.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control action specification that specifies the number of artificially-infected vectors to be released at each household.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

clear infection upon vector migration
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that, when set to true, results in the simulator clearing each simulated artificially-infected vector of its simulated infection whenever it migrates out of the simulated population location.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator action specification that, when set to true, results in the simulator clearing each simulated artificially-infected vector of its simulated infection whenever it migrates out of the simulated population location.
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.

SNOMED concept identifier
type: Class
subclass of: identifier
definition: An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy.
Unique Apollo Label: SnomedId

probability
type: Class
subclass of: data item
definition: A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents.
Unique Apollo Label: Probability
comment: The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'.

minimum eggs per oviposition site
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the minimum number of eggs that any simulated female mosquito will oviposit during a gonotrophic cycle.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator action specification that specifies the minimum number of eggs that any simulated female mosquito will oviposit during a gonotrophic cycle.
Unique Apollo Label: minimumEggsPerOviposition

age-dependent fecundity reduction
type: Class
subclass of: rate measurement datum
definition: A rate measurement datum that measures the percentage decrease per unit time (typically per day) in the number of offspring to which a female mosquito passes an infection with a particular pathogen (e.g., Wolbachia).
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A rate measurement datum that measures the percentage decrease per unit time (typically per day) in the number of offspring to which a female mosquito passes an infection with a particular pathogen (e.g., Wolbachia).
Unique Apollo Label: ageDependentFecundityReduction

carrying capacity per house
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house.
Unique Apollo Label: carryingCapacityPerHouse
comment: Mosquitos can sense eggs in ovisite so tend to lay in places not at max.

reactive control measure operator
type: Class
subclass of: epidemic simulator action specification
definition: An epidemic simulator action specification that specifies the comparison operation to use to determine whether some value, relative to a threshold, is one that should trigger the implementation of a control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An epidemic simulator action specification that specifies the comparison operation to use to determine whether some value, relative to a threshold, is one that should trigger the implementation of a control measure.
Unique Apollo Label: reactiveControlMeasureOperator

gonotrophic period duration
type: Class
definition: A time measurement datum of the length of the temporal interval occupied by a gonotropic period.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A time measurement datum of the length of the temporal interval occupied by a gonotropic period.
deprecated: true

description
type: Class
subclass of: textual entity
definition: A textual entity that specifies characteristics of some entity.
definition editor: Matthew Diller
definition editor: William Hogan
elucidation: A textual entity that specifies characteristics of some entity.
Unique Apollo Label: description

parametric probability distribution
type: Class
subclass of: probability distribution
definition: A probability distribution where the probability of each outcome is the range of a function (whose domain is the outcomes) that is calculated using one or more constant values (called parameters).
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A probability distribution where the probability of each outcome is the range of a function (whose domain is the outcomes) that is calculated using one or more constant values (called parameters).
Unique Apollo Label: ParametricProbabilityDistribution

seed infections into vector population control measure
type: Class
subclass of: vector control strategy
definition: A vector control strategy that has 1) an action specification that is realized in releasing artificially-infected vector organisms into a vector population, and 2) an objective specification of spreading this infection throughtout the vector population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A vector control strategy that has 1) an action specification that is realized in releasing artificially-infected vector organisms into a vector population, and 2) an objective specification of spreading this infection throughtout the vector population.
comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.

ovisite carrying capacity
type: Class
subclass of: calculated datum
definition: A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining.

geographical movement of organism
type: Class
subclass of: behavior
definition: A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification.

cut-off point specification
type: Class
subclass of: action specification
definition: An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An action specification that delineates some minimum value or maximum value for some test statistic within a continuous probability distribution that is meant to serve as a lower bound or upper bound, respectively, for some population or sample of interest.
Unique Apollo Label: cutTailAt

prodromal period duration
type: Class
subclass of: duration
definition: A duration that measures a temporal region occupied by a prodromal period.
definition editor: Matthew Diller
definition editor: William R. Hogan

fulminant period duration
type: Class
subclass of: duration
definition: A duration that measures a temporal region occupied by a fulminant period.
definition editor: Matthew Diller
definition editor: William R. Hogan

identifier of species of diseased organism
type: Class
subclass of: taxonomy identifier
definition: A taxonomy identifier curated by the NCBI taxonomy database that has been used to specify the species of some organism in which some disease has been realized.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the NCBI taxonomy database that has been used to specify the species of some organism in which some disease has been realized.
Unique Apollo Label: speciesWithDiseasae

identifier for species of case
type: Class
subclass of: taxonomy identifier
definition: A taxonomy identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the NCBI taxonomy database that has been used to identify the species of some organism that meets a case definition.
Unique Apollo Label: speciesOfCase

travel-related infectious disease control strategy
type: Class
subclass of: infectious disease control strategy
editor preferred term: infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem
definition: An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem.
definition editor: William R. Hogan
elucidation: An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem.

travel recommendation control strategy
type: Class
subclass of: travel-related infectious disease control strategy
editor preferred term: travel recommendation infectious disease control strategy
definition: A travel-related infectious disease control strategy that has an action specification that is realized by making recommendations to travelers to either (1) avoid travel to an ecosystem with an ongoing infection such as an epidemic, (2) take precautions when traveling to such an ecosystem, (3) receive certain vaccinations prior to traveling to such an ecosystem, or (4) take certain medications when traveling to such an ecosystem
definition editor: William R. Hogan
elucidation: A travel-related infectious disease control strategy that recommends to travelers to either (1) avoid travel to a region with an ongoing infection such as an epidemic, (2) take precautions when traveling to such a region, (3) receive certain vaccinations prior to traveling to such a region, or (4) take certain medications when traveling to such a region

contact isolation control measure
type: Class
subclass of: case isolation control strategy
definition: A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms.
Unique Apollo Label: ContactIsolationControlMeasure

colonization duration
type: Class
subclass of: duration
definition: A duration that measures the temporal interval occupied by some colonization.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A duration that measures the temporal interval occupied by some colonization.
Unique Apollo Label: colonizationDuration

identifier of species of population
type: Class
subclass of: taxonomy identifier
definition: A taxonomy identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms.
Unique Apollo Label: populationSpecies

RxNorm drug concept identifier
type: Class
subclass of: identifier
definition: An identifier curated by the National Library of Medicine as a unique string of integer numerals to be used as a standard way of denoting each concept in the RxNorm terminology.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the National Library of Medicine as a unique string of integer numerals to be used as a standard way of denoting each concept in the RxNorm terminology.
Unique Apollo Label: RxNormId

LOINC identifier
type: Class
subclass of: identifier
definition: An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database.
Unique Apollo Label: LoincId

laboratory test LOINC identifier
type: Class
subclass of: LOINC identifier
definition: A LOINC identifier that refers to some clinical laboratory test conducted in a particular context..
definition editor: Matthew Diller
definition editor: Willliam R. Hogan
elucidation: A LOINC identifier that refers to some clinical laboratory test conducted in a particular context..
Unique Apollo Label: testLoincId

PubMed identifier
type: Class
subclass of: identifier
definition: An identifier curated by the United States National Library of Medicine and National Institutes of Health that denotes some publication record in the MEDLINE database.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by the United States National Library of Medicine and National Institutes of Health that denotes some publication record in the MEDLINE database.
Unique Apollo Label: pubMedId

ORCID
type: Class
definition: An identifier curated by ORCID, Inc. to denote some academic author.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier curated by ORCID, Inc. to denote some academic author.
term replaced by: ORCID identifier
Unique Apollo Label: orcId
deprecated: true

count of disease cases
type: Class
subclass of: population count
definition: A count of individuals in a population who meet the criteria of some case definition during some time interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A count of individuals in a population who meet the criteria of some case definition during some time interval.
Unique Apollo Label: CaseCount

count of cases in an epidemic
type: Class
subclass of: count of disease cases
definition: A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval.
Unique Apollo Label: EpidemicCaseCounts

insecticide-treated net control measure
type: Class
subclass of: adult vector control strategy
definition: An adult vector control strategy that has 1) an action specification that is realized by the use of insecticide-treated nets within households, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An adult vector control strategy that has 1) an action specification that is realized by the use of insecticide-treated nets within households, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host.
Unique Apollo Label: InsecticideTreatedNetControlMeasure

schedule
type: Class
subclass of: plan specification
definition: A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A plan specification that specifies 1) the quantity of which some material entity will be allocated to the eventual realization of some action specification, and 2) the temporal regions in which each action specification is to be realized.
Unique Apollo Label: Schedule

population colonization census
type: Class
subclass of: population census
definition: A population census about the organisms specific to that population that were the host in some colonization acquisition.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A population census about the organisms specific to that population that were the host in some colonization acquisition.
Unique Apollo Label: PopulationColonizationCensus

drug treatment efficacy
type: Class
subclass of: efficacy
definition: The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome.
Unique Apollo Label: drugTreatmentEfficacy
comment: While we understand that 'drug efficacy' can have multiple interpretations, this class is specifically referring to drug efficacy in the context of clinical outcomes. As such, our definition excludes any mention of efficacy as it relates to pharmacodynamics.

latitude and longitude coordinate pair
type: Class
subclass of: geodetic datum
definition: A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set that comprises exactly one latitude measurement datum and exactly one longitude measurement datum as its elements, and optiionally the geodetic datum used as the coordinate system for the measurements, and each of these measurements is about the same zero-dimensional geographical region.
Unique Apollo Label: LatLongPair

age in years datum
type: Class
subclass of: time measurement datum
definition: A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A time measurement datum that refers to the temporal interval occupied by the life course of some organism and that takes 'years' as its measurement unit label.
Unique Apollo Label: ageInYears

contamination period duration
type: Class
subclass of: duration
definition: A duration that measures a temporal region occupied by some contamination.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A duration that measures a temporal region occupied by some contamination.
Unique Apollo Label: contaminationDuration

healthcare facility identifier
type: Class
subclass of: facility identifier
definition: A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function.
Unique Apollo Label: healthcareFacilityId

disease transmission model identifier
type: Class
subclass of: identifier
definition: An identifier that refers to some disease transmission model model.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that refers to some disease transmission model model.
Unique Apollo Label: modelId

facility identifier
type: Class
subclass of: identifier
definition: An identifier that denotes some architectural structure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that denotes some architectural structure.
Unique Apollo Label: FacilityId

taxonomy identifier
type: Class
subclass of: identifier
definition: An identifier that denotes a biological taxonomic group.
definition editor: Matthew Diller
definition editor: William R. Hogan
Unique Apollo Label: taxonId

disease case identifier
type: Class
subclass of: identifier
definition: An identifier that denotes an organism included in some infection case count.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that denotes an organism included in some infection case count.
Unique Apollo Label: caseId

infection acquisition through sexual activity with infectious host
type: Class
subclass of: infection acquisition from infectious host
definition: An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting
definition editor: Matthew Diller
comment: Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika.

rate of hydrological precipitation
type: Class
subclass of: rate measurement datum
definition: A rate measurement datum that is the result of the measurement of the volume of water produced by some hydrological precipitation process at a particular geographical region divided by the number of temporal intervals of equal duration over which the precipitation occurred.
definition editor: Matthew Diller
definition editor: William R. Hogan

mean rate of hydrological precipitation
type: Class
subclass of: average value
definition: An average value that takes, as input, some set of rate of hydrological precipitation data that were recorded over a particular duration of time.
definition editor: Matthew Diller
definition editor: William R. Hogan

mean air temperature
type: Class
subclass of: average value
definition: An average value that takes, as input, some set of air temperature measurement data that were recorded over a particular duration of time.
definition editor: Matthew Diller
definition editor: William R. Hogan

potentially infectious sexual contacting
type: Class
subclass of: sexual activity
definition: A sexual activity with at least one infectious host as participant where the infectious host(s) are infected with a pathogen that has a disposition to infect the tissues of the non-infected host that came into physical contact with the infectious host during the activity.
definition editor: Matthew Diller
definition editor: William R. Hogan

host population
type: Class
subclass of: population
editor preferred term: host population
definition: A population of organisms some of which were susceptible to infection with a particular pathogen at some point in their lives.
definition editor: William R. Hogan
alternative label: population of host organisms

prioritization scheme for control measure
type: Class
subclass of: action specification
definition: An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure.
Unique Apollo Label: controlMeasureNamedPrioritizationScheme

one-way sensitivity analysis of a continuous variable
type: Class
subclass of: data transformation
definition: A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data transformation that takes as its input exactly one continuous variable as a value and assesses whether any statistically significant change to that variable will produce some change to the model's output.
comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.

citation identifier
type: Class
subclass of: identifier
definition: An identifier that is an integer numeral that denotes some citation.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that is an integer numeral that denotes some citation.
Unique Apollo Label: referenceId

location of sampling process
type: Class
subclass of: geographical region
definition: A geographic region that contains a sampling process.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A geographic region that contains a sampling process.
Unique Apollo Label: whereSampled

infection acquisition from vertical transmission
type: Class
subclass of: infection acquisition from infectious host
definition: An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: congenital infection acquisition
alternative label: infection acquisition from mother-to-child transmission
elucidation: An infection acquisition from infectious host by an embryo, fetus, or baby from its infectious mother while in utero, in egg at any point prior to hatching (even after laying), or during childbirth.

source code repository
type: Class
subclass of: data set
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 term: 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 term: 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.

compiled software code
type: Class
subclass of: software
editor preferred term: machine instructions compiled from software source code
definition: A software that is the specified output of some compilation of software process
definition editor: William R. Hogan

scale-free network model
type: Class
subclass of: algorithm
definition: An algorithm that models some scale-free network.
definition editor: Matthew Diller
definition editor: William R. Hogan

scale-free network
type: Class
subclass of: graph of vertices
definition: A graph of vertices in which, for some fraction of vertices, P(k), the number of connections, k, varies as a power of some parameter, γ. In other words, P(k) ~ k^(-γ), where 2 < γ < 3.
definition editor: Matthew Diller
definition editor: William R. Hogan

synthetic ecosystem data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: ecosystem
definition: A data set that represents 1) one or more collections of organisms at some time and some geographical region; and optionally 2) the school facilities, workplace facilities, and health care facilities in that region.
definition editor: Matthew Diller
definition editor: William R. Hogan
Unique Apollo Label: SyntheticEcosystem
comment: The interactions between each organism as they move between these facilities may also be included in the data set.

conditional probability
type: Class
subclass of: probability
definition: A probability whose value is dependent upon the occurrence, known or presumed, of some process.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A probability whose value is dependent upon the occurrence, known or presumed, of some process.
Unique Apollo Label: conditionalProbability

probability of infection over time
type: Class
subclass of: conditional probability
definition: A conditional probability whose value is dependent upon the duration of some colonization or infection.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A conditional probability whose value is dependent upon the duration of some colonization or infection.
Unique Apollo Label: probabilityOfInfectionOverTime

epidemic threshold
type: Class
subclass of: data item
definition: A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population.
definition editor: Matthew Diller
definition editor: William R. Hogan

human travel
type: Class
subclass of: geographical movement of organism
definition: A geographical migration of an organism belonging to the species Homo sapiens.
definition editor: Matthew Diller
definition editor: William R. Hogan

human air travel
type: Class
subclass of: human travel
definition: Human travel that involves 1) movement from one geographical region to another through the air as a temporal proper part, and 2) the use of some processed material (e.g., airplane, hang glider) for propulsion that has some function of mechanical flight.
definition editor: Matthew Diller
definition editor: William R. Hogan

human mobility data item
type: Class
subclass of: data item
definition: A data item that is about one or more instances of human travel, and that specifies the geographical start location, geographical end location, and the geographical regions visited throughout the process.
definition editor: Matthew Diller
definition editor: William R. Hogan

software license
type: Class
subclass of: copyright license
definition: A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A copyright license that is about some software and contains one or more conditional specifications that specify the use and redistribution of the software.

complete software license identifier
type: Class
subclass of: identifier
definition: An identifier that refers to a specific software license.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that refers to a specific software license.
Unique Apollo Label: SoftwareLicenseIdentification

software license version identifier
type: Class
subclass of: identifier
definition: An identifier that, as part of a complete software license identifier, refers to one specific version of the software license.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that, as part of a complete software license identifier, refers to one specific version of the software license.
Unique Apollo Label: licenseVersion

software license identifier
type: Class
subclass of: identifier
definition: An identifier that refers to all versions of a specific software license.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An identifier that refers to all versions of a specific software license.
Unique Apollo Label: licenseName

software license URL
type: Class
subclass of: unique resource locator
definition: A unique resource locator that constitutes a reference to some software license.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A unique resource locator that constitutes a reference to some software license.
Unique Apollo Label: licenseLocation

population dynamics model
type: Class
subclass of: simulation software application
editor preferred term: model of population dynamics software application
definition: An simulation software application that when realized simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An algorithm that simulates changes in the size and life stage distribution of a population or populations of organisms of a particular biological taxon.

disease surveillance objective specification
type: Class
subclass of: objective specification
editor preferred term: disease surveillance objective specification
definition: An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval.

mortality data
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: population
editor preferred term: population mortality data set
definition: A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon.

pathogen evolution model
type: Class
subclass of: simulation software application
editor preferred term: pathogen evolution model software application
definition: A simulation software application that simulates the evolution over time of a particular pathogen of a particular biological taxon.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: Simulation software that simulates the evolution over time of a particular pathogen of a particular biological taxon.

disease surveillance
type: Class
subclass of: planned process
definition: A planned process that is the realization of a disease surveillance objective specification.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A planned process that is the realization of a disease surveillance objective specification.

self-initiated travel avoidance behavior
type: Class
subclass of: individual human behavior
definition: Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: Individual human behavior that involves either 1) remaining in some susceptible population or some exposed population or 2) human movement away from or around an infectious population, in order to avoid being participant in some infection acquisition.

social interaction data item
type: Class
subclass of: data item
definition: A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s).
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that is about one or more instances of social interaction between two or more individuals, and that specifies the temporal duration of interaction, spatial distance of individuals, geographical location of individuals, and the number of individuals participant in some social behavior(s).

Susceptible-Infected-Susceptible model
type: Class
subclass of: compartmental disease transmission model
definition: A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A compartmental disease transmission model that represents some infection in ecosystem in which there is only a susceptible population and an infectious population, such that individuals who aren't infectious are susceptible.

Susceptible-Infected-Resistant model
type: Class
subclass of: compartmental disease transmission model
definition: A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, infectious individuals, and recovered individuals, such that recovered individuals are immune to future infection.

contact tracing
type: Class
subclass of: infectious disease control strategy
definition: An infectious disease control strategy that identifies and treats contacted organisms in a host population.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An infectious disease control strategy that identifies and treats contacted organisms in a host population.

Susceptible-Exposed-Infectious-Recovered model
type: Class
subclass of: compartmental disease transmission model
definition: A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A compartmental disease transmission model that represents some infection in ecosystem in which there are compartments for susceptible individuals, exposed individuals, infectious individuals, and immune inviduals, such that exposed individuals are infected but cannot transmit the pathogen.

metapopulation disease transmission model
type: Class
subclass of: disease transmission model
definition: A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A disease transmission model that is about two or more collections of organisms of a particular biological taxon in separate geographical locations and some geographical migration of organisms between them.

two-strain Susceptible-Infectious-Resistant model
type: Class
subclass of: Susceptible-Infected-Resistant model
definition: A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens.

disease surveillance data
type: Class
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: disease surveillance
definition: A data set that is about some disease surveillance.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set that is about some disease surveillance.

disease transmission tree estimator
type: Class
subclass of: software application
editor preferred term: disease transmission tree estimator software application
definition: A software application that implements an algorithm that has specified output some transmission tree.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An algorithm that has specified output some transmission tree.

mechanical flight function
type: Class
subclass of: function
definition: A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in.

infectious disease forecaster
type: Class
subclass of: simulation software application
editor preferred term: software application that forecasts disease transmission
definition: A simulation software application that has as output one or more predicted count data items that are about a host population and that predict how many infections will occur at or will have occurred at some temporal region relative to when the data items are created.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: disease forecasting software
alternative label: infectious disease forecasting software application

case series
type: Class
equivalent class: Class
  intersection of: investigation
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: disease state design
  intersection of: Restriction
    on property: has occurrent part
    some values from: Class
      intersection of: population survey
      intersection of: Restriction
        on property: has_specified_input
        some values from: case definition
subclass of: investigation
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: disease state design
subclass of: Restriction
  on property: has occurrent part
  some values from: Class
    intersection of: population survey
    intersection of: Restriction
      on property: has_specified_input
      some values from: case definition
definition: An investigation that realizes the concretization of some disease state design and that has as an occurrent part some population survey that has specified input some case definition.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An investigation following a disease state study design that includes a population survey as part, where a case definition used in the population survey to ascertain disease state.
Unique Apollo Label: CaseSeries

case series data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: case series
definition: A data set that is the output of a case series investigation.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set that is the output of a case series investigation.

epidemic data set
type: Class
equivalent class: Restriction
  on property: is about
  some values from: epidemic
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: epidemic
definition: A data set about an instance of an epidemic.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data set about an instance of an epidemic.

disease transmission model software
type: Class
subclass of: simulation software application
editor preferred term: disease transmission model software application
definition editor: Matthew Diller
definition editor: William R. Hogan

data format converter
type: Class
subclass of: software application
editor preferred term: data format converter software application
definition editor: Matthew Diller
definition editor: William R. Hogan

phylogenetic tree constructor
type: Class
subclass of: software application
editor preferred term: phylogenetic tree constructor software application
definition: A software application that implements an algorithm that has specified output a phylogenetic tree
definition editor: William R. Hogan

data visualizer
type: Class
subclass of: software application
editor preferred term: data visualizer software application
definition: A software application that implements an algorithm that has some data visualizer software objective specification as part.
definition editor: Matthew Diller
definition editor: William R. Hogan

computational modeling toolkit
type: Class
subclass of: software application
editor preferred term: computational modeling toolkit software application
definition editor: Matthew Diller
definition editor: William R. Hogan

data parsing
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: data set
editor preferred term: data parsing process
definition: A data transformation that has a dataset, encoded in a particular data format specification, as input and extracts certain elements or parts of the dataset, typically into the volatile memory of a computer.
definition editor: William R. Hogan
alternative label: data reading process
alternative label: reading data

synthetic ecosystem constructor
type: Class
subclass of: software
editor preferred term: synthetic ecosystem constructor software
definition: A software that when compiled and run, has specified output of an agent-level ecosystem data set.
definition editor: William R. Hogan
alternative label: software for creating a synthetic ecosystem dataset
comment: example: Synthia, SPEW

total fatal disease cases
type: Class
subclass of: data item
definition: A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that is the output of some infection case count and that represents the number of infectious disease cases that ended in death.
Unique Apollo Label: totalFatalCaseCount

total disease cases
type: Class
equivalent class: Class
  intersection of: population count
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: bearer of
        some values from: disease
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: population infection survey
subclass of: population count
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: bearer of
      some values from: disease
subclass of: Restriction
  on property: is_specified_output_of
  some values from: population infection survey
definition: A count of the total number of diseased indivduals in a population during a particular time interval.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: The total number of diseased individuals in a population at a point in time.
Unique Apollo Label: totalCaseCount

employment status data item
type: Class
subclass of: data item
definition: A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: A data item that denotes some context in which an individual realizes some employee role if he or she is a member of the labor force, or the context in which he or she is not a member of the labor force according to certain prespecified conditions.
Unique Apollo Label: employmentStatus
comment: If an individual is a member of the labor force, the criteria that this status is selected from includes whether they are in the armed forces, employed and working, employed but absent from work for a week, and unemployed. The criteria for those not in the labor force includes whether the individual is a houseworker, suffering from a physical impairment that prevents them from working, in school, or other miscellaneous reasons.

contaminated abiotic thing
type: Class
subclass of: abiotic ecosystem element
definition: An abiotic ecosystem element that is participant in some biological contamination process.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An abiotic ecosystem element that is participant in some biological contamination process.
Unique Apollo Label: contaminatedAbioticThing

odor-baited trap control strategy
type: Class
subclass of: adult vector control strategy
definition: An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An adult vector control strategy that has 1) an action specification that is realized by the use of mosquito traps that leverage natural or synthetic human odors as bait, and 2) an objective specification that is realized by preventing potentially infectious contacting between some mosquito vector and some human host.

zoo-prophylaxis control strategy
type: Class
subclass of: infectious disease control strategy
definition: An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans.
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An infectious disease control strategy that attempts to prevent infection of susceptible human host organisms in a particular geographical region by increasing the population of domesticated animals in that region, such that less mosquitoes feed on humans.

acute respiratory illness
type: Class
subclass of: clinical phenotype
definition: A clinical phenotype that is causally preceded by some infection or some adverse drug reaction; and that is accompanied by a fever greater than or equal to 37.8 degrees Celsius, and a cough or sore throat.
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: influenza-like illness

epidemic start week
type: Class
subclass of: scalar value specification
definition: A scalar value specification whose measurement unit label is 'week' and that is part of the first predicted data item that is greater than the epidemic threshold set for that data item.
definition editor: Amanda Hicks
definition editor: Matthew Diller
definition editor: William R. Hogan

epidemic peak week
type: Class
subclass of: scalar value specification
definition: A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity.
definition editor: Amanda Hicks
definition editor: Matthew Diller
definition editor: William R. Hogan

epidemic peak intensity
type: Class
subclass of: calculated datum
definition: A predicted data item that is about some aggregate of cases in an epidemic and whose value specification contains the maximum value in a data set that is about the epidemic.
definition editor: Amanda Hicks
definition editor: Matthew Diller
definition editor: William R. Hogan

aggregate of disease courses
type: Class
subclass of: process
definition: A process that (1) has as occurrent parts at least two disease courses that realize the same type of disease, and (2) has as participants two or more hosts that are members of a particular host population.
definition editor: Amanda Hicks
definition editor: Matthew Diller
definition editor: William R. Hogan

infectious disease forecast
type: Class
subclass of: planned process
definition: A planned process that realizes some infectious disease forecasting software.
definition editor: Matthew Diller
definition editor: William R. Hogan

infectious disease nowcast
type: Class
subclass of: infectious disease forecast
definition: An infectious disesae forecast that realizes some infectious disease nowcasting software.
definition editor: Matthew Diller
definition editor: William R. Hogan

infectious disease forecast objective specification
type: Class
subclass of: objective specification
definition: An objective specification that is realized by the estimation of one or more predicted data items that are about 1) some infection in ecosystem and 2) potential changes to its number of participants (e.g., individuals within a host population, individuals within a vector population) relative to a particular temporal region; and is part of some infectious disease forecasting software.
definition editor: Matthew Diller
definition editor: William R. Hogan

infectious disease nowcast objective specification
type: Class
subclass of: infectious disease forecast objective specification
definition: An infectious disease forecasting objective specification that is realized by the estimation of one or more predicted data items that are about some infection in ecosystem as they are occurring in real time, and is part of some infectious disease nowcasting software.
definition editor: Matthew Diller
definition editor: William R. Hogan

infectious disease nowcaster
type: Class
subclass of: infectious disease forecaster
editor preferred term: infectious disease nowcasting software application
definition: An infectious disease forecasting software application that predicts how many infections are occurring within the same temporal interval that the data items are being estimated.
definition editor: Matthew Diller
definition editor: William R. Hogan

prospective infectious disease forecast
type: Class
subclass of: infectious disease forecast
definition: An infectious disease forecast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized.
definition editor: Matthew Diller
definition editor: William R. Hogan

prospective infectious disease nowcast
type: Class
subclass of: infectious disease nowcast
definition: An infectious disease nowcast that has specified input some data set, the data items of which are about an infection in ecosystem that is current concomitant with the forecasting software’s executable code being realized.
definition editor: Matthew Diller
definition editor: William R. Hogan

infectious disease forecast time specification
type: Class
subclass of: action specification
definition: An action specification that specifies the duration of time that is to elapse between each calculation of each predicted data item that is the output of some infectious disease forecast.
definition editor: Matthew Diller
definition editor: William R. Hogan

intensive care unit encounter
type: Class
subclass of: inpatient encounter
definition: An inpatient encounter in which the health care provider role is realized by some person employed by the intensive care department of some health care facility, and the patient role is realized by someone admitted to that intensive care department.

data visualization objective specification
type: Class
subclass of: objective specification
definition: An objective specification that is realized when a diagram is drawn from one or more data sets.
definition editor: Matthew Diller
definition editor: William R. Hogan

treatment in the ICU control strategy
type: Class
subclass of: individual treatment control strategy
editor preferred term: treatment in the intensive care unit control strategy
definition: an individual treatment control strategy that is realized by one or more intensive care unit encounters for infected individuals in the population
definition editor: William R. Hogan
elucidation: an individual treatment control strategy that is realized by treating one or more infected individuals in an intensive care unit

website with data
type: Class
equivalent class: Class
  intersection of: website
  intersection of: Restriction
    on property: has proper continuant part at all times
    some values from: data item
subclass of: website
subclass of: Restriction
  on property: has proper continuant part at all times
  some values from: data item
editor preferred term: website that has data as a part
definition editor: William R. Hogan
comment: This class was created for use case for MIDAS Digital Repository to index websites that have useful data in them, albeit rarely as machine-interpretable, downloadable datasets. Much of the data are locked in PDF or other text-based formats.

climate data set
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Class
    union of: Restriction
      on property: is about
      some values from: environmental system process
    union of: Restriction
      on property: is about
      some values from: Class
        intersection of: continuant
        intersection of: Restriction
subclass of: data set
editor preferred term: climate data set
definition: A data set that is an aggregate of data items that are about an environmental system process (e.g., hydrological precipitation) or a participant in an environmental system process.
definition editor: Matt Diller
definition editor: William R. Hogan

metagenomics analysis software
type: Class
subclass of: software application
editor preferred term: metagenomics analysis software application
definition: A software application that has as part an objective specification that is achieved by only a metagenomics analysis.
definition editor: Matthew Diller
definition editor: William R. Hogan

abiotic ecosystem data set
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Restriction
    on property: is about
    some values from: Class
      union of: abiotic ecosystem
      union of: abiotic ecosystem element
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: abiotic ecosystem
    union of: abiotic ecosystem element
editor preferred term: abiotic ecosystem data set
definition: A data set that is about some abiotic ecosystem or abiotic ecosystem element.
definition editor: William R. Hogan
alternative label: abiotic ecosystem dataset
alternative label: data set about an abiotic ecosystem or abiotic ecosystem element
elucidation: A data set that is about an abiotic ecosystem or some abiotic ecosystem element.

atmospheric data set
type: Class
equivalent class: Class
  intersection of: abiotic ecosystem data set
  intersection of: Restriction
    on property: is about
    some values from: Restriction
      on property: part of
      has value: atmosphere of the Earth
subclass of: abiotic ecosystem data set
subclass of: Restriction
  on property: is about
  some values from: Restriction
    on property: part of
    has value: atmosphere of the Earth
editor preferred term: data set about Earth's atmosphere or some part of it
definition: A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere.
definition editor: William R. Hogan
elucidation: A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere.

treatment facility census
type: Class
subclass of: Class
  intersection of: census
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: facility
editor preferred term: census of treatment facility
definition: A census that counts the number of treatment facilities of some kind in a particular geographical region.
definition editor: William R. Hogan
alternative label: census of treatment facilities
alternative label: treatment facilities census
alternative label: treatment facility census
elucidation: A census that counts the number of treatment facilities of some kind in a particular geographical region.
comment: NOTE: this class counts the facilities themselves, not patients (people) in those facilities. For example, how many hospitals in a state. Not how many patients are in a hospital or hospitals in a state.

symbiosis
type: Class
subclass of: biological process involved in interspecies interaction between organisms
editor preferred term: symbiosis
definition: An interspecies interaction between two or more organisms in intimate association.
definition editor: Matthew Diller
definition editor: William R. Hogan
definition source: Martin BD, Schwab E. Current usage of symbiosis and associated terminology. International Journal of Biology. 2013 Jan 1;5(1):32. Available from: https://web.archive.org/web/20190723160720/https://www.researchgate.net/publication/233865641_Current_Usage_of_Symbiosis_and_Associated_Terminology
comment: By "intimate interaction," we mean any interaction between two or more organisms that involves (1) physical contact or (2) multi-organism behavior in which all interacting organisms are participant.

data format validator
type: Class
subclass of: software application
editor preferred term: data format validator software application
definition: A software application that takes a data set as input and outputs a determination of whether the dataset is in compliance with one or more given data format specifications.
definition editor: William R. Hogan

disease identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    some values from: disease
subclass of: identifier
subclass of: Restriction
  on property: denotes
  some values from: disease
editor preferred term: disease identifier
definition: an identifier that denotes a disease.
definition editor: William R. Hogan
contributor: Mathias Brochhausen
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:01:41Z

infection acquisition dataset
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Restriction
    on property: is about
    some values from: infection acquisition
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: infection acquisition
editor preferred term: dataset about infectious disease acquisitions
example of usage: The dataset at this link is rdf:type this class: https://figshare.com/articles/dataset/COVID19_settings_of_transmission_-_collected_reports_database/12173343
definition: a dataset that is about infectious disease acquisitions at particular times and particular places.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:16:26Z
comment: The dataset may include sites (e.g. types of facilities, rooms), events (e.g., church service whether in or outdoors), dates, times, geographical regions, etc. in which the sites/events are located, and so on.

hospital stay dataset
type: Class
subclass of: data set
editor preferred term: dataset about hospital stays
example of usage: The datasets at this link are rdf:type this class: https://www.opendataphilly.org/dataset/covid-hospitalizations
definition: a dataset that is about two or more hospital stays involving two or more patients.
definition editor: William R. Hogan
alternative label: hospital discharge dataset
alternative label: hospitalization dataset
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:20:48Z
comment: The dataset may be limited to stays in one hospital, but hospital discharge datasets as compiled by state departments of health typically contain stays from multiple hospitals (typically every hospital) in the geographical region over which they have jurisdiction

human daily movement
type: Class
subclass of: individual human behavior
editor preferred term: human daily movement behavior
definition: an individual human behavior that is the movements from one location to another throughout the day (e.g., work, home, stores, church, relatives' homes) in the areas adjacent to where the human lives at the time.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:29:53Z

human daily movement data set
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Restriction
    on property: is about
    some values from: human daily movement
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: human daily movement
editor preferred term: human daily movement behavior data set
example of usage: https://www.google.com/covid19/mobility/
definition: a data set that is about the human daily movement behavior of the individual huamns in a given population.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:32:39Z

potentially infectious contact data set
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Restriction
    on property: is about
    some values from: potentially infectious contacting
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: potentially infectious contacting
editor preferred term: potentially infectious contact process data set in a population
definition: a data set that is about one or more potentially infectious contact processes in a population of host organisms.
definition editor: William R. Hogan
alternative label: contact data set
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:39:24Z

control strategy census
type: Class
equivalent class: Class
  intersection of: census
  intersection of: Restriction
    on property: is about
    some values from: infectious disease control strategy
subclass of: census
subclass of: Restriction
  on property: is about
  some values from: infectious disease control strategy
editor preferred term: infectious disease control strategy census
definition: a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:43:04Z

school closure control strategy census
type: Class
equivalent class: Class
  intersection of: control strategy census
  intersection of: Restriction
    on property: is about
    some values from: school closure control strategy
subclass of: control strategy census
subclass of: Restriction
  on property: is about
  some values from: school closure control strategy
editor preferred term: school closure infectious disease control strategy census
definition: an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region.
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:44:03Z
comment: This class represents datasets about strategies for school closure. Datasets about individual actual school closures go elsewhere.

vaccination control strategy census
type: Class
equivalent class: Class
  intersection of: control strategy census
  intersection of: Restriction
    on property: is about
    some values from: vaccination control strategy
subclass of: control strategy census
subclass of: Restriction
  on property: is about
  some values from: vaccination control strategy
editor preferred term: vaccination infectious disease control strategy census
definition editor: William R. Hogan
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:47:09Z
comment: This class is an inventory of vaccination control strategies, not vaccinations themselves. So it should be a list of things like "Publix vaccination plan", "Alachua county vaccination plan", "Sam's Club vaccination plan", etc. And not a list of individual vaccinations given to actual patients (see population vaccination census)

vaccination administration census
type: Class
equivalent class: Class
  intersection of: population treatment census
  intersection of: Restriction
    on property: is about
    some values from: vaccination
subclass of: population treatment census
subclass of: Restriction
  on property: is about
  some values from: vaccination
editor preferred term: population vaccination census
example of usage: vaccine / immunization registry data, vaccination / immunization records extracted from an EHR
definition: a population treatment census that is about one or more vaccinations of organisms in a population.
definition editor: William R. Hogan
alternative label: vaccination census
creator: http://orcid.org/0000-0002-9881-1017
date: 2021-03-16T16:48:42Z

excess mortality dataset
type: Class
subclass of: mortality data
editor preferred term: dataset about excess mortality in a population
definition: A population mortality dataset that compares deaths in the population during one time interval to deaths in the population during a previous time interval and reports an estimate of how many more or less deaths occurred in the later time interval.
definition editor: William R. Hogan
comment: Often used during epidemics or pandemics to estimate the death toll.

census of vaccination supplies
type: Class
subclass of: control strategy inventory census
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: vaccine
editor preferred term: census of supplies of vaccine products
definition: A control strategy inventory census that counts available vaccine doses of one or more similar vaccines.
definition editor: William R. Hogan
alternative label: vaccine availability
creator: https://orcid.org/0000-0002-9881-1017
date: 2022-02-01T00:03:00Z
comment: Motivated my MIDAS coordination center indexing of COVID-19 data, software, etc. By "similar vaccines" we typically mean same pathogen, but could be similar in other ways (requiring refrigeration of a certain kind).

laboratory testing facility census
type: Class
subclass of: census
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: facility
editor preferred term: census of facilities that conduct clinical laboratory tests
definition: A census of facilities that conduct clinical laboratory testing.
definition editor: William R. Hogan
alternative label: testing availability
creator: https://orcid.org/0000-0002-9881-1017
date: 2022-02-01T00:10:00Z
comment: The census might also include information about each facility such as operating hours, address, accessibility, and so on.

parameter estimation model
type: Class
subclass of: algorithm
editor preferred term: model for disease transmission parameter estimation
definition: An algoirthm that is used to estimate the "true" values of certain parameters of disease transmission and/or forecasting.
definition editor: William R. Hogan
date: 2022-09-18T17:51:00
comment: Examples of parameters estimated include R0, transmissibility, infectious period.

network model
type: Class
subclass of: algorithm
definition: An algorithm that operates on a representation of some portion of reality and that representation has a structure with nodes that stand for certain entities and edges that state some direct or indirect relationship between pairs of entities.
definition editor: William R. Hogan
date: 2022-09-18T18:00:00
comment: The algorithm might involve also generating or creating the network structure in addition to operating on it.

laboratory testing capacity
type: Class
subclass of: action specification
editor preferred term: laboratory testing capacity action specification
definition: An action specification giving the number of laboratory tests of a certain type that it is possible to perform in a given population during a specific time interval.
definition editor: William R. Hogan
date: 2022-09-18T18:21

weather data set
type: Class
equivalent class: Class
  intersection of: data set
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: atmospheric weather
      intersection of: Restriction
        on property: characteristic of
        has value: atmosphere of the Earth
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: atmospheric weather
    intersection of: Restriction
      on property: characteristic of
      has value: atmosphere of the Earth
editor preferred term: data set about Earth's atmospheric weather
definition: A data set about the Earth's atmospheric weather
definition editor: William R. Hogan
date: 2022-09-18T18:34:00

human monkeypox
type: Class
equivalent class: Class
  intersection of: monkeypox
  intersection of: Restriction
    on property: characteristic of
    some values from: Homo sapiens
subclass of: monkeypox
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
editor preferred term: monkeypox disease inhering in a human being
definition: A monkeypox disease inhering in a human being.
definition editor: William R. Hogan
date: 2022-09-18T18:51:00
comment: requested by MIDAS CC

wastewater disease surveillance
type: Class
subclass of: disease surveillance
definition: A disease surveillance that detects evidence of the presence of pathogens in sewage.
definition editor: Matthew Diller
alternative label: sewage disease surveillance
contributor: William R. Hogan
comment: See the CDC's explanation of wastewater surveillance, and how it uses the term 'wastewater' synonymously with 'sewage', here: https://www.cdc.gov/nwss/wastewater-surveillance.html.

population count
type: Class
subclass of: count
definition: A count of simulated or physical individuals in a population.
definition editor: Matthew Diller

wastewater surveillance data set
type: Class
subclass of: disease surveillance data
definition: A disease surveillance data set that is about some wastewater disease surveillance.
definition editor: Matthew Diller
alternative label: sewage surveillance data
contributor: William R. Hogan

population density datum
type: Class
subclass of: scalar measurement datum
definition: A scalar measurement datum that is about some population and is normalized by unit land area in a particular geographical region.
definition editor: Matthew Diller
contributor: William R. Hogan

physical distancing infectious disease control measure
type: Class
subclass of: individual treatment control strategy
definition: An individual treatment control strategy in which individuals maintain a certain distance from other individuals during a social act.
definition editor: Matthew Diller
contributor: William R. Hogan

lockdown infectious disease control measure
type: Class
subclass of: place closure control strategy
definition: A place closure control strategy in which only selected places in a geographical region are permitted to stay open and travel is permitted only for people employed by certain organizations.
definition editor: Matthew Diller
contributor: William R. Hogan
comment: The places that are allowed to stay open are typically selected by the local or state government, and often include hospitals, many healthcare facilities, food stores and food banks, and law enforcement and emergency services.

cumulative epidemic case count
type: Class
subclass of: count of cases in an epidemic
subclass of: cumulative case count
definition: A count of cases in an epidemic that is about the entire temporal interval occupied by the epidemic.
definition editor: William R. Hogan
elucidation: A count of cases from the beginning of the epidemic until recently.
comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin.

incident epidemic case count
type: Class
subclass of: count of cases in an epidemic
subclass of: incident case count
definition: A count of cases in an epidemic that is about a proper part of the temporal interval occupied by the epidemic.
definition editor: William R. Hogan
elucidation: A count of cases in an epidemic that spans a shorter interval, such as a particular day or a week.
comment: Incident case counts are measured according to regular intervals, typically day or week.
comment: The count is also nearly always geographically localized, for example, the case count for the state of Pennsylvania or the case count for Waukesha County, Wisconsin.

count of events occurring in a population
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: has_participant
      some values from: Restriction
        on property: member of
        some values from: population
definition: A count of processes in which a population and/or its members participate during a given temporal region.
definition editor: William R. Hogan
elucidation: A count of certain type of event that occurs within a population, such as deaths, infections, births, and so on during a particular time.
comment: As the population is typically geographically defined (among other ways), the count is most often constrained to particular location in addition to a given time.

count of deaths in a population
type: Class
subclass of: count of events occurring in a population
definition: A count of death events that occurred in a population in a given temporal region.
definition editor: William R. Hogan
alternative label: population death count

count of vaccinations in a population
type: Class
subclass of: count of events occurring in a population
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: vaccination
    intersection of: Restriction
      on property: has_participant
      some values from: Restriction
        on property: member of
        some values from: population
definition: A count of vaccination events that occurred in a population during a temporal region.
definition editor: William R. Hogan
alternative label: population vaccination count
elucidation: A count of vaccinations in a population during a particular time.

count of hospital stays in a population
type: Class
subclass of: count of events occurring in a population
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: hospitalization
    intersection of: Restriction
      on property: has_participant
      some values from: Restriction
        on property: member of
        some values from: population
definition: A count of hospital stays in a population during a temporal region.
definition editor: William R. Hogan
alternative label: population hospitalization count
elucidation: A count of hospitalizations in a population during a particular time.

count of infections in a population
type: Class
subclass of: count of events occurring in a population
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: infection
    intersection of: Restriction
      on property: has_participant
      some values from: Restriction
        on property: member of
        some values from: population
definition: A count of infections (process) that occurred in a population in a given temporal region.
definition editor: William R. Hogan
alternative label: population infection count
elucidation: A count of infections in a population during a particular time.

cumulative epidemic infection count
type: Class
subclass of: cumulative infection count
definition: A cumulative infection count where the infections are an occurrent part of the same epidemic, and the reference interval is the interval occupied by the entire epidemic.
definition editor: William R. Hogan

incident epidemic infection count
type: Class
subclass of: incident infection count
definition: An incident infection count where the infections are an occurrent part of the same epidemic, and the temporal interval over which the count is made is a proper part of the reference interval.
definition editor: William R. Hogan

cumulative epidemic death count
type: Class
subclass of: cumulative death count
definition: A cumulative death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic.
definition editor: William R. Hogan

incident epidemic death count
type: Class
subclass of: incident death count
definition: An incident death count where the deaths are an occurrent part of the same epidemic, the deaths are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval.
definition editor: William R. Hogan

cumulative epidemic hospitalization count
type: Class
subclass of: cumulative hospitalization count
definition: A cumulative hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the reference interval is the interval occupied by the entire epidemic.
definition editor: William R. Hogan

incident epidemic hospitalization count
type: Class
subclass of: incident hospitalization count
definition: An incident hospitalization count where the hospitalizations are an occurrent part of the same epidemic, the hospitalizations are attributed to the epidemic disease, and the temporal interval over which the count is made is a proper part of the reference interval.
definition editor: William R. Hogan

cumulative epidemic vaccination count
type: Class
subclass of: cumulative vaccination count
definition: A cumulative vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the reference interval is the temporal interval occupied by the entire epidemic.
definition editor: William R. Hogan

incident epidemic vaccination count
type: Class
subclass of: incident vaccination count
definition: An incident vaccination count where the vaccinations are an occurrent part of the same epidemic, the vaccinations are against the type of pathogen causing the epidemic, and the temporal region over which the count is made is a proper part of the reference interval.
definition editor: William R. Hogan

intent to be vaccinated
type: Class
subclass of: intentionality
definition: An intentionality directed at future participation in a vaccination as the recipient of a vaccine or other immunization.
definition editor: William R. Hogan
elucidation: An intent to be vaccinated in the future.

intent to vaccinate
type: Class
subclass of: intentionality
definition: An intentionality directed at future participation in a vaccination as the administrator of a vaccine or other immunization to an organism with an immune system.
definition editor: William R. Hogan
elucidation: An intention to give a vaccine to someone or an animal.

vaccination with nirsevimab
type: Class
subclass of: vaccination
definition: A vaccination against respiratory syncytial virus via the administration of the monoclonal antibody nirsevimab.
definition editor: William R. Hogan

cumulative vaccination count
type: Class
subclass of: count of vaccinations in a population
definition: A count of vaccinations in a population that is the total number of a given type of vaccines administered during a reference temporal interval.
definition editor: William R. Hogan
comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic or vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

incident vaccination count
type: Class
subclass of: count of vaccinations in a population
definition: A count of vaccinations in a population that is the number of a given type of vaccines administered during a proper occurrent part of a reference temporal interval.
definition editor: William R. Hogan
comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, vaccination campaign, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

cumulative infection count
type: Class
subclass of: count of infections in a population
definition: A count of infections in a population that is the total number of infections that occur during a reference temporal interval.
definition editor: William R. Hogan
comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

incident infection count
type: Class
subclass of: count of infections in a population
definition: A count of infections in a population that is the number of infections of a given type that occurred during a proper occurrent part of a reference temporal interval.
definition editor: William R. Hogan
comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

cumulative hospitalization count
type: Class
subclass of: count of hospital stays in a population
definition: A count of hospital stays in a population that is the total number of hospitalizations that occur during a reference temporal interval.
definition editor: William R. Hogan
comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

incident hospitalization count
type: Class
subclass of: count of hospital stays in a population
definition: A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval.
definition editor: William R. Hogan
comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

cumulative death count
type: Class
subclass of: count of deaths in a population
definition: A count of deaths in a population that is the total number of deaths that occur during a reference temporal interval.
definition editor: William R. Hogan
comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

incident death count
type: Class
subclass of: count of deaths in a population
definition: A count of deaths in a population that is the number of deaths that occurred during a proper part of a reference temporal interval.
definition editor: William R. Hogan
comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

cumulative case count
type: Class
subclass of: count of disease cases
definition: A count of disease cases that is the total number of individuals who come to meet the criteria of some case definition during a reference temporal interval.
definition editor: William R. Hogan
comment: The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

incident case count
type: Class
subclass of: count of disease cases
definition: A count of cases in a population that is the number of individuals who come to meet the criteria of some case definition during a proper part of a reference temporal interval.
definition editor: William R. Hogan
comment: The interval over which the count is made is typically either one calendar day or one calendar week. The reference interval is usually relative to (i.e., occupied by) a major event like an epidemic, or it is a specific calendar-defined interval like a given calendar year or a set of consecutive "epidemiological weeks" as defined by CDC or another national or subnational public health organization.

intent to have a ward vaccinated
type: Class
subclass of: intentionality
editor preferred term: guardian's intent to have a ward under their care vaccinated
definition: An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role.
definition editor: William R. Hogan
elucidation: The intent of a guardian to have a ward under their care vaccinated in the near future.
comment: Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE.

reproduction
type: Class
equivalent class: Class
  union of: viral life cycle
  union of: sexual reproduction
  union of: asexual reproduction
subclass of: biological_process
editor preferred term: organism reproduction
definition: The process by which new organisms are created from existing ones.
definition editor: William R. Hogan
Unique Apollo Label: Reproduction

intent to have a child vaccinated
type: Class
subclass of: intent to have a ward vaccinated
definition: An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child.
definition editor: William R. Hogan
elucidation: Intent to have one's child vaccinated.
comment: The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist.

epidemic simulator action specification
type: Class
subclass of: action specification
editor preferred term: epidemic simulator action specification
definition editor: William R. Hogan

infectious disease control strategy action specification
type: Class
subclass of: action specification
editor preferred term: infectious disease control strategy action specification
definition editor: William R. Hogan

individual treatment control strategy action specification
type: Class
subclass of: infectious disease control strategy action specification
editor preferred term: individual treatment control strategy action specification
definition editor: William R. Hogan

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

creating a copyright license
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: copyright license
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: copyright license
editor preferred term: creating a copyright license
definition: A planned process that has a copyright license as its specified output.
definition editor: William R. Hogan
alternative label: copyright license creation
comment: Note: for less than 24 hours, this class was a bit more specific to software licenses, but it did not have the equivalent class axiom during that time.

copyright license
type: Class
subclass of: document
editor preferred term: copyright license for a creative work
definition: A document that is about the legal rights, claims, and obligations of a legal person (person or organization) under copyright law, and how that legal person intends for those rights, claims, and obligations to be handled/managed by users of the creative work to which this document is attached.
definition editor: William R. Hogan
comment: Can be for any creative work including fiction. But the license itself is an ICE, and refers to real claims and obligations.

data service software
type: Class
subclass of: software application
editor preferred term: data service software application
definition: A software application that implements a data service.
definition editor: William R. Hogan

TODO
type: Class
subclass of: entity

facultative role
type: Class
subclass of: role
editor preferred term: facultative role
definition: A role borne by an organism in virtue of the fact that it is in intimate association with one or more organisms of different species, and is realized by bodily benefit to that organism as an occurrent part of a symbiosis with the other organisms. This bodily benefit takes the place of the organism or some relatively isolated part of the organism realizing some normal homeostasis disposition itself.

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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

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
subclass of: Restriction
  on property: part of
  all values from: continuant
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
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
subclass of: Restriction
  on property: part of
  all values from: occurrent
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.
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
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: characteristic
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])
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

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.
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
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)
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
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.
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
type: Class
subclass of: characteristic
subclass of: Restriction
  on property: part of
  all values from: realizable
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.
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]
label: realizable entity

Axiom
annotated source: realizable
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
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
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
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: characteristic
subclass of: Restriction
  on property: part of
  all values from: quality
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
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

characteristic
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: characteristic
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.
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.
label: specifically dependent continuant

Axiom
annotated source: characteristic
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: characteristic
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: characteristic
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: characteristic
annotated property: has associated axiom(fol)
annotated target: (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 axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: characteristic
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
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.
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
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object
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]
label: fiat object part

Axiom
annotated source: fiat object
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
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]
comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
comment: Synonyms: substance aggregate
label: object aggregate

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)
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
subclass of: Restriction
  on property: part of
  all values from: generically dependent 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])
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.
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).
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]
Unique Apollo Label: Interval

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
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
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
disjoint with: Restriction
  on property: has part
  some values from: material entity
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

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 label: 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.
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

antiviral drug
type: Class
subclass of: role
comment: The usage or intended usage of a drug product to act against a viral infection of a host.

Zika fever
type: Class
subclass of: infectious disease
definition: A viral infectious disease that has_material_basis in Zika virus, which is transmitted_by Aedes aegypti mosquitoes and targets neural progenitor cells and neuronal cells in all stages of maturity and has_symptom fever, has_symptom rash, has_symptom headaches and has_symptom joint pain.
imported from: http://purl.obolibrary.org/obo/doid.owl
database_cross_reference: ICD10:U06
database_cross_reference: ICD10CM:A92.8
database_cross_reference: MESH:D000071243
has_exact_synonym: Zika virus disease

dengue disease
type: Class
subclass of: infectious disease
definition: A viral infectious disease that results_in infection, has_material_basis_in Dengue virus [NCBITaxon:12637] with four serotypes (Dengue virus 1, 2, 3 and 4), which are transmitted_by Aedes mosquito bite. The infection has_symptom fever, has_symptom severe headache, has_symptom severe pain behind the eyes, has_symptom joint pain, has_symptom muscle and bone pain, has_symptom rash, and has_symptom mild bleeding.
imported from: http://purl.obolibrary.org/obo/doid.owl
has_alternative_id: DOID:0050142
database_cross_reference: ICD10CM:A90
database_cross_reference: ICD9CM:061
database_cross_reference: MESH:D003715
database_cross_reference: NCI:C34528
database_cross_reference: SNOMEDCT_US_2016_03_01:154345006
database_cross_reference: SNOMEDCT_US_2016_03_01:266194002
database_cross_reference: SNOMEDCT_US_2016_03_01:38362002
database_cross_reference: UMLS_CUI:C0011311
has_exact_synonym: Dengue Fever
has_exact_synonym: breakbone fever
has_exact_synonym: classic dengue
has_obo_namespace: disease_ontology
has_related_synonym: classical dengue
id: DOID:12205
in_subset: zoonotic infectious disease

dengue hemorrhagic fever
type: Class
subclass of: dengue disease
definition: A dengue disease that occurs when a person experiences a second infection with a heterologous Dengue virus serotype, which is transmitted_by Aedes mosquito bite. The infection has_symptom hemorrhagic lesions of the skin, has_symptom thrombocytopenia, has_symptom reduction in the fluid part of the blood, and has_symptom high fever.
imported from: http://purl.obolibrary.org/obo/doid.owl
database_cross_reference: ICD10CM:A91
database_cross_reference: MESH:D019595
database_cross_reference: NCI:C34683
database_cross_reference: SNOMEDCT_US_2016_03_01:186598001
database_cross_reference: SNOMEDCT_US_2016_03_01:186599009
database_cross_reference: SNOMEDCT_US_2016_03_01:20927009
database_cross_reference: UMLS_CUI:C0019100
has_exact_synonym: DHF
has_obo_namespace: disease_ontology
has_related_synonym: Dengue haemorrhagic fever
id: DOID:12206
in_subset: zoonotic infectious disease

monkeypox
type: Class
subclass of: infectious disease
definition: A viral infectious disease that results in infection of primates, rodents and humans, located in skin, has_material_basis_in Monkeypox virus, which is transmitted by contact with the animal's blood, body fluids, rash, or with the body fluids of a sick person, transmitted by fomites, and transmitted by respiratory droplets. The infection has symptom fever, has symptom muscle ache, has symptom headache, and has symptom lymphadenopathy.
imported from: http://purl.obolibrary.org/obo/doid/releases/2022-08-29/doid.owl
dc:type: ECO_0007637
database_cross_reference: GARD:10722
database_cross_reference: ICD10CM:B04
database_cross_reference: ICD9CM:059.01
database_cross_reference: MESH:D045908
database_cross_reference: NCI:C128421
database_cross_reference: SNOMEDCT_US_2021_09_01:240466002
database_cross_reference: UMLS_CUI:C0276180
database_cross_reference: url:http://www.cdc.gov/ncidod/monkeypox/factsheet2.htm
has_obo_namespace: disease_ontology
id: DOID:3292
in_subset: NCIthesaurus
in_subset: zoonotic infectious disease

influenza
type: Class
subclass of: infectious disease
definition: A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness.
imported from: http://purl.obolibrary.org/obo/doid.owl
has_alternative_id: DOID:8468
database_cross_reference: ICD10CM:J11.1
database_cross_reference: ICD9CM:487
database_cross_reference: MESH:D007251
database_cross_reference: NCI:C53482
database_cross_reference: SNOMEDCT_US_2016_03_01:155559006
database_cross_reference: SNOMEDCT_US_2016_03_01:155562009
database_cross_reference: SNOMEDCT_US_2016_03_01:195931008
database_cross_reference: SNOMEDCT_US_2016_03_01:266353003
database_cross_reference: SNOMEDCT_US_2016_03_01:266393000
database_cross_reference: SNOMEDCT_US_2016_03_01:6142004
database_cross_reference: UMLS_CUI:C0021400
has_exact_synonym: Influenza with non-respiratory manifestation (disorder)
has_exact_synonym: Influenza with other manifestations
has_exact_synonym: Influenza with other manifestations (disorder)
has_exact_synonym: Influenza with other manifestations NOS (disorder)
has_exact_synonym: flu
has_exact_synonym: influenza with non-respiratory manifestation
has_obo_namespace: disease_ontology
id: DOID:8469

drug product
type: Class
subclass of: object
definition: a material entity (1) containing at least one scattered molecular aggregate as part (the active ingredient) and (2) that is the bearer of a clinical drug role
definition editor: William Hogan
imported from: http://purl.obolibrary.org/obo/dron.owl
creator: William Hogan

environmental material
type: Class
subclass of: material entity
definition: A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
imported from: http://purl.obolibrary.org/obo/envo.owl
has_exact_synonym: portion of environmental material
has_obo_namespace: ENVO
id: ENVO:00010483
comment: Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.

environmental condition
type: Class
subclass of: physical quality
has curation status: organizational term
definition: An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
imported from: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl
created by: ORCID:0000-0002-4366-3088
creation date: 2013-04-07T14:35:18Z
database_cross_reference: DOI:10.1186/2041-1480-4-43
in_subset: envoPolar
comment: A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.

water vapour
type: Class
subclass of: gaseous environmental material
definition: Water vapour is a vapour which is the gas phase of water.
imported from: http://purl.obolibrary.org/obo/envo.owl
created by: ORCID:0000-0002-4366-3088
creation date: 2013-10-10T07:58:18Z
has_exact_synonym: aqueous vapor
has_exact_synonym: aqueous vapour
has_exact_synonym: water vapor
has_obo_namespace: ENVO
id: ENVO:01000266
comment: Perhaps a better relation between water vapour and water can be found in or added to RO?

atmospheric water vapour
type: Class
subclass of: water vapour
definition: Atmospheric water vapour is water vapour that is part of an atmosphere.
imported from: http://purl.obolibrary.org/obo/envo.owl
created by: ORCID:0000-0002-4366-3088
creation date: 2013-10-10T08:22:07Z
has_exact_synonym: atmospheric water vapor
has_obo_namespace: ENVO
id: ENVO:01000268

hydrological precipitation process
type: Class
subclass of: environmental system process
definition: Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
imported from: http://purl.obolibrary.org/obo/envo.owl
has_broad_synonym: precipitation
comment: "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)

air temperature
type: Class
subclass of: temperature of air
definition: A temperature that inheres in some portion of air.
editor note: Draft class. In discussion in Issue #278.
imported from: http://purl.obolibrary.org/obo/envo.owl

gaseous environmental material
type: Class
subclass of: environmental material
definition: A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
editor note: This class is to be populated by inference.
imported from: http://purl.obolibrary.org/obo/envo.owl
has_narrow_synonym: gas

weather
type: Class
subclass of: environmental variability
definition: Environmental variability which inheres in an astronomical body part or in outer space.
imported from: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl
database_cross_reference: https://en.wikipedia.org/wiki/Space_weather
database_cross_reference: https://en.wikipedia.org/wiki/Weather
comment: This class refers to all weather, including atmospheric and space weather. Please use a subclass for more specificity.

atmospheric weather
type: Class
subclass of: weather
definition: Weather which inheres in an atmosphere.
imported from: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl
database_cross_reference: https://en.wikipedia.org/wiki/Weather
comment: This class refers to the common usage of "weather", referencing the state of a (part of) an astronomical body's atmosphere.

environmental variability
type: Class
subclass of: environmental condition
definition: A condition which inheres in an environmental system by virtue of that system undergoing variation in its composition, the distribution of the qualities its components bear, and/or in the processes which occur within it and which it participates in.
imported from: http://purl.obolibrary.org/obo/envo/releases/2021-05-14/envo.owl
comment: This class is very general, but the nature of environmental variability is indeed quite variable. This class may be refined once we have more subclasses to consider.

environmental system process
type: Class
subclass of: process
imported from: http://purl.obolibrary.org/obo/envo.owl
comment: Should environmental feature become something more towards a disposition, the assert would be updated to something like "has participant (environmental system or (material entity and has disposition some environmental feature))". There are several issues surrounding the reconcilliation of environmental feature and environmental system, both theoretical and practical.

temperature of environmental material
type: Class
subclass of: temperature
definition: The temperature of a environmental material.
imported from: http://purl.obolibrary.org/obo/envo.owl
has_exact_synonym: environmental material temperature

temperature of air
type: Class
subclass of: temperature of environmental material
definition: The temperature of a air.
imported from: http://purl.obolibrary.org/obo/envo.owl
has_exact_synonym: air temperature

metagenomics analysis
type: Class
subclass of: planned process
has curation status: metadata incomplete
definition: A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research.
definition editor: PERSON: Nicole Vasilevsky
alternative label: community genomic analysis
alternative label: ecogenomic analysis
alternative label: environmental genomic analysis
definition source: http://en.wikipedia.org/wiki/Metagenomics
imported from: http://purl.obolibrary.org/obo/ero.owl

website
type: Class
subclass of: document
definition: A set of related web pages containing content such as text, images, video, audio, etc., prepared and maintained as a collection of information on a particular subject.
imported from: http://purl.obolibrary.org/obo/fbcv.owl
has_obo_namespace: pub_type
id: FBcv:0000667

journal
type: Class
subclass of: information content entity
definition: A publication issued on a regular, ongoing basis containing separate research articles and other writings such as reviews, comments and conference reports.
imported from: http://purl.obolibrary.org/obo/fbcv.owl
created by: djs93
creation date: 2012-07-10T04:08:06Z
database_cross_reference: MeSH:D020492
has_obo_namespace: pub_type
has_related_synonym: Periodicals
id: FBcv:0000787

geopolitical entity
type: Class
subclass of: Obsolete Class
definition: An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii)
definition editor: William R. Hogan
comment: In some cases, geopolitical entities possess uninhabited geographical regions. However, it is that case that it controls the movement of people in and out of those regions, and its laws apply to those regions.
deprecated: true

obsolete group of governmental organizations
type: Class
equivalent class: Restriction
  on property: is aggregate of
  some values from: Class
    union of: geopoli organization
    union of: governmental organization
subclass of: independent continuant
subclass of: Restriction
  on property: is aggregate of
  some values from: Class
    union of: geopoli organization
    union of: governmental organization
editor preferred term: obsolete aggregate of governmental organizations
definition: An aggregate of geopoliticial entities. Examples include the group of states of the United States, the nations of North America, and so on.
definition editor: William R. Hogan
comment: taken over by GEO_0000000401
deprecated: true

nation
type: Class
subclass of: Obsolete Class
definition: A geopolitical entity that is self contained and recognizes no higher political authority than itself.
definition editor: William R. Hogan
deprecated: true

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

major administrative subdivision
type: Class
subclass of: subnational entity
definition: A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation.
definition editor: Amanda Hicks
definition editor: William R. Hogan
Unique Apollo Label: administrativeLocations
comment: examples: Northern Ireland, Florida

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

aggregate of major administrative subdivisions
type: Class
equivalent class: Class
  intersection of: Class
    complement of: major administrative subdivision
  intersection of: Restriction
    on property: is aggregate of
    all values from: major administrative subdivision
  intersection of: Restriction
    on property: is aggregate of
    min qualified cardinality: 2
    on class: major administrative subdivision
subclass of: aggregate of governmental organizations
subclass of: Restriction
  on property: is aggregate of
  some values from: major administrative subdivision
definition: An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common.
definition editor: Amanda Hicks
comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc.
label: group of major administrative subdivisions

aggregate of dependencies
type: Class
equivalent class: Class
  intersection of: Class
    complement of: geopolitical dependency
  intersection of: Restriction
    on property: is aggregate of
    all values from: geopolitical dependency
  intersection of: Restriction
    on property: is aggregate of
    min qualified cardinality: 2
    on class: geopolitical dependency
subclass of: aggregate of governmental organizations
subclass of: Restriction
  on property: is aggregate of
  some values from: geopolitical dependency
definition: An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.
definition editor: Amanda Hicks
comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies.
label: group of dependencies

subcontinental land mass
type: Class
subclass of: land mass
subclass of: Restriction
  on property: proper part of continuant at all times
  some values from: continent

contiguous land mass
type: Class
subclass of: subcontinental land mass
alternative label: contiguous continental land mass
comment: per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. At some point, we need an 'adjacent to' relation if BFO doesn't provide it. One question is whether this class encompasses fiat parts of islands.

aggregate of governmental organizations
type: Class
equivalent class: Class
  intersection of: Class
    complement of: governmental organization
  intersection of: Restriction
    on property: is aggregate of
    all values from: governmental organization
  intersection of: Restriction
    on property: is aggregate of
    min qualified cardinality: 2
    on class: governmental organization
subclass of: independent continuant
subclass of: Restriction
  on property: is aggregate of
  some values from: governmental organization
definition: An aggregate of organizations that is not itself a governmental organization, has only governmental organizations as members, and has at least two governmental organizations as members.
definition editor: William R. Hogan

contiguous island land mass
type: Class
subclass of: subcontinental land mass
definition: A subcontinental land mass that is part of an island and includes part of the land surface of the island.
definition editor: William R. Hogan
comment: It cannot be a part of the island, for example, that is below water.

aggregate of contiguous land masses
type: Class
equivalent class: Restriction
  on property: is aggregate of
  some values from: land mass
subclass of: land mass
subclass of: aggregate of geographical entities
subclass of: Restriction
  on property: is aggregate of
  some values from: land mass

geographical entity
type: Class
subclass of: material entity
editor preferred term: geographical entity of astronomical body
definition: A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface).
definition editor: Mathias Brochhausen
definition editor: Matt Diller
definition editor: William R. Hogan
comment: Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example.
comment: Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc.
comment: We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities.
comment: We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc.

geographical feature
type: Class
subclass of: geographical entity
definition: A geographical entity that has at least one bona fide boundary.

geographical region
type: Class
subclass of: geographical entity
definition: A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface.
definition: A site designated by some relative spatial orientation.
definition editor: François Modave
definition editor: Mathias Brochhausen
definition editor: Matt Diller
definition editor: Matthew Diller
definition editor: William R. Hogan
elucidation: An arbitrary part of the Earth defined by human-made boundaries and/or natural features such as rivers.
Unique Apollo Label: Location

body of water
type: Class
subclass of: geographical region

continent
type: Class
subclass of: land mass

land mass
type: Class
subclass of: geographical region

island
type: Class
subclass of: subcontinental land mass

aggregate of geographical entities
type: Class
equivalent class: Restriction
  on property: is aggregate of
  some values from: geographical entity
subclass of: object_aggregate
subclass of: Restriction
  on property: is aggregate of
  some values from: geographical entity
definition: An object aggregate of geographical entities

aggregate of geographical features
type: Class
equivalent class: Restriction
  on property: is aggregate of
  some values from: geographical feature
subclass of: aggregate of geographical entities
subclass of: Restriction
  on property: is aggregate of
  some values from: geographical feature

aggregate of islands
type: Class
equivalent class: Restriction
  on property: is aggregate of
  some values from: island
subclass of: aggregate of contiguous land masses
subclass of: Restriction
  on property: is aggregate of
  some values from: island

geopoli organization
type: Class
subclass of: organization
editor preferred term: geopolitical organization
definition editor: Amanda Hicks

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

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

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

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

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".
definition editor: Amanda Hicks
comment: IMPORTANT: The label "geopolitical organization" was previously used for OMRSE_00000044 (governmental organization). "geopoli organization" is a label for a new and different class.

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

obsolete aggregate of dependencies
type: Class
subclass of: aggregate of governmental organizations
definition: An aggregate of governmental organizations that is not itself a geopolitical dependency and whose members are only geopolitical dependencies that have some feature in common.
definition editor: Amanda Hicks
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Examples: all the dependencies of the United States, all of the dependencies whose territory is located in the Carribean Sea, French Overseas Collectivities, Biritish Crown Dependencies.
deprecated: true

obsolete aggregate of major administrative subdivisions
type: Class
subclass of: aggregate of governmental organizations
definition: An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common
definition editor: Amanda Hicks
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Examples: all the major administrative subdivisions of the United States (which is different from the U.S. itself), all the major administrative subdivisions with a bicameral legislature, all the major administrative subdivisions with a judiciary, etc.
deprecated: true

aggregate of sovereign states
type: Class
equivalent class: Class
  intersection of: Class
    complement of: sovereign state
  intersection of: Restriction
    on property: is aggregate of
    all values from: sovereign state
  intersection of: Restriction
    on property: is aggregate of
    min qualified cardinality: 2
    on class: sovereign state
subclass of: aggregate of governmental organizations
subclass of: Restriction
  on property: is aggregate of
  some values from: sovereign state
definition: An aggregate of governmental organizations that is not itself a sovereign state and whose members are only sovereign states that have some feature in common
definition editor: William R. Hogan
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: examples: all the sovereign states in North America, all the sovereign states with a GDP below or exceeding a particular quantity of money, all the sovereign states with a constitutional monarchy, all the sovereign states who belong to the U.N. (which is different than the U.N. itself), etc.

geodetic coordinate measurement datum
type: Class
equivalent class: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has_specified_input
        some values from: geodetic datum
  intersection of: Restriction
    on property: has value specification
    some values from: Class
      intersection of: value specification
      intersection of: Restriction
        on property: has measurement unit label
        has value: angular degree
subclass of: measurement datum
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: has_specified_input
      some values from: geodetic datum
subclass of: Restriction
  on property: has value specification
  some values from: Class
    intersection of: value specification
    intersection of: Restriction
      on property: has measurement unit label
      has value: angular degree
editor preferred term: geodetic coordinate measurement datum
definition: A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum.
definition editor: Josh Hanna
definition editor: William R. Hogan
comment: latitude and longitude are key subtypes

geodetic datum
type: Class
subclass of: information content entity
editor preferred term: geodetic datum
definition: A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects).
definition editor: Josh Hanna
definition editor: William R. Hogan
definition source: Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum Date accessed: 2015-04-13
comment: Every latitude and longitude measurement is with respect to a geodetic datum. Most common ones in use are NAD83 and WGS84.

plane angle measurement unit label
type: Class
subclass of: measurement unit label
editor preferred term: planar angular measurement unit label

de jure sovereign state
type: Class
subclass of: sovereign state
definition: A sovereign state whose political sovereignty has been recognized by the United Nations, in accordance with international law.
definition editor: Matthew Diller
alternative label: de jure state
comment: Sovereignty, in the legal sense, is acquired by a state upon receiving recognition by the international community. However, without specifying that this recognition can only be acquired through full membership to the United Nations, a non-arbitrary standard would be difficult, if not impossible, to come by since there are a good many sovereign states whose sovereignty is not explicitly recognized by one or more states. Given that the de facto criteria for sovereignty must be achieved prior to membership to the UN General Assembly and that every member therein is considered to be "international recognized," full membership to the UN is a sufficient criterion for de jure sovereignty. This can be further justified by noting that, in cases where UN member X claims to not recognize the sovereign status of UN member Y, the diplomatic and political behavior of member X towards Y nevertheless tacitly implies that it recognizes Y's sovereignty.

molecular_function
type: Class
subclass of: process
disjoint with: biological_process
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
has_exact_synonym: molecular function
id: GO:0003674
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
comment: This is the same as GO molecular function
label: gene product or complex activity

Axiom
annotated source: molecular_function
annotated property: definition
annotated target: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
database_cross_reference: GOC:pdt

immune response
type: Class
subclass of: biological_process
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl

behavior
type: Class
subclass of: multicellular organismal process
subclass of: bodily process
definition: The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
imported from: go.owl
created by: jl
creation date: 2012-09-20T14:06:08Z
has_alternative_id: GO:0023032
has_alternative_id: GO:0044708
has_alternative_id: GO:0044709
database_cross_reference: Wikipedia:Behavior
has_exact_synonym: behavioral response to stimulus
has_exact_synonym: behaviour
has_exact_synonym: behavioural response to stimulus
has_obo_namespace: biological_process
has_related_synonym: single-organism behavior
id: GO:0007610
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim flybase ribbon
comment: 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).

Axiom
annotated source: behavior
annotated property: definition
annotated target: The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
database_cross_reference: GOC:ems
database_cross_reference: GOC:jl
database_cross_reference: ISBN:0395448956
database_cross_reference: PMID:20160973

biological_process
type: Class
subclass of: process
disjoint with: planned process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
definition: A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
term tracker item: https://github.com/geneontology/go-ontology/issues/24968
imported from: go.owl
created by: jl
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
comment: A biological process is an evolved process
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
label: biological process

Axiom
annotated source: biological_process
annotated property: definition
annotated target: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
database_cross_reference: GOC:pdt

viral process
type: Class
subclass of: biological_process
definition: A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
has_alternative_id: GO:0022415
database_cross_reference: Wikipedia:Viral_life_cycle
has_exact_synonym: virus process
has_obo_namespace: biological_process
has_related_synonym: viral infection
has_related_synonym: virulence
id: GO:0016032
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim virus
comment: See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.

Axiom
annotated source: viral process
annotated property: definition
annotated target: A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl
database_cross_reference: GOC:mah

Axiom
annotated source: viral process
annotated property: has_exact_synonym
annotated target: virus process
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

kinase activity
type: Class
subclass of: molecular_function
subclass of: Restriction
  on property: is kinase activity
  has self: true
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: Reactome:R-HSA-6788855
database_cross_reference: Reactome:R-HSA-6788867
has_exact_synonym: phosphokinase activity
id: GO:0016301
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.

Axiom
annotated source: kinase activity
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
database_cross_reference: ISBN:0198506732

FN3KRP phosphorylates PsiAm, RibAm
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788855

FN3K phosphorylates ketosamines
type: Axiom
annotated source: kinase activity
annotated property: database_cross_reference
annotated target: Reactome:R-HSA-6788867

viral life cycle
type: Class
subclass of: reproduction
subclass of: viral process
definition: A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
has_alternative_id: GO:0019067
has_narrow_synonym: viral assembly, maturation, egress, and release
has_obo_namespace: biological_process
has_related_synonym: lytic viral life cycle
has_related_synonym: viral infectious cycle
has_related_synonym: viral replication
id: GO:0019058
in_subset: goslim virus

Axiom
annotated source: viral life cycle
annotated property: definition
annotated target: A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
database_cross_reference: ISBN:1555811272

Axiom
annotated source: viral life cycle
annotated property: has_narrow_synonym
annotated target: viral assembly, maturation, egress, and release
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

Axiom
annotated source: viral life cycle
annotated property: has_related_synonym
annotated target: viral infectious cycle
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

Axiom
annotated source: viral life cycle
annotated property: has_related_synonym
annotated target: viral replication
database_cross_reference: GOC:bf
database_cross_reference: GOC:jl

reproductive behavior
type: Class
equivalent class: Class
  intersection of: behavior
  intersection of: multicellular organismal reproductive process
subclass of: behavior
subclass of: multicellular organismal reproductive process
definition: The specific behavior of an organism that is associated with reproduction.
term tracker item: https://github.com/geneontology/go-ontology/issues/23491
imported from: go.owl
created by: jl
creation date: 2012-09-19T16:01:37Z
has_alternative_id: GO:0033057
has_alternative_id: GO:0044704
has_alternative_id: GO:0044705
has_exact_synonym: reproductive behavior in a multicellular organism
has_exact_synonym: reproductive behaviour
has_narrow_synonym: multi-organism reproductive behavior
has_narrow_synonym: multicellular organism reproductive behavior
has_obo_namespace: biological_process
has_related_synonym: single-organism reproductive behavior
id: GO:0019098

Axiom
annotated source: reproductive behavior
annotated property: definition
annotated target: The specific behavior of an organism that is associated with reproduction.
database_cross_reference: GOC:jl
database_cross_reference: GOC:pr

sexual reproduction
type: Class
subclass of: reproduction
subclass of: reproductive process
definition: A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
term tracker item: https://github.com/geneontology/go-ontology/issues/22929
database_cross_reference: Wikipedia:Sexual_reproduction
has_obo_namespace: biological_process
id: GO:0019953
comment: Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.

Axiom
annotated source: sexual reproduction
annotated property: definition
annotated target: A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).
database_cross_reference: Wikipedia:Sexual_reproduction

asexual reproduction
type: Class
subclass of: reproduction
subclass of: reproductive process
definition: A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.
term tracker item: https://github.com/geneontology/go-ontology/issues/22929
database_cross_reference: Wikipedia:Asexual_reproduction
has_obo_namespace: biological_process
has_related_synonym: parthenogenesis
id: GO:0019954

Axiom
annotated source: asexual reproduction
annotated property: definition
annotated target: A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.
database_cross_reference: ISBN:0387520546
database_cross_reference: PMID:22977071
database_cross_reference: PMID:28779329
database_cross_reference: PMID:29559496

Axiom
annotated source: asexual reproduction
annotated property: has_related_synonym
annotated target: parthenogenesis
database_cross_reference: Wikipedia:Parthenogenesis

reproductive process
type: Class
subclass of: biological_process
definition: A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
term tracker item: https://github.com/geneontology/go-ontology/issues/27054
created by: jl
creation date: 2012-09-19T15:56:06Z
has_alternative_id: GO:0044702
database_cross_reference: Wikipedia:Reproduction
has_obo_namespace: biological_process
has_related_synonym: single organism reproductive process
id: GO:0022414
in_subset: gocheck do not annotate
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim flybase ribbon
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim plant ribbon

Axiom
annotated source: reproductive process
annotated property: definition
annotated target: A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete

multicellular organismal process
type: Class
subclass of: biological_process
definition: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
term tracker item: https://github.com/geneontology/go-ontology/issues/27189
created by: jl
creation date: 2012-09-19T16:07:47Z
has_alternative_id: GO:0044707
has_alternative_id: GO:0050874
has_exact_synonym: organismal physiological process
has_obo_namespace: biological_process
has_related_synonym: single-multicellular organism process
id: GO:0032501
in_subset: gocheck do not annotate
in_subset: goslim pir
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.

Axiom
annotated source: multicellular organismal process
annotated property: definition
annotated target: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
database_cross_reference: GOC:curators
database_cross_reference: GOC:dph
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:tb

obsolete multicellular organism reproduction
type: Class
definition: OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
term tracker item: https://github.com/geneontology/go-ontology/issues/27054
term replaced by: GO:0048609
has_obo_namespace: biological_process
id: GO:0032504
comment: The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.
deprecated: true

Axiom
annotated source: obsolete multicellular organism reproduction
annotated property: definition
annotated target: OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
database_cross_reference: GOC:isa_complete
database_cross_reference: GOC:jid

biological process involved in symbiotic interaction
type: Class
subclass of: biological process involved in interspecies interaction between organisms
definition: A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
term tracker item: https://github.com/geneontology/go-ontology/issues/14807
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
has_alternative_id: GO:0043298
has_alternative_id: GO:0044404
has_alternative_id: GO:0072519
has_alternative_id: GO:0085031
has_narrow_synonym: commensalism
has_narrow_synonym: host-pathogen interaction
has_narrow_synonym: parasitism
has_obo_namespace: biological_process
has_related_synonym: symbiosis
has_related_synonym: symbiosis, encompassing mutualism through parasitism
has_related_synonym: symbiotic interaction
has_related_synonym: symbiotic interaction between host and organism
has_related_synonym: symbiotic interaction between organisms
has_related_synonym: symbiotic interaction between species
has_related_synonym: symbiotic process
id: GO:0044403
in_subset: goslim chembl

Axiom
annotated source: biological process involved in symbiotic interaction
annotated property: definition
annotated target: A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
database_cross_reference: GOC:cc
database_cross_reference: PMID:31257129

entry into host
type: Class
subclass of: biological process involved in interaction with host
subclass of: multi-organism process
definition: Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.
definition: Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
term tracker item: https://github.com/geneontology/go-ontology/issues/18563
imported from: go.owl
has_alternative_id: GO:0030260
has_alternative_id: GO:0044411
has_alternative_id: GO:0051806
has_alternative_id: GO:0051828
has_alternative_id: GO:0051830
has_alternative_id: GO:0075052
has_alternative_id: GO:0085027
has_alternative_id: GO:0085028
has_exact_synonym: entry into host
has_exact_synonym: host invasion
has_exact_synonym: host penetration
has_exact_synonym: invasion into host
has_exact_synonym: invasion of host
has_exact_synonym: penetration into host
has_narrow_synonym: entry into cell of other organism during symbiotic interaction
has_narrow_synonym: entry into host cell via penetration peg
has_narrow_synonym: entry into host via a specialized structure during symbiotic interaction
has_narrow_synonym: entry into host via enzymatic degradation of host anatomical structure
has_narrow_synonym: entry into host via enzymatic degradation of host cuticle
has_narrow_synonym: penetration into host via a specialized structure
has_narrow_synonym: penetration into host via a specialized structure during symbiotic interaction
has_obo_namespace: biological_process
has_related_synonym: entry into cell of other organism involved in symbiotic interaction
has_related_synonym: entry into host through host barriers
has_related_synonym: entry into other organism during symbiotic interaction
has_related_synonym: entry into other organism involved in symbiotic interaction
has_related_synonym: invasion into other organism
has_related_synonym: invasion of other organism
has_related_synonym: invasive growth
has_related_synonym: other organism invasion
id: GO:0044409
in_subset: goslim virus
label: symbiont entry into host

Axiom
annotated source: entry into host
annotated property: definition
annotated target: Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.
database_cross_reference: GOC:vw

Axiom
annotated source: entry into host
annotated property: has_exact_synonym
annotated target: host penetration
database_cross_reference: GOC:vw

Axiom
annotated source: entry into host
annotated property: has_exact_synonym
annotated target: penetration into host
database_cross_reference: GOC:vw

Axiom
annotated source: entry into host
annotated property: has_narrow_synonym
annotated target: entry into cell of other organism during symbiotic interaction
database_cross_reference: GOC:tb

Axiom
annotated source: entry into host
annotated property: has_narrow_synonym
annotated target: penetration into host via a specialized structure
database_cross_reference: GOC:vw

Axiom
annotated source: entry into host
annotated property: has_narrow_synonym
annotated target: penetration into host via a specialized structure during symbiotic interaction
database_cross_reference: GOC:vw

Axiom
annotated source: entry into host
annotated property: has_related_synonym
annotated target: entry into other organism during symbiotic interaction
database_cross_reference: GOC:tb

biological process involved in interspecies interaction between organisms
type: Class
subclass of: biological_process
definition: Any process evolved to enable an interaction with an organism of a different species.
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
has_exact_synonym: interaction with another species
has_exact_synonym: interspecies interaction
has_exact_synonym: interspecies interaction between organisms
has_exact_synonym: interspecies interaction with other organisms
has_obo_namespace: biological_process
id: GO:0044419
in_subset: gocheck do not annotate
in_subset: goslim candida
in_subset: goslim pir

Axiom
annotated source: biological process involved in interspecies interaction between organisms
annotated property: definition
annotated target: Any process evolved to enable an interaction with an organism of a different species.
database_cross_reference: GOC:cc

multicellular organismal reproductive process
type: Class
subclass of: reproductive process
definition: The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
term tracker item: https://github.com/geneontology/go-ontology/issues/27054
has_broad_synonym: organismal reproductive process
has_exact_synonym: reproductive process in a multicellular organism
has_obo_namespace: biological_process
id: GO:0048609
in_subset: gocheck do not annotate
in_subset: goslim drosophila

Axiom
annotated source: multicellular organismal reproductive process
annotated property: definition
annotated target: The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
database_cross_reference: GOC:dph
database_cross_reference: GOC:jid
database_cross_reference: GOC:tb

establishment of localization
type: Class
subclass of: biological_process
definition: Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
imported from: go.owl
imported from: Gene Ontology: http://purl.obolibrary.org/obo/go.owl

biological process involved in interaction with host
type: Class
subclass of: biological process involved in symbiotic interaction
definition: An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
term tracker item: https://github.com/geneontology/go-ontology/issues/20191
has_alternative_id: GO:0044112
has_alternative_id: GO:0044116
has_alternative_id: GO:0044117
has_alternative_id: GO:0044119
has_alternative_id: GO:0044121
has_alternative_id: GO:0044123
has_alternative_id: GO:0044125
has_exact_synonym: interaction with host
has_narrow_synonym: growth of symbiont in host
has_narrow_synonym: growth of symbiont in host cell
has_narrow_synonym: growth of symbiont in host organelle
has_narrow_synonym: growth of symbiont in host vacuole
has_obo_namespace: biological_process
id: GO:0051701

Axiom
annotated source: biological process involved in interaction with host
annotated property: definition
annotated target: An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
database_cross_reference: GOC:cc

multi-organism process
type: Class
subclass of: biological_process
definition: A biological process which involves another organism of the same or different species.
imported from: go.owl

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

objective specification
type: Class
subclass of: directive information entity
editor preferred term: 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 label: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

narrative object
type: Class
subclass of: information content entity
editor preferred term: 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

data item label
type: Class
subclass of: information content entity
editor preferred term: data item label
editor preferred term: datum label
has curation status: ready for release
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
definition: An information content entity that is part of some data item and is used to partially define the denotation of that data item.
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
definition editor: GROUP: IAO
alternative label: datum label
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
imported from: http://purl.obolibrary.org/obo/obi.owl
label: datum label

software
type: Class
subclass of: plan specification
editor preferred term: 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 term: 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 term: 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
subclass of: Restriction
  on property: concretizes
  some values from: information content entity
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 label: data

symbol
type: Class
subclass of: information content entity
editor preferred term: 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 term: 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 term: 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

integer numeral
type: Class
subclass of: numeral
editor preferred term: 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
editor preferred term: scalar measurement datum
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.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: http://purl.obolibrary.org/obo/obi.owl

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable
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

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

obsolete_study interpretation
type: Class
subclass of: Obsolete Class
editor preferred term: 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 label: conclusion
definition source: OBI_0000005
has obsolescence reason: failed exploratory term
deprecated: true

dot plot
type: Class
subclass of: graph
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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

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

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 term: 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, 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: 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
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 editor: Clint Dowland
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
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 term: 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
editor preferred term: 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: http://purl.obolibrary.org/obo/obi.owl

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 term: 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 term: 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 term: 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 label: 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 term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete
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
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: information content entity
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 label: 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
subclass of: Restriction
  on property: bearer of
  some values from: Restriction
    on property: concretizes
    some values from: photograph
editor preferred term: 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
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
  one of: out of scope
subclass of: data about an ontology part
editor preferred term: 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 term: 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 label: text

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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

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 term: 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 label: 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 term: 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 label: scientific publication

patent
type: Class
subclass of: document
editor preferred term: 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 term: 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 term: 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 label: 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 term: 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 label: background
alternative label: introduction
alternative label: 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 term: 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 label: experimental
alternative label: experimental methods
alternative label: experimental procedures
alternative label: experimental section
alternative label: method
alternative label: methodology
alternative label: 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 term: 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 label: results

discussion section of a publication about an investigation
type: Class
subclass of: document part
editor preferred term: 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 label: discussion
alternative label: discussion section
alternative label: 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 term: 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 label: literature cited
alternative label: reference
alternative label: reference list
alternative label: 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 term: 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 term: 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 term: 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 label: author contributions
alternative label: authors' contribution
alternative label: authors' contributions
alternative label: authors' roles
alternative label: contributions by the authors
alternative label: contributorship
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

acknowledgements section
type: Class
subclass of: document part
editor preferred term: 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 label: acknowledgement
alternative label: acknowledgements
alternative label: acknowledgment
alternative label: 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 term: 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 label: endnote
alternative label: 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 term: 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 label: additional file
alternative label: additional files
alternative label: additional information
alternative label: appendix
alternative label: electronic supplementary material
alternative label: electronic supplementary materials
alternative label: supplemental data
alternative label: supplemental information
alternative label: supplemental material
alternative label: supplementary data
alternative label: supplementary files
alternative label: supplementary information
alternative label: supplementary material
alternative label: supplementary materials
alternative label: supporting information
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/234

table of contents
type: Class
subclass of: table
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: hypothesis textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete
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
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 term: 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 term: 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
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

line graph
type: Class
subclass of: graph
editor preferred term: 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 label: 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 label: 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: 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 label: 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 label: 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 label: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls

centrally registered identifier registry
type: Class
subclass of: code set
example of usage: PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
definition editor: Justin Whorton
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative label: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237

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 label: 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 label: experimental time series

written name
type: Class
subclass of: textual entity
editor preferred term: 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 term: 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 term: 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 label: abbreviation and acronyms
alternative label: abbreviation list
alternative label: abbreviations
alternative label: abbreviations and acronyms
alternative label: abbreviations list
alternative label: abbreviations used
alternative label: definitions for abbreviations
alternative label: list of abbreviations
alternative label: list of abbreviations used
alternative label: non-standard abbreviations
alternative label: nonstandard abbreviations
alternative label: 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 term: 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 label: author information
alternative label: authors’ information
alternative label: biographies
alternative label: 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 term: 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 term: 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 label: author summary
alternative label: summary
alternative label: 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 term: 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 term: 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 label: availability
alternative label: availability of data
alternative label: data archiving
alternative label: data availability
alternative label: data availability statement
alternative label: 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 term: 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 term: 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 label: case presentation
alternative label: 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 term: 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 term: 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 label: concluding remarks
alternative label: conclusion
alternative label: conclusions
alternative label: findings
alternative label: 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 term: 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 label: authors' disclosures of potential conflicts of interest
alternative label: competing financial interests
alternative label: competing interests
alternative label: conflict of interest
alternative label: conflict of interest statement
alternative label: conflict of interests
alternative label: conflicts of interest
alternative label: declaration of competing interest
alternative label: declaration of competing interests
alternative label: declaration of interest
alternative label: declaration of interests
alternative label: disclosure of conflict of interest
alternative label: disclosure of potential conflicts of interest
alternative label: duality of interest
alternative label: 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 term: 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 term: 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 label: consent
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

consent textual entity
type: Class
subclass of: textual entity
editor preferred term: 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 term: 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 label: ethical approval
alternative label: ethical requirements
alternative label: ethics
alternative label: 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 term: 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 term: 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 label: 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 term: 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 label: financial support
alternative label: funding
alternative label: funding information
alternative label: funding sources
alternative label: funding statement
alternative label: funding/support
alternative label: grants
alternative label: role of the funding source
alternative label: source of funding
alternative label: sources of funding
alternative label: 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 term: 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 term: 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 label: future challenges
alternative label: future considerations
alternative label: future developments
alternative label: future directions
alternative label: future outlook
alternative label: future perspectives
alternative label: future plans
alternative label: future prospects
alternative label: future research
alternative label: future research directions
alternative label: future studies
alternative label: future work
alternative label: 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 term: 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 term: 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 label: 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 term: 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 term: 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 term: 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 label: 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 term: 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 label: limitations
alternative label: 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 term: 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 term: 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 label: materials
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

notes section
type: Class
subclass of: document part
editor preferred term: 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 label: 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 term: 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 term: 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 term: 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 label: notice of republication
alternative label: 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 term: 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 term: 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 label: related literature
alternative label: 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 term: 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 term: 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 label: requirements
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/183

requirements textual entity
type: Class
subclass of: textual entity
editor preferred term: 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 term: 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 term: 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 label: 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 term: 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 label: 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 label: 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 term: 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 label: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 label: 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

ORCID identifier
type: Class
subclass of: centrally registered identifier
has curation status: pending final vetting
definition: A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
editor note: "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]
editor note: This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)
definition editor: http://orcid.org/0000-0002-1595-3213
alternative label: ORCID ID
alternative label: ORCiD
alternative label: Open Researcher and Contributor ID
alternative label: Open Researcher and Contributor Identifier
definition source: https://orcid.org/
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/259

identifier
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: denotes
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: identifier creating process
equivalent class: Class
  intersection of: Restriction
    on property: denotes
    some values from: entity
  intersection of: Restriction
    on property: is_specified_output_of
    all values from: identifier creating process
subclass of: information content entity
subclass of: Restriction
  on property: denotes
  some values from: entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: identifier creating process
editor preferred term: 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.
definition: An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
definition editor: Justin Whorton
definition editor: Mathias Brochhausen
alternative label: proper name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen
comment: Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)

grapheme
type: Class
subclass of: information content entity
example of usage: alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems
definition: An information content entity that is a fundamental unit in a written language.
definition editor: Justin Whorton
definition source: http://en.wikipedia.org/wiki/Grapheme
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen
comment: Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there.

identifier creating process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: identifier
equivalent class: Restriction
  on property: has_specified_output
  some values from: identifier
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: identifier
definition: A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
definition: An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
definition editor: Justin Whorton
definition editor: Mathias Brochhausen
alternative label: dubbing process
alternative label: naming
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
creator: Mathias Brochhausen

personal name
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: denotes
    all values from: Homo sapiens
subclass of: identifier
definition: A personal name is a proper name identifying an individual person.
definition: An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.
definition editor: Justin Whorton
definition editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Personal_name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
comment: Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
comment: Personal names to not include names of fictional characters, e.g. Sherlock Holmes.
comment: Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)

given name
type: Class
subclass of: personal name
definition: A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
definition editor: Justin Whorton
definition editor: Mathias Brochhausen
alternative label: first name
definition source: http://en.wikipedia.org/wiki/Given_name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237

family name
type: Class
subclass of: identifier
definition: An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
definition editor: Justin Whorton
definition editor: Mathias Brochhausen
alternative label: last name
alternative label: surname
definition source: http://en.wikipedia.org/wiki/Family_name
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237

code set
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: identifier
definition: An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate.
definition: An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
definition editor: Alan Ruttenberg
definition editor: Justin Whorton
definition editor: Mathias Brochhausen
alternative label: code map
alternative label: code system
alternative label: codeset
alternative label: coding system
alternative label: controlled vocabulary
term tracker item: https://github.com/information-artifact-ontology/IAO/issues/237
contributor: Alan Ruttenberg
contributor: Clint Dowland
contributor: Matt Diller
contributor: Sarah Bost
contributor: William R. Hogan
comment: Code sets might include non-entities/things (e.g. missing thumbs).
comment: Does not imply absence vs. presence of any taxonomy.
comment: Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.
comment: Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).
comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).
comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.
comment: Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.
comment: The information content entities do not denote each other.

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 is in need of being perceived.
definition editor: Mathias Brochhausen
comment: The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. Thanks to W.R. Hogan for finding the Reinach quote.

deontic declaration
type: Class
subclass of: social act
definition: A social act that creates or revokes a deontic role.
definition editor: Mathias Brochhausen

ontology module
type: Class
subclass of: data about an ontology part
editor preferred term: 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 label: 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 term: 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 term: 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 label: source ontology module

main release ontology module
type: Class
subclass of: ontology module
editor preferred term: 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 term: 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 term: 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 label: import file

subset ontology module
type: Class
subclass of: ontology module
editor preferred term: 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 label: ontology slim
alternative label: subset ontology

curation subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: 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 term: 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 term: 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 label: ribbon subset

exclusion subset ontology module
type: Class
subclass of: subset ontology module
editor preferred term: 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 label: antislim

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

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

reasoned ontology module
type: Class
subclass of: ontology module
editor preferred term: 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 term: 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 term: 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 term: taxonomic bridge ontology module

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

obo basic subset ontology module
type: Class
subclass of: ontology module subsetted by expressivity
editor preferred term: 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 term: ontology module subsetted by OWL profile

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

opportunistic infectious disposition
type: Class
subclass of: infectious disposition
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: transmission process
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: An infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
alternative label: opportunitistic pathogenic disposition
comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).

primary infectious disposition
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: transmission process
      intersection of: Restriction
        on property: has part
        some values from: Class
subclass of: infectious disposition
definition: An infectious disposition to become part of a disorder in organisms that have intact defenses.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
comment: A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease."

pathogenic disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: material entity
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: results in formation of
        some values from: disorder
disjoint with: immunocompetence
disjoint with: disease
definition: A disposition to initiate processes that result in a disorder.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
alternative label: pathogenicity
comment: A pathogenic disposition is realized in processes that create a disorder.
comment: The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.

infectious disposition
type: Class
subclass of: pathogenic disposition
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has part
        some values from: transmission process
definition: A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder.

zoonotic disposition
type: Class
subclass of: infectious disposition
definition: An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis.

reverse zoonotic disposition
type: Class
subclass of: infectious disposition
definition: An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.

immunocompetent organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: immunocompetence
subclass of: organism
subclass of: Restriction
  on property: has disposition
  some values from: immunocompetence
definition: An organism that has immunocompetence.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

infectious agent transmissibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: infectious agent
definition: A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.

infectivity
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: This quality is measured by the proportion of exposed who become infected.

virulence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: infectious agent
definition: A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal.

susceptibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
definition: A quality that inheres in an entity and is the degree to which it can be harmed by another entity.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.

infectious disease incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.

infection incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.

infectious disease incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
alternative label: cumulative incidence of infectious disease
comment: An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.

infection incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
alternative label: cumulative incidence of infection
comment: An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.

infectious disease incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.

infection incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the infection incidence proportion per unit time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.

infectious disease prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.

infection prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.

infectious disease lifetime prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.

infectious agent seroprevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.

infectious disease mortality rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.

infectious disease endemicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic.

infectious disease sporadicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: characteristic of
  some values from: organism population
definition: A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease.

organism population
type: Class
subclass of: object_aggregate
definition: An aggregate of organisms of the same Species.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.

pathogen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: pathogenic disposition
subclass of: material entity
subclass of: Restriction
  on property: has disposition
  some values from: pathogenic disposition
definition: A material entity with a pathogenic disposition.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

primary pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: primary infectious disposition
subclass of: infectious agent
subclass of: Restriction
  on property: has disposition
  some values from: primary infectious disposition
definition: An infectious agent with a primary infectious disposition.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
alternative label: principal pathogen

host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: host role
subclass of: organism
subclass of: Restriction
  on property: has role
  some values from: host role
definition: An organism bearing a host role.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
subclass of: pathogen
subclass of: organism
subclass of: Restriction
  on property: has disposition
  some values from: infectious disposition
definition: An organism that has an infectious disposition.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

immunosuppression
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: negatively regulates
    some values from: immune response
subclass of: process
subclass of: Restriction
  on property: negatively regulates
  some values from: immune response
definition: A process that attenuates an immune response.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

immunocompetence
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
  intersection of: Restriction
    on property: is realized by
    all values from: immune response
disjoint with: disease
definition: A disposition that is the ability to mount a normal immune response.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response.

communicability
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: is realized by
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has part
        some values from: horizontal pathogen transmission process
subclass of: infectious disposition
definition: An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The disposition is realized in a direct, horizontal transmission process between members of the same Species.

establishment of localization in host
type: Class
equivalent class: Restriction
  on property: occurs in
  some values from: host
subclass of: establishment of localization
subclass of: Restriction
  on property: occurs in
  some values from: host
definition: An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature.
editor note: Requested addition of this term to the GO.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA.

appearance of disorder
type: Class
equivalent class: Restriction
  on property: results in formation of
  some values from: disorder
subclass of: process
subclass of: Restriction
  on property: results in formation of
  some values from: disorder
definition: A process by which a disorder comes into existence.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

host role
type: Class
subclass of: organism role
subclass of: Restriction
  on property: characteristic of
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: Class
        intersection of: extended organism
        intersection of: Restriction
definition: A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

opportunistic pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: opportunistic infectious disposition
subclass of: infectious agent
subclass of: Restriction
  on property: has disposition
  some values from: opportunistic infectious disposition
definition: An infectious agent with an opportunistic infectious disposition.
definition editor: Albert Goldfain
definition editor: Alex Diehl
definition editor: Lindsay Cowell
alternative label: opportunist

horizontal pathogen transmission process
type: Class
subclass of: transmission process
definition: A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship.
definition editor: Lindsay Cowell

intentionality
type: Class
subclass of: mental quality
definition: Intentionality is the fundamental quality of conscious mental processes of always having content, of being directed towards, or about something.

bodily quality
type: Class
subclass of: quality
definition: A bodily quality is a quality that inheres in some extended organism.

mental quality
type: Class
subclass of: bodily quality
definition: A mental quality is a bodily quality that inheres in those structures of the extended organism that are essential for mental functioning.

sexual activity
type: Class
subclass of: reproductive behavior
imported from: http://purl.obolibrary.org/obo/MF.owl
created by: George Gkoutos
creation date: 2011-04-14T01:03:39Z
def: "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG]
namespace: behavior_ontology

Mus musculus
type: Class
subclass of: Eukaryota
editor preferred term: Mus musculus
definition editor: William R. Hogan
alternative label: House mouse

Viruses
type: Class
subclass of: organism
imported from: ncbitaxon.owl
label: Virus

Poxviridae
type: Class
subclass of: dsDNA viruses, no RNA stage

Chordopoxvirinae
type: Class
subclass of: Poxviridae

Orthopoxvirus
type: Class
subclass of: Chordopoxvirinae

Monkeypox virus
type: Class
subclass of: Orthopoxvirus
definition editor: Mirela L Vasconcelos
alternative label: monkey pox virus

Variola virus
type: Class
subclass of: Orthopoxvirus

H5N1 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H5N1 subtype of Influenza A virus

Herpesviridae
type: Class
subclass of: Herpesvirales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Alphaherpesvirinae
type: Class
subclass of: Herpesviridae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Simplexvirus
type: Class
subclass of: Alphaherpesvirinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Human alphaherpesvirus 1
type: Class
subclass of: Simplexvirus
has_rank: NCBITaxon species
has_broad_synonym: HSV-1
has_broad_synonym: HSV1
database_cross_reference: GC_ID:1
has_exact_synonym: Herpes simplex virus type 1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Herpes simplex virus 1
has_related_synonym: Human Herpesvirus-1
has_related_synonym: Human herpesvirus 1
has_related_synonym: Human herpesvirus type 1
has_related_synonym: herpes simplex virus 1 HSV-1
has_related_synonym: herpes simplex virus HSV-1
has_related_synonym: herpes simplex virus type 1 HSV-1
has_related_synonym: herpes simplex virus type 1 HSV1
has_related_synonym: herpes simplex virus type-1 HSV-1

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_broad_synonym
annotated target: HSV-1
has_synonym_type: acronym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_broad_synonym
annotated target: HSV1
has_synonym_type: acronym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_exact_synonym
annotated target: Herpes simplex virus type 1
has_synonym_type: genbank common name

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: Herpes simplex virus 1
has_synonym_type: genbank synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: Human Herpesvirus-1
has_synonym_type: misspelling

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: Human herpesvirus 1
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: Human herpesvirus type 1
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: herpes simplex virus 1 HSV-1
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: herpes simplex virus HSV-1
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: herpes simplex virus type 1 HSV-1
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: herpes simplex virus type 1 HSV1
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 1
annotated property: has_related_synonym
annotated target: herpes simplex virus type-1 HSV-1
has_synonym_type: synonym

Human alphaherpesvirus 2
type: Class
subclass of: Simplexvirus
has_rank: NCBITaxon species
has_broad_synonym: HSV2
database_cross_reference: GC_ID:1
has_exact_synonym: Herpes simplex virus type 2 (HSV-2)
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Herpes simplex virus (type 2)
has_related_synonym: Herpes simplex virus 2
has_related_synonym: Herpes simplex virus II
has_related_synonym: Herpes simplex virus type 2
has_related_synonym: Human herpesvirus 2
has_related_synonym: herpes simplex virus type 2 HSV-2

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_broad_synonym
annotated target: HSV2
has_synonym_type: acronym

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_exact_synonym
annotated target: Herpes simplex virus type 2 (HSV-2)
has_synonym_type: equivalent name

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_related_synonym
annotated target: Herpes simplex virus (type 2)
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_related_synonym
annotated target: Herpes simplex virus 2
has_synonym_type: genbank synonym

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_related_synonym
annotated target: Herpes simplex virus II
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_related_synonym
annotated target: Herpes simplex virus type 2
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_related_synonym
annotated target: Human herpesvirus 2
has_synonym_type: synonym

Axiom
annotated source: Human alphaherpesvirus 2
annotated property: has_related_synonym
annotated target: herpes simplex virus type 2 HSV-2
has_synonym_type: synonym

Varicellovirus
type: Class
subclass of: Alphaherpesvirinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Human herpesvirus 3
type: Class
subclass of: Varicellovirus
has_rank: NCBITaxon species
has_broad_synonym: HHV-3
has_broad_synonym: VZV
database_cross_reference: GC_ID:1
has_exact_synonym: Varicella-zoster virus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Human alphaherpesvirus 3
has_related_synonym: Human herpes virus 3
has_related_synonym: Varicella Zoster Virus
has_related_synonym: varicella zoster virus VZV
has_related_synonym: varicella-zoster virus VZV

Axiom
annotated source: Human herpesvirus 3
annotated property: has_broad_synonym
annotated target: HHV-3
has_synonym_type: genbank acronym

Axiom
annotated source: Human herpesvirus 3
annotated property: has_broad_synonym
annotated target: VZV
has_synonym_type: acronym

Axiom
annotated source: Human herpesvirus 3
annotated property: has_exact_synonym
annotated target: Varicella-zoster virus
has_synonym_type: genbank common name

Axiom
annotated source: Human herpesvirus 3
annotated property: has_related_synonym
annotated target: Human alphaherpesvirus 3
has_synonym_type: synonym

Axiom
annotated source: Human herpesvirus 3
annotated property: has_related_synonym
annotated target: Human herpes virus 3
has_synonym_type: synonym

Axiom
annotated source: Human herpesvirus 3
annotated property: has_related_synonym
annotated target: Varicella Zoster Virus
has_synonym_type: synonym

Axiom
annotated source: Human herpesvirus 3
annotated property: has_related_synonym
annotated target: varicella zoster virus VZV
has_synonym_type: synonym

Axiom
annotated source: Human herpesvirus 3
annotated property: has_related_synonym
annotated target: varicella-zoster virus VZV
has_synonym_type: synonym

Suid herpesvirus 1
type: Class
subclass of: Varicellovirus
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:44156
has_broad_synonym: PRV
database_cross_reference: GC_ID:1
has_exact_synonym: Pseudorabies virus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Alphaherpesvirus pseudorabies virus PRV
has_related_synonym: Aujeszky's disease virus
has_related_synonym: Pseudorabies Virus PRV
has_related_synonym: Suid herpesvirus type 1

Axiom
annotated source: Suid herpesvirus 1
annotated property: has_broad_synonym
annotated target: PRV
has_synonym_type: acronym

Axiom
annotated source: Suid herpesvirus 1
annotated property: has_exact_synonym
annotated target: Pseudorabies virus
has_synonym_type: genbank common name

Axiom
annotated source: Suid herpesvirus 1
annotated property: has_related_synonym
annotated target: Alphaherpesvirus pseudorabies virus PRV
has_synonym_type: synonym

Axiom
annotated source: Suid herpesvirus 1
annotated property: has_related_synonym
annotated target: Aujeszky's disease virus
has_synonym_type: synonym

Axiom
annotated source: Suid herpesvirus 1
annotated property: has_related_synonym
annotated target: Pseudorabies Virus PRV
has_synonym_type: synonym

Axiom
annotated source: Suid herpesvirus 1
annotated property: has_related_synonym
annotated target: Suid herpesvirus type 1
has_synonym_type: synonym

Hepadnaviridae
type: Class
subclass of: Retro-transcribing viruses
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_exact_synonym: hepatitis B-type viruses
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Hepadnaviridae
annotated property: has_exact_synonym
annotated target: hepatitis B-type viruses
has_synonym_type: genbank common name

Orthohepadnavirus
type: Class
subclass of: Hepadnaviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_exact_synonym: mammalian hepatitis B-type viruses
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Orthohepadnavirus
annotated property: has_exact_synonym
annotated target: mammalian hepatitis B-type viruses
has_synonym_type: genbank common name

Hepatitis B virus
type: Class
subclass of: Orthohepadnavirus
has_rank: NCBITaxon species
has_broad_synonym: HBV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Human hepatitis B virus
has_related_synonym: hepatitis B virus (HBV)
has_related_synonym: hepatitis B virus HBV
has_related_synonym: hepatitis B virus, HBV
has_related_synonym: human hepatitis B virus HBV

Axiom
annotated source: Hepatitis B virus
annotated property: has_broad_synonym
annotated target: HBV
has_synonym_type: acronym

Axiom
annotated source: Hepatitis B virus
annotated property: has_related_synonym
annotated target: Human hepatitis B virus
has_synonym_type: synonym

Axiom
annotated source: Hepatitis B virus
annotated property: has_related_synonym
annotated target: hepatitis B virus (HBV)
has_synonym_type: synonym

Axiom
annotated source: Hepatitis B virus
annotated property: has_related_synonym
annotated target: hepatitis B virus HBV
has_synonym_type: synonym

Axiom
annotated source: Hepatitis B virus
annotated property: has_related_synonym
annotated target: hepatitis B virus, HBV
has_synonym_type: synonym

Axiom
annotated source: Hepatitis B virus
annotated property: has_related_synonym
annotated target: human hepatitis B virus HBV
has_synonym_type: synonym

Escherichia coli O157
type: Class
subclass of: Escherichia coli
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Aedini
type: Class
subclass of: Culicinae

canis group
type: Class
subclass of: Ehrlichia
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

phagocytophilum group
type: Class
subclass of: Anaplasma
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
has_exact_synonym: phagocytophila group
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: phagocytophilum group
annotated property: has_exact_synonym
annotated target: phagocytophila group
has_synonym_type: equivalent name

Reoviridae
type: Class
subclass of: dsRNA viruses
definition editor: Mirela L Vasconcelos

Rotavirus
type: Class
subclass of: Sedoreovirinae
definition editor: Mirela L Vasconcelos
alternative label: Rotaviruses

Togaviridae
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage

Alphavirus
type: Class
subclass of: Togaviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_exact_synonym: arboviruses group A
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Alphaviridae

Axiom
annotated source: Alphavirus
annotated property: has_exact_synonym
annotated target: arboviruses group A
has_synonym_type: genbank common name

Axiom
annotated source: Alphavirus
annotated property: has_related_synonym
annotated target: Alphaviridae
has_synonym_type: synonym

Barmah Forest virus
type: Class
subclass of: Alphavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Eastern equine encephalitis virus
type: Class
subclass of: EEEV complex
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eastern equine encephalomyelitis virus
has_related_synonym: eastern equine encephalomyelitis EEE
has_related_synonym: eastern equine encephalomyelitis virus EEEV

Axiom
annotated source: Eastern equine encephalitis virus
annotated property: has_related_synonym
annotated target: Eastern equine encephalomyelitis virus
has_synonym_type: synonym

Axiom
annotated source: Eastern equine encephalitis virus
annotated property: has_related_synonym
annotated target: eastern equine encephalomyelitis EEE
has_synonym_type: synonym

Axiom
annotated source: Eastern equine encephalitis virus
annotated property: has_related_synonym
annotated target: eastern equine encephalomyelitis virus EEEV
has_synonym_type: synonym

Ross River virus
type: Class
subclass of: Alphavirus
has_rank: NCBITaxon species
has_broad_synonym: RRV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Ross River virus
annotated property: has_broad_synonym
annotated target: RRV
has_synonym_type: acronym

Western equine encephalitis virus
type: Class
subclass of: WEEV complex
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Western equine encephaliomyelitis virus
has_related_synonym: Western equine encephalomyelitis virus

Axiom
annotated source: Western equine encephalitis virus
annotated property: has_related_synonym
annotated target: Western equine encephaliomyelitis virus
has_synonym_type: misspelling

Axiom
annotated source: Western equine encephalitis virus
annotated property: has_related_synonym
annotated target: Western equine encephalomyelitis virus
has_synonym_type: synonym

Rubivirus
type: Class
subclass of: Togaviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Rubella virus
type: Class
subclass of: Rubivirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Flaviviridae
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage

Flavivirus
type: Class
subclass of: Flaviviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_exact_synonym: arboviruses group B
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Flavivirus
annotated property: has_exact_synonym
annotated target: arboviruses group B
has_synonym_type: genbank common name

Dengue virus group
type: Class
subclass of: Flavivirus

Dengue virus 1
type: Class
subclass of: Dengue virus

Dengue virus 2
type: Class
subclass of: Dengue virus

Dengue virus 3
type: Class
subclass of: Dengue virus

Dengue virus 4
type: Class
subclass of: Dengue virus

Japanese encephalitis virus group
type: Class
subclass of: Flavivirus
has_rank: NCBITaxon subgenus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Japanese encephalitis viruses

Axiom
annotated source: Japanese encephalitis virus group
annotated property: has_related_synonym
annotated target: Japanese encephalitis viruses
has_synonym_type: synonym

Japanese encephalitis virus
type: Class
subclass of: Japanese encephalitis virus group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Japanese encephalitis
has_related_synonym: Japanese encephalitis (JE) virus
has_related_synonym: Japanese encephalitis virus JE
has_related_synonym: Japanese encephalitis virus JEV

Axiom
annotated source: Japanese encephalitis virus
annotated property: has_related_synonym
annotated target: Japanese encephalitis
has_synonym_type: misspelling

Axiom
annotated source: Japanese encephalitis virus
annotated property: has_related_synonym
annotated target: Japanese encephalitis (JE) virus
has_synonym_type: synonym

Axiom
annotated source: Japanese encephalitis virus
annotated property: has_related_synonym
annotated target: Japanese encephalitis virus JE
has_synonym_type: synonym

Axiom
annotated source: Japanese encephalitis virus
annotated property: has_related_synonym
annotated target: Japanese encephalitis virus JEV
has_synonym_type: synonym

Murray Valley encephalitis virus
type: Class
subclass of: Japanese encephalitis virus group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

St. Louis encephalitis virus
type: Class
subclass of: Japanese encephalitis virus group
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:64321
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Saint Louis encephalitis virus
has_related_synonym: St. Louis encephalitis virus SLEV

Axiom
annotated source: St. Louis encephalitis virus
annotated property: has_related_synonym
annotated target: Saint Louis encephalitis virus
has_synonym_type: synonym

Axiom
annotated source: St. Louis encephalitis virus
annotated property: has_related_synonym
annotated target: St. Louis encephalitis virus SLEV
has_synonym_type: misnomer

West Nile virus
type: Class
subclass of: Japanese encephalitis virus group
has_rank: NCBITaxon species
has_broad_synonym: WNV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: West Nile virus
annotated property: has_broad_synonym
annotated target: WNV
has_synonym_type: genbank acronym

Powassan virus
type: Class
subclass of: tick-borne encephalitis virus group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Flavivirus powassan

Axiom
annotated source: Powassan virus
annotated property: has_related_synonym
annotated target: Flavivirus powassan
has_synonym_type: synonym

Yellow fever virus
type: Class
subclass of: Yellow fever virus group
has_rank: NCBITaxon species
has_broad_synonym: YFV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Flavivirus febricis
has_related_synonym: yellow fever virus YFV

Axiom
annotated source: Yellow fever virus
annotated property: has_broad_synonym
annotated target: YFV
has_synonym_type: genbank acronym

Axiom
annotated source: Yellow fever virus
annotated property: has_related_synonym
annotated target: Flavivirus febricis
has_synonym_type: synonym

Axiom
annotated source: Yellow fever virus
annotated property: has_related_synonym
annotated target: yellow fever virus YFV
has_synonym_type: synonym

Hepacivirus
type: Class
subclass of: Flaviviridae
definition editor: Mirela L Vasconcelos
alternative label: Hepatitis C virus group
alternative label: Hepatitis C viruses
alternative label: Hepatitis C-like viruses

Hepatitis C virus
type: Class
subclass of: Hepacivirus
definition editor: Mirela L Vasconcelos
alternative label: hepatitis C virus HCV
alternative label: human hepatitis C virus
alternative label: human hepatitis C virus HCV
alternative label: human hepatitis virus C HCV
alternative label: post-transfusion hepatitis non A non B virus

Coronaviridae
type: Class
subclass of: Nidovirales
editor preferred term: Coronaviridae
imported from: http://purl.obolibrary.org/obo/obi.owl

Chlamydia/Chlamydophila group
type: Class
subclass of: Chlamydiaceae
definition editor: Mirela L Vasconcelos

pseudomallei group
type: Class
subclass of: Burkholderia
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Mononegavirales
type: Class
subclass of: ssRNA negative-strand virus

Paramyxoviridae
type: Class
subclass of: Mononegavirales

Paramyxovirinae
type: Class
subclass of: Paramyxoviridae

Mumps virus
type: Class
subclass of: Rubulavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Morbillivirus
type: Class
subclass of: Paramyxoviridae
definition editor: Mirela L Vasconcelos
alternative label: Morbilliviruses

Measles virus
type: Class
subclass of: Morbillivirus

Pneumoviridae
type: Class
subclass of: Mononegavirales
definition editor: Mirela L Vasconcelos
alternative label: Pneumovirinae

Pneumovirus
type: Class
subclass of: Pneumoviridae
definition editor: Mirela L Vasconcelos

Filoviridae
type: Class
subclass of: Mononegavirales

Marburg marburgvirus
type: Class
subclass of: Marburgvirus
has_rank: NCBITaxon species
has_broad_synonym: MBG
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Lake Victoria marburgvirus
has_related_synonym: Marburg virus MBG

Axiom
annotated source: Marburg marburgvirus
annotated property: has_broad_synonym
annotated target: MBG
has_synonym_type: acronym

Axiom
annotated source: Marburg marburgvirus
annotated property: has_related_synonym
annotated target: Lake Victoria marburgvirus
has_synonym_type: synonym

Axiom
annotated source: Marburg marburgvirus
annotated property: has_related_synonym
annotated target: Marburg virus MBG
has_synonym_type: synonym

Rhabdoviridae
type: Class
subclass of: Mononegavirales
definition editor: Mirela L Vasconcelos

Lyssavirus
type: Class
subclass of: Rhabdoviridae
definition editor: Mirela L Vasconcelos

Rabies lyssavirus
type: Class
subclass of: Lyssavirus
definition editor: Mirela L Vasconcelos
alternative label: Rabies virus

Orthomyxoviridae
type: Class
subclass of: ssRNA negative-strand virus

Influenza A virus
type: Class
subclass of: Influenzavirus A

spotted fever group
type: Class
subclass of: Rickettsia
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
database_cross_reference: PMID:9734038
has_obo_namespace: ncbi_taxonomy

typhus group
type: Class
subclass of: Rickettsia
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

H1N1 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H1N1 subtype of Influenza A virus

H2N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H2N2 subtype of Influenza A virus

Influenza B virus
type: Class
subclass of: Influenzavirus B
definition editor: Mirela L Vasconcelos
alternative label: Influenza virus type B

Bunyaviridae
type: Class
subclass of: ssRNA negative-strand virus
definition editor: Mirela L Vasconcelos
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Orthobunyavirus
type: Class
subclass of: Peribunyaviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bunyavirus
has_related_synonym: Bunyaviruses

Axiom
annotated source: Orthobunyavirus
annotated property: has_related_synonym
annotated target: Bunyavirus
has_synonym_type: synonym

Axiom
annotated source: Orthobunyavirus
annotated property: has_related_synonym
annotated target: Bunyaviruses
has_synonym_type: synonym

La Crosse virus
type: Class
subclass of: California encephalitis orthobunyavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bunyavirus la crosse

Axiom
annotated source: La Crosse virus
annotated property: has_related_synonym
annotated target: Bunyavirus la crosse
has_synonym_type: synonym

Snowshoe hare virus
type: Class
subclass of: California encephalitis orthobunyavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bunyavirus snowshoe hare
has_related_synonym: Snowshoe hare bunyavirus

Axiom
annotated source: Snowshoe hare virus
annotated property: has_related_synonym
annotated target: Bunyavirus snowshoe hare
has_synonym_type: synonym

Axiom
annotated source: Snowshoe hare virus
annotated property: has_related_synonym
annotated target: Snowshoe hare bunyavirus
has_synonym_type: synonym

Phlebovirus
type: Class
subclass of: Bunyaviridae
definition editor: Mirela L Vasconcelos
alternative label: Phleboviruses

Rift Valley fever virus
type: Class
subclass of: Rift Valley fever phlebovirus
definition editor: Mirela L Vasconcelos

Hantavirus
type: Class
subclass of: Bunyaviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Hantaviurs

Axiom
annotated source: Hantavirus
annotated property: has_related_synonym
annotated target: Hantaviurs
has_synonym_type: misspelling

Arenaviridae
type: Class
subclass of: ssRNA negative-strand virus
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Junin mammarenavirus
type: Class
subclass of: Mammarenavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Junin arenavirus
has_related_synonym: Junin virus
has_related_synonym: Junn mammarenavirus

Axiom
annotated source: Junin mammarenavirus
annotated property: has_related_synonym
annotated target: Junin arenavirus
has_synonym_type: synonym

Axiom
annotated source: Junin mammarenavirus
annotated property: has_related_synonym
annotated target: Junin virus
has_synonym_type: synonym

Axiom
annotated source: Junin mammarenavirus
annotated property: has_related_synonym
annotated target: Junn mammarenavirus
has_synonym_type: synonym

Lassa mammarenavirus
type: Class
subclass of: Mammarenavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Lassa virus

Axiom
annotated source: Lassa mammarenavirus
annotated property: has_related_synonym
annotated target: Lassa virus
has_synonym_type: synonym

Machupo mammarenavirus
type: Class
subclass of: Mammarenavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Machupo virus

Axiom
annotated source: Machupo mammarenavirus
annotated property: has_related_synonym
annotated target: Machupo virus
has_synonym_type: synonym

Retroviridae
type: Class
subclass of: Retro-transcribing viruses

Lentivirus
type: Class
subclass of: Orthoretrovirinae
alternative label: Lentivirinae

Primate lentivirus group
type: Class
subclass of: Lentivirus
alternative label: Primate immunodeficiency viruses

Human immunodeficiency virus 1
type: Class
subclass of: Primate lentivirus group
alternative label: HIV-1
alternative label: Human immunodeficiency virus type 1
alternative label: human immunodeficiency virus 1 HIV-1
alternative label: human immunodeficiency virus HIV-1
alternative label: human immunodeficiency virus type 1 HIV 1
alternative label: human immunodeficiency virus type 1 HIV-1
alternative label: human immunodeficiency virus type 1 HIV1
alternative label: human immunodeficiency virus type 1, HIV-1
alternative label: human immunodeficiency virus type I HIV-1
alternative label: human immunodeficiency virus type-1 HIV-1
alternative label: human immunodeficiency virus-1 HIV-1

Human immunodeficiency virus 2
type: Class
subclass of: Primate lentivirus group
alternative label: HIV type 2
alternative label: HIV-2
alternative label: Human immunodeficiency virus type 2
alternative label: Human immunodeficiency virus-2
alternative label: human immunodeficiency virus type 2 HIV-2
alternative label: human immunodeficiency virus type 2, HIV-2

Teleostomi
type: Class
subclass of: Gnathostomata

Euteleostomi
type: Class
subclass of: Teleostomi
alternative label: bony vertebrates

Brucellaceae
type: Class
subclass of: Rhizobiales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Brucellaceae Breed et al. 1957

Axiom
annotated source: Brucellaceae
annotated property: has_related_synonym
annotated target: Brucellaceae Breed et al. 1957
has_synonym_type: synonym

Coxiellaceae
type: Class
subclass of: Legionellales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16280474
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Coxiella group

Axiom
annotated source: Coxiellaceae
annotated property: has_related_synonym
annotated target: Coxiella group
has_synonym_type: synonym

Legionellales
type: Class
subclass of: Gammaproteobacteria
has_rank: NCBITaxon order
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16280474
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Legionellaceae group
has_related_synonym: Legionellales Garrity et al. 2005

Axiom
annotated source: Legionellales
annotated property: has_related_synonym
annotated target: Legionellaceae group
has_synonym_type: synonym

Axiom
annotated source: Legionellales
annotated property: has_related_synonym
annotated target: Legionellales Garrity et al. 2005
has_synonym_type: synonym

Burkholderiaceae
type: Class
subclass of: Burkholderiales
has_rank: NCBITaxon family
has_alternative_id: NCBITaxon:119063
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16403855
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Burkholderia group

Axiom
annotated source: Burkholderiaceae
annotated property: has_related_synonym
annotated target: Burkholderia group
has_synonym_type: synonym

Enoplea
type: Class
subclass of: Nematoda
has_rank: NCBITaxon class
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Chromadorea
type: Class
subclass of: Nematoda
has_rank: NCBITaxon class
has_alternative_id: NCBITaxon:27837
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Adenophorea

Axiom
annotated source: Chromadorea
annotated property: has_related_synonym
annotated target: Adenophorea
has_synonym_type: synonym

H3N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H3N2 subtype of Influenza A virus

H7N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H7N2 subtype of Influenza A virus

H7N7 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H7N7 subtype of Influenza A virus

H5N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H5N2 subtype of Influenza A virus

Caliciviridae
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage
definition editor: Mirela L Vasconcelos

Picornaviridae
type: Class
subclass of: Picornavirales

Enterovirus
type: Class
subclass of: Picornaviridae

Ecdysozoa
type: Class
subclass of: Protostomia

Human poliovirus 1
type: Class
subclass of: Enterovirus C
alternative label: Human poliovirus type 1
alternative label: Poliovirus type 1
alternative label: poliovirus type 1 PV1

Human poliovirus 3
type: Class
subclass of: Enterovirus C
alternative label: Human poliovirus type 3
alternative label: Poliovirus type 3

Hepatovirus
type: Class
subclass of: Picornaviridae
definition editor: Mirela L Vasconcelos

Hepatovirus A
type: Class
subclass of: Hepatovirus
definition editor: Mirela L Vasconcelos
alternative label: Hepatitis A virus

Aphthovirus
type: Class
subclass of: Picornaviridae
definition editor: Mirela L Vasconcelos

Foot-and-mouth disease virus
type: Class
subclass of: Aphthovirus
definition editor: Mirela L Vasconcelos
alternative label: Foot and mouth disease virus
alternative label: foot and mouth disease virus FMDV
alternative label: foot-and-mouth disease virus FMDV

Nipah henipavirus
type: Class
subclass of: Henipavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Nipah virus

Axiom
annotated source: Nipah henipavirus
annotated property: has_related_synonym
annotated target: Nipah virus
has_synonym_type: synonym

Proteobacteria
type: Class
subclass of: Bacteria
definition editor: Mirela L Vasconcelos
alternative label: Alphaproteobacteraeota
alternative label: purple bacteria
alternative label: purple bacteria and relatives
alternative label: purple non-sulfur bacteria
alternative label: purple photosynthetic bacteria
alternative label: purple photosynthetic bacteria and relatives

Gammaproteobacteria
type: Class
subclass of: Proteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Proteobacteria gamma subdivision
alternative label: Purple bacteria, gamma subdivision
alternative label: gamma proteobacteria
alternative label: gamma subdivision
alternative label: gamma subgroup

Firmicutes
type: Class
subclass of: Terrabacteria group
alternative label: Gram-postive bacterium

Hepatitis E virus
type: Class
subclass of: Orthohepevirus A
has_broad_synonym: HEV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Hepatitis E virus HEV

Axiom
annotated source: Hepatitis E virus
annotated property: has_broad_synonym
annotated target: HEV
has_synonym_type: acronym

Axiom
annotated source: Hepatitis E virus
annotated property: has_related_synonym
annotated target: Hepatitis E virus HEV
has_synonym_type: synonym

Hepatitis delta virus
type: Class
subclass of: Deltavirus
definition editor: Mirela L Vasconcelos
alternative label: Hepatitis D virus
alternative label: hepatitis delta virus HDV

Dengue virus
type: Class
subclass of: Dengue virus group

Staphylococcus
type: Class
subclass of: Staphylococcaceae
editor preferred term: Staphylococcus
alternative label: Aurococcus

Vibrio cholerae O1
type: Class
subclass of: Vibrio cholerae
definition editor: Mirela L Vasconcelos
alternative label: Vibrio cholerae serogroup O1

Staphylococcus aureus
type: Class
subclass of: Staphylococcus
editor preferred term: Staphylococcus aureus
alternative label: Micrococcus aureus
alternative label: Micrococcus pyogenes
alternative label: Staphlococcus pyogenes citreus
alternative label: Staphylococcus pyogenes aureus
alternative label: Streptococcus aureus

Conoidasida
type: Class
subclass of: Apicomplexa
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Respiratory syncytial virus
type: Class
subclass of: Pneumovirus
definition editor: Mirela L Vasconcelos
alternative label: respiratory syncytial virus RS
alternative label: respiratory syncytial virus RS virus
alternative label: respiratory syncytial virus RSV

Streptococcaceae
type: Class
subclass of: Lactobacillales
definition editor: Mirela L Vasconcelos

Streptococcus
type: Class
subclass of: Streptococcaceae
definition editor: Mirela L Vasconcelos

Streptophytina
type: Class
subclass of: Streptophyta
has_rank: NCBITaxon subphylum
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Charophyta/Embryophyta group
has_related_synonym: charophyte/embryophyte group

Axiom
annotated source: Streptophytina
annotated property: has_related_synonym
annotated target: Charophyta/Embryophyta group
has_synonym_type: synonym

Axiom
annotated source: Streptophytina
annotated property: has_related_synonym
annotated target: charophyte/embryophyte group
has_synonym_type: synonym

Streptococcus pneumoniae
type: Class
subclass of: Streptococcus
definition editor: Mirela L Vasconcelos
alternative label: Diplococcus pneumoniae
alternative label: Micrococcus pneumoniae

Archelosauria
type: Class
subclass of: Sauria
database_cross_reference: GC_ID:1
database_cross_reference: PMID:22839753
database_cross_reference: PMID:25450099
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Archosauria-Testudines
has_related_synonym: Testudines + Archosauria group

Axiom
annotated source: Archelosauria
annotated property: has_related_synonym
annotated target: Archosauria-Testudines
has_synonym_type: synonym

Axiom
annotated source: Archelosauria
annotated property: has_related_synonym
annotated target: Testudines + Archosauria group
has_synonym_type: synonym

Middle East respiratory syndrome coronavirus
type: Class
subclass of: Betacoronavirus

Dipnotetrapodomorpha
type: Class
subclass of: Sarcopterygii

Vibrionales
type: Class
subclass of: Gammaproteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Vibrionaceae group

Pasteurellales
type: Class
subclass of: Gammaproteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Pasteruellaceae group

Spirochaetales
type: Class
subclass of: Spirochaetia
has_rank: NCBITaxon order
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11075904
database_cross_reference: PMID:11542017
database_cross_reference: PMID:16558735
database_cross_reference: PMID:1917844
database_cross_reference: PMID:23908650
has_obo_namespace: ncbi_taxonomy
has_related_synonym: spirochetes

Axiom
annotated source: Spirochaetales
annotated property: has_related_synonym
annotated target: spirochetes
has_synonym_type: blast name

Spirochaetaceae
type: Class
subclass of: Spirochaetales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:23908650
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Treponemataceae

Axiom
annotated source: Spirochaetaceae
annotated property: has_related_synonym
annotated target: Treponemataceae
has_synonym_type: in part

Borrelia
type: Class
subclass of: Borreliaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:24744012
database_cross_reference: PMID:8863409
database_cross_reference: PMID:8863416
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Relapsing Fever Borrelia

Axiom
annotated source: Borrelia
annotated property: has_related_synonym
annotated target: Relapsing Fever Borrelia
has_synonym_type: synonym

Bacillales
type: Class
subclass of: Bacilli

Bacillus
type: Class
subclass of: Bacillaceae

Enterovirus A
type: Class
subclass of: Enterovirus
definition editor: Mirela L Vasconcelos
alternative label: Coxsackievirus A
alternative label: Enterovirus EV-A
alternative label: Human coxsackievirus A
alternative label: Human enterovirus A

Enterovirus C
type: Class
subclass of: Enterovirus
alternative label: Enterovirus EV-C
alternative label: Human enterovirus C
alternative label: Poliovirus

Enterovirus D
type: Class
subclass of: Enterovirus

Bacillus anthracis
type: Class
subclass of: Bacillus cereus group
definition editor: Mirela L Vasconcelos
alternative label: Bacillus cereus var. anthracis
alternative label: Bacteridium anthracis
alternative label: anthrax
alternative label: anthrax bacterium

Norovirus
type: Class
subclass of: Caliciviridae
definition editor: Mirela L Vasconcelos
alternative label: Norwalk-like viruses

Boreoeutheria
type: Class
subclass of: Eutheria
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11743200
database_cross_reference: PMID:11791233
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Boreotheria

Axiom
annotated source: Boreoeutheria
annotated property: has_related_synonym
annotated target: Boreotheria
has_synonym_type: synonym

Trichinella murrelli
type: Class
subclass of: Trichinella
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:92178
database_cross_reference: GC_ID:1
database_cross_reference: PMID:10701576
has_exact_synonym: Trichinella T5
has_exact_synonym: Trichinella sp. T5
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Trichinella murrelli
annotated property: has_exact_synonym
annotated target: Trichinella T5
has_synonym_type: equivalent name

Axiom
annotated source: Trichinella murrelli
annotated property: has_exact_synonym
annotated target: Trichinella sp. T5
has_synonym_type: equivalent name

Dorylaimia
type: Class
subclass of: Enoplea
has_rank: NCBITaxon subclass
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Saccharomycotina
type: Class
subclass of: saccharomyceta
has_rank: NCBITaxon subphylum
database_cross_reference: GC_ID:1
has_exact_synonym: true yeasts
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Saccharomycotina
annotated property: has_exact_synonym
annotated target: true yeasts
has_synonym_type: genbank common name

Pezizomycotina
type: Class
subclass of: saccharomyceta
has_rank: NCBITaxon subphylum
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Euascomycota

Axiom
annotated source: Pezizomycotina
annotated property: has_related_synonym
annotated target: Euascomycota
has_synonym_type: synonym

Eurotiomycetes
type: Class
subclass of: leotiomyceta
has_rank: NCBITaxon class
has_alternative_id: NCBITaxon:147540
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Loculoascomycetes
has_related_synonym: Plectomycetes
has_related_synonym: bitunicate ascomycetes

Axiom
annotated source: Eurotiomycetes
annotated property: has_related_synonym
annotated target: Loculoascomycetes
has_synonym_type: in part

Axiom
annotated source: Eurotiomycetes
annotated property: has_related_synonym
annotated target: Plectomycetes
has_synonym_type: in part

Axiom
annotated source: Eurotiomycetes
annotated property: has_related_synonym
annotated target: bitunicate ascomycetes
has_synonym_type: in part

Rhinovirus A
type: Class
subclass of: Enterovirus
editor preferred term: Rhinovirus A

Clostridium
type: Class
subclass of: Clostridiaceae
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:69207
database_cross_reference: GC_ID:11
database_cross_reference: PMID:26643615
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anaerobacter

Axiom
annotated source: Clostridium
annotated property: has_related_synonym
annotated target: Anaerobacter
has_synonym_type: synonym

Clostridium botulinum
type: Class
subclass of: Clostridium
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:29368
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10028279
database_cross_reference: PMID:15244052
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus botulinus
has_related_synonym: Bacillus putrificus
has_related_synonym: Botulobacillus botulinus
has_related_synonym: Clostridium putrificum
has_related_synonym: Ermengemillus botulinus
has_related_synonym: Pacinia putrifica

Axiom
annotated source: Clostridium botulinum
annotated property: has_related_synonym
annotated target: Bacillus botulinus
has_synonym_type: synonym

Axiom
annotated source: Clostridium botulinum
annotated property: has_related_synonym
annotated target: Bacillus putrificus
has_synonym_type: synonym

Axiom
annotated source: Clostridium botulinum
annotated property: has_related_synonym
annotated target: Botulobacillus botulinus
has_synonym_type: synonym

Axiom
annotated source: Clostridium botulinum
annotated property: has_related_synonym
annotated target: Clostridium putrificum
has_synonym_type: synonym

Axiom
annotated source: Clostridium botulinum
annotated property: has_related_synonym
annotated target: Ermengemillus botulinus
has_synonym_type: synonym

Axiom
annotated source: Clostridium botulinum
annotated property: has_related_synonym
annotated target: Pacinia putrifica
has_synonym_type: synonym

Clostridioides difficile
type: Class
subclass of: Clostridioides
definition editor: Mirela L Vasconcelos
alternative label: Bacillus difficilis
alternative label: Clostridium difficile
alternative label: Peptoclostridium difficile

Clostridium tetani
type: Class
subclass of: Clostridium
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus tetani

Axiom
annotated source: Clostridium tetani
annotated property: has_related_synonym
annotated target: Bacillus tetani
has_synonym_type: synonym

Clavispora/Candida clade
type: Class
subclass of: Clavispora
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Galloanserae
type: Class
subclass of: Neognathae
database_cross_reference: GC_ID:1
has_exact_synonym: ducks, geese, chickens, fowl, quail, currasows and allies
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Galloanseri

Axiom
annotated source: Galloanserae
annotated property: has_exact_synonym
annotated target: ducks, geese, chickens, fowl, quail, currasows and allies
has_synonym_type: equivalent name

Axiom
annotated source: Galloanserae
annotated property: has_related_synonym
annotated target: Galloanseri
has_synonym_type: synonym

Treponema
type: Class
subclass of: Spirochaetaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:23961314
database_cross_reference: PMID:9019153
database_cross_reference: PMID:9734025
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Microspironema

Axiom
annotated source: Treponema
annotated property: has_related_synonym
annotated target: Microspironema
has_synonym_type: synonym

Onygenales incertae sedis
type: Class
subclass of: Onygenales
has_alternative_id: NCBITaxon:34383
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Treponema pallidum
type: Class
subclass of: Treponema
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Microspironema pallidum
has_related_synonym: Spirillum pallidum
has_related_synonym: Spirochaeta pallida
has_related_synonym: Spironema pallidum

Axiom
annotated source: Treponema pallidum
annotated property: has_related_synonym
annotated target: Microspironema pallidum
has_synonym_type: synonym

Axiom
annotated source: Treponema pallidum
annotated property: has_related_synonym
annotated target: Spirillum pallidum
has_synonym_type: synonym

Axiom
annotated source: Treponema pallidum
annotated property: has_related_synonym
annotated target: Spirochaeta pallida
has_synonym_type: synonym

Axiom
annotated source: Treponema pallidum
annotated property: has_related_synonym
annotated target: Spironema pallidum
has_synonym_type: synonym

Treponema pallidum subsp. pallidum
type: Class
subclass of: Treponema pallidum
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:11
has_exact_synonym: Treponema pallidum pallidum
has_exact_synonym: syphilis treponeme
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Treponema pallidum subsp. pallidum
annotated property: has_exact_synonym
annotated target: Treponema pallidum pallidum
has_synonym_type: equivalent name

Axiom
annotated source: Treponema pallidum subsp. pallidum
annotated property: has_exact_synonym
annotated target: syphilis treponeme
has_synonym_type: genbank common name

Listeria
type: Class
subclass of: Listeriaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10408878
database_cross_reference: PMID:15709360
database_cross_reference: PMID:1713054
database_cross_reference: PMID:1899799
database_cross_reference: PMID:8427807
database_cross_reference: PMID:8782674
database_cross_reference: PMID:9226919
database_cross_reference: PMID:9542083
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Listerella

Axiom
annotated source: Listeria
annotated property: has_related_synonym
annotated target: Listerella
has_synonym_type: synonym

Listeria ivanovii
type: Class
subclass of: Listeria
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:8782698
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Listeria bulgarica
has_related_synonym: Listeria monocytogenes subsp. perhaemolytica
has_related_synonym: Listeria perhaemolytica

Axiom
annotated source: Listeria ivanovii
annotated property: has_related_synonym
annotated target: Listeria bulgarica
has_synonym_type: synonym

Axiom
annotated source: Listeria ivanovii
annotated property: has_related_synonym
annotated target: Listeria monocytogenes subsp. perhaemolytica
has_synonym_type: synonym

Axiom
annotated source: Listeria ivanovii
annotated property: has_related_synonym
annotated target: Listeria perhaemolytica
has_synonym_type: synonym

Listeria monocytogenes
type: Class
subclass of: Listeria
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1634566
database_cross_reference: GC_ID:11
database_cross_reference: PMID:17773427
database_cross_reference: PMID:1906732
database_cross_reference: PMID:8782698
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacterium monocytogenes
has_related_synonym: Bacterium monocytogenes hominis
has_related_synonym: Corynebacterium infantisepticum
has_related_synonym: Corynebacterium parvulum
has_related_synonym: Erysipelothrix monocytogenes
has_related_synonym: Listerella hepatolytica
has_related_synonym: Listeria momocytogenes
has_related_synonym: Lysteria monocytogenes

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Bacterium monocytogenes
has_synonym_type: synonym

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Bacterium monocytogenes hominis
has_synonym_type: synonym

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Corynebacterium infantisepticum
has_synonym_type: synonym

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Corynebacterium parvulum
has_synonym_type: synonym

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Erysipelothrix monocytogenes
has_synonym_type: synonym

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Listerella hepatolytica
has_synonym_type: synonym

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Listeria momocytogenes
has_synonym_type: misspelling

Axiom
annotated source: Listeria monocytogenes
annotated property: has_related_synonym
annotated target: Lysteria monocytogenes
has_synonym_type: misspelling

Plasmodiidae
type: Class
subclass of: Haemosporida
definition editor: Mirela L Vasconcelos

Listeria grayi
type: Class
subclass of: Listeria
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1644
has_alternative_id: NCBITaxon:47986
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1736964
has_exact_synonym: Listeria grayi grayi
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Listeria grayi murrayi
has_related_synonym: Listeria grayi subsp. grayi
has_related_synonym: Listeria murrayi
has_related_synonym: Murraya grayi
has_related_synonym: Murraya grayi subsp. grayi

Axiom
annotated source: Listeria grayi
annotated property: has_exact_synonym
annotated target: Listeria grayi grayi
has_synonym_type: equivalent name

Axiom
annotated source: Listeria grayi
annotated property: has_related_synonym
annotated target: Listeria grayi murrayi
has_synonym_type: synonym

Axiom
annotated source: Listeria grayi
annotated property: has_related_synonym
annotated target: Listeria grayi subsp. grayi
has_synonym_type: synonym

Axiom
annotated source: Listeria grayi
annotated property: has_related_synonym
annotated target: Listeria murrayi
has_synonym_type: synonym

Axiom
annotated source: Listeria grayi
annotated property: has_related_synonym
annotated target: Murraya grayi
has_synonym_type: synonym

Axiom
annotated source: Listeria grayi
annotated property: has_related_synonym
annotated target: Murraya grayi subsp. grayi
has_synonym_type: synonym

Borreliaceae
type: Class
subclass of: Spirochaetales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:23908650
has_obo_namespace: ncbi_taxonomy

Leptospirales
type: Class
subclass of: Spirochaetia
database_cross_reference: GC_ID:11
database_cross_reference: PMID:23908650
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Leptospiriales

Axiom
annotated source: Leptospirales
annotated property: has_related_synonym
annotated target: Leptospiriales
has_synonym_type: synonym

Yersinia pseudotuberculosis complex
type: Class
subclass of: Yersinia <bacteria>
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Corynebacteriaceae
type: Class
subclass of: Corynebacteriales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19244447
has_exact_synonym: Coryneform bacteria
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Corynebacteriaceae
annotated property: has_exact_synonym
annotated target: Coryneform bacteria
has_synonym_type: genbank common name

Mammarenavirus
type: Class
subclass of: Arenaviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Orthohepevirus
type: Class
subclass of: Hepeviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Orthohepevirus A
type: Class
subclass of: Orthohepevirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Leptospiraceae
type: Class
subclass of: Leptospirales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16014471
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Treponemataceae

Axiom
annotated source: Leptospiraceae
annotated property: has_related_synonym
annotated target: Treponemataceae
has_synonym_type: in part

Leptospira
type: Class
subclass of: Leptospiraceae
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:29512
has_alternative_id: NCBITaxon:29514
has_alternative_id: NCBITaxon:29516
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425768
database_cross_reference: PMID:1581182
database_cross_reference: PMID:19868121
database_cross_reference: PMID:9103653
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Ancona
has_related_synonym: Canela
has_related_synonym: Jequitaia

Axiom
annotated source: Leptospira
annotated property: has_related_synonym
annotated target: Ancona
has_synonym_type: misnomer

Axiom
annotated source: Leptospira
annotated property: has_related_synonym
annotated target: Canela
has_synonym_type: misnomer

Axiom
annotated source: Leptospira
annotated property: has_related_synonym
annotated target: Jequitaia
has_synonym_type: misnomer

Corynebacterium
type: Class
subclass of: Corynebacteriaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425754
database_cross_reference: PMID:19661509
database_cross_reference: PMID:7547284
database_cross_reference: PMID:7547291
database_cross_reference: PMID:7547293
has_obo_namespace: ncbi_taxonomy

Corynebacterium diphtheriae
type: Class
subclass of: Corynebacterium
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:7729671
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus diphtheriae
has_related_synonym: Bacterium diphtheriae
has_related_synonym: Microsporon diphthericum
has_related_synonym: Microsporon diphtheriticum
has_related_synonym: Mycobacterium diphtheriae
has_related_synonym: Pacinia loeffleri

Axiom
annotated source: Corynebacterium diphtheriae
annotated property: has_related_synonym
annotated target: Bacillus diphtheriae
has_synonym_type: synonym

Axiom
annotated source: Corynebacterium diphtheriae
annotated property: has_related_synonym
annotated target: Bacterium diphtheriae
has_synonym_type: synonym

Axiom
annotated source: Corynebacterium diphtheriae
annotated property: has_related_synonym
annotated target: Microsporon diphthericum
has_synonym_type: synonym

Axiom
annotated source: Corynebacterium diphtheriae
annotated property: has_related_synonym
annotated target: Microsporon diphtheriticum
has_synonym_type: synonym

Axiom
annotated source: Corynebacterium diphtheriae
annotated property: has_related_synonym
annotated target: Mycobacterium diphtheriae
has_synonym_type: synonym

Axiom
annotated source: Corynebacterium diphtheriae
annotated property: has_related_synonym
annotated target: Pacinia loeffleri
has_synonym_type: synonym

Actinobacteria <class>
type: Class
subclass of: Actinobacteria <phylum>
alternative label: Actinomycetes
alternative label: High GC gram-positive bacteria

Mycobacteriaceae
type: Class
subclass of: Corynebacteriales

Mycobacterium
type: Class
subclass of: Mycobacteriaceae
alternative label: Mycobacterium Lehmann and Neumann 1896

Mycobacterium leprae
type: Class
subclass of: Mycobacterium
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus leprae
has_related_synonym: Mycoplasma leprae

Axiom
annotated source: Mycobacterium leprae
annotated property: has_related_synonym
annotated target: Bacillus leprae
has_synonym_type: synonym

Axiom
annotated source: Mycobacterium leprae
annotated property: has_related_synonym
annotated target: Mycoplasma leprae
has_synonym_type: misnomer

Mycobacterium tuberculosis
type: Class
subclass of: Mycobacterium tuberculosis complex
alternative label: Bacillus tuberculosis
alternative label: Bacterium tuberculosis
alternative label: Mycobacterium tuberculosis typus humanus
alternative label: Mycobacterium tuberculosis var. hominis

EEEV complex
type: Class
subclass of: Alphavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

WEEV complex
type: Class
subclass of: Alphavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

SFV complex
type: Class
subclass of: Alphavirus

PVC group
type: Class
subclass of: Bacteria
definition editor: Mirela L Vasconcelos

Terrabacteria group
type: Class
subclass of: Bacteria
definition editor: Mirela L Vasconcelos

Ebolavirus
type: Class
subclass of: Filoviridae
alternative label: Ebola-like virus

Marburgvirus
type: Class
subclass of: Filoviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Marburg-like viruses

Axiom
annotated source: Marburgvirus
annotated property: has_related_synonym
annotated target: Marburg-like viruses
has_synonym_type: synonym

Zaire ebolavirus
type: Class
subclass of: Ebolavirus

Reston ebolavirus
type: Class
subclass of: Ebolavirus
alternative label: Ebola virus Reston
alternative label: REBOV
alternative label: Reston Ebola virus

Sudan ebolavirus
type: Class
subclass of: Ebolavirus
alternative label: Ebolavirus Sudan
alternative label: SEBOV
alternative label: Sudan Ebola virus

Tai Forest ebolavirus
type: Class
subclass of: Ebolavirus
alternative label: CIEBOV
alternative label: Côte d'Ivoire Ebola virus
alternative label: Côte d'Ivoire ebolavirus
alternative label: Ivory Coast ebolavirus

Clostridia
type: Class
subclass of: Firmicutes
definition editor: Mirela L Vasconcelos

Clostridiales
type: Class
subclass of: Clostridia
definition editor: Mirela L Vasconcelos

Peptostreptococcaceae
type: Class
subclass of: Clostridiales
definition editor: Mirela L Vasconcelos
alternative label: Clostridium cluster XI

Bacillaceae
type: Class
subclass of: Bacillales

Listeriaceae
type: Class
subclass of: Bacillales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:20212322
has_obo_namespace: ncbi_taxonomy

Lactobacillales
type: Class
subclass of: Bacilli
definition editor: Mirela L Vasconcelos

Clostridioides
type: Class
subclass of: Peptostreptococcaceae
definition editor: Mirela L Vasconcelos

Yersiniaceae
type: Class
subclass of: Enterobacterales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:27620848
has_obo_namespace: ncbi_taxonomy

Rift Valley fever phlebovirus
type: Class
subclass of: Phlebovirus
definition editor: Mirela L Vasconcelos

California encephalitis orthobunyavirus
type: Class
subclass of: Orthobunyavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Guaroa orthobunyavirus
type: Class
subclass of: Orthobunyavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Campylobacter
type: Class
subclass of: Campylobacteraceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11542086
database_cross_reference: PMID:12361288
database_cross_reference: PMID:16627635
database_cross_reference: PMID:1704793
database_cross_reference: PMID:19801389
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Ampylobacter

Axiom
annotated source: Campylobacter
annotated property: has_related_synonym
annotated target: Ampylobacter
has_synonym_type: misspelling

Pancrustacea
type: Class
subclass of: Mandibulata

Mandibulata
type: Class
subclass of: Arthropoda

Influenzavirus A
type: Class
subclass of: Orthomyxoviridae

Influenzavirus B
type: Class
subclass of: Orthomyxoviridae
definition editor: Mirela L Vasconcelos

Bunyavirales
type: Class
subclass of: ssRNA negative-strand virus
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Nairoviridae
type: Class
subclass of: Bunyavirales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Peribunyaviridae
type: Class
subclass of: Bunyavirales
has_rank: NCBITaxon family
has_alternative_id: NCBITaxon:11571
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bunyaviridae

Axiom
annotated source: Peribunyaviridae
annotated property: has_related_synonym
annotated target: Bunyaviridae
has_synonym_type: synonym

Orthonairovirus
type: Class
subclass of: Nairoviridae
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:11592
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Nairovirus
has_related_synonym: Nairoviruses

Axiom
annotated source: Orthonairovirus
annotated property: has_related_synonym
annotated target: Nairovirus
has_synonym_type: synonym

Axiom
annotated source: Orthonairovirus
annotated property: has_related_synonym
annotated target: Nairoviruses
has_synonym_type: synonym

Crimean-Congo hemorrhagic fever orthonairovirus
type: Class
subclass of: Orthonairovirus
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:11593
has_broad_synonym: CCHFV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Crimean Congo Hemorrhagic Fever virus
has_related_synonym: Crimean-Congo haemorrhagic fever virus
has_related_synonym: Crimean-Congo hemorrhagic fever nairovirus
has_related_synonym: Crimean-Congo hemorrhagic fever virus
has_related_synonym: Crimean-Congo hemorrhagic virus

Axiom
annotated source: Crimean-Congo hemorrhagic fever orthonairovirus
annotated property: has_broad_synonym
annotated target: CCHFV
has_synonym_type: acronym

Axiom
annotated source: Crimean-Congo hemorrhagic fever orthonairovirus
annotated property: has_related_synonym
annotated target: Crimean Congo Hemorrhagic Fever virus
has_synonym_type: misspelling

Axiom
annotated source: Crimean-Congo hemorrhagic fever orthonairovirus
annotated property: has_related_synonym
annotated target: Crimean-Congo haemorrhagic fever virus
has_synonym_type: synonym

Axiom
annotated source: Crimean-Congo hemorrhagic fever orthonairovirus
annotated property: has_related_synonym
annotated target: Crimean-Congo hemorrhagic fever nairovirus
has_synonym_type: synonym

Axiom
annotated source: Crimean-Congo hemorrhagic fever orthonairovirus
annotated property: has_related_synonym
annotated target: Crimean-Congo hemorrhagic fever virus
has_synonym_type: synonym

Axiom
annotated source: Crimean-Congo hemorrhagic fever orthonairovirus
annotated property: has_related_synonym
annotated target: Crimean-Congo hemorrhagic virus
has_synonym_type: synonym

Coccidioides posadasii
type: Class
subclass of: Coccidioides
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

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

Actinobacteria <phylum>
type: Class
subclass of: Terrabacteria group
alternative label: 'Actinobacteria'
alternative label: not Actinobacteria Cavalier-Smith 2002

Spirochaetes
type: Class
subclass of: Bacteria
has_rank: NCBITaxon phylum
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11837318
database_cross_reference: PMID:26654112
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Spirochaetae
has_related_synonym: Spirochaetaeota

Axiom
annotated source: Spirochaetes
annotated property: has_related_synonym
annotated target: Spirochaetae
has_synonym_type: synonym

Axiom
annotated source: Spirochaetes
annotated property: has_related_synonym
annotated target: Spirochaetaeota
has_synonym_type: synonym

Spirochaetia
type: Class
subclass of: Spirochaetes
has_rank: NCBITaxon class
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11837318
database_cross_reference: PMID:25288668
database_cross_reference: PMID:26654112
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Spirochaetes

Axiom
annotated source: Spirochaetia
annotated property: has_related_synonym
annotated target: Spirochaetes
has_synonym_type: synonym

Chlamydiae
type: Class
subclass of: PVC group
definition editor: Mirela L Vasconcelos
alternative label: Chlamydaeota

Chlamydiia
type: Class
subclass of: Chlamydiae
definition editor: Mirela L Vasconcelos
alternative label: Chlamydiae

Neisseriales
type: Class
subclass of: Betaproteobacteria
definition editor: Mirela L Vasconcelos

Fornicata
type: Class
subclass of: Eukaryota
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Diplomonadida group

Axiom
annotated source: Fornicata
annotated property: has_related_synonym
annotated target: Diplomonadida group
has_synonym_type: synonym

Helicobacter
type: Class
subclass of: Helicobacteraceae
definition editor: Mirela L Vasconcelos

Helicobacter pylori
type: Class
subclass of: Helicobacter
definition editor: Mirela L Vasconcelos
alternative label: Campylobacter pylori
alternative label: Campylobacter pylori subsp. pylori
alternative label: Campylobacter pyloridis
alternative label: Helicobacter nemestrinae

Campylobacterales
type: Class
subclass of: Epsilonproteobacteria
definition editor: Mirela L Vasconcelos

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

Psoroptidia
type: Class
subclass of: Astigmata
has_alternative_id: NCBITaxon:261182
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Sarcoptidia

Axiom
annotated source: Psoroptidia
annotated property: has_related_synonym
annotated target: Sarcoptidia
has_synonym_type: synonym

SARS coronavirus
type: Class
subclass of: Betacoronavirus

H5N8 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H5N8 subtype of Influenza A virus

Brucella
type: Class
subclass of: Brucellaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:8573514
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Brucella Meyer and Shaw 1920

Axiom
annotated source: Brucella
annotated property: has_related_synonym
annotated target: Brucella Meyer and Shaw 1920
has_synonym_type: synonym

Brucella abortus
type: Class
subclass of: Brucella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_exact_synonym: Brucella melitensis bv. Abortus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacterium abortus
has_related_synonym: Brucella melitensis biovar Abortus

Axiom
annotated source: Brucella abortus
annotated property: has_exact_synonym
annotated target: Brucella melitensis bv. Abortus
has_synonym_type: equivalent name

Axiom
annotated source: Brucella abortus
annotated property: has_related_synonym
annotated target: Bacterium abortus
has_synonym_type: synonym

Axiom
annotated source: Brucella abortus
annotated property: has_related_synonym
annotated target: Brucella melitensis biovar Abortus
has_synonym_type: genbank synonym

Cryptosporidium hominis
type: Class
subclass of: Cryptosporidium
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Henipavirus
type: Class
subclass of: Paramyxoviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Francisella
type: Class
subclass of: Francisellaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19783615
database_cross_reference: PMID:8123561
has_obo_namespace: ncbi_taxonomy

Francisella tularensis
type: Class
subclass of: Francisella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacterium tularense
has_related_synonym: Brucella tularensis
has_related_synonym: Francisella tularense
has_related_synonym: Pasteurella tularensis

Axiom
annotated source: Francisella tularensis
annotated property: has_related_synonym
annotated target: Bacterium tularense
has_synonym_type: synonym

Axiom
annotated source: Francisella tularensis
annotated property: has_related_synonym
annotated target: Brucella tularensis
has_synonym_type: synonym

Axiom
annotated source: Francisella tularensis
annotated property: has_related_synonym
annotated target: Francisella tularense
has_synonym_type: synonym

Axiom
annotated source: Francisella tularensis
annotated property: has_related_synonym
annotated target: Pasteurella tularensis
has_synonym_type: synonym

Metschnikowiaceae
type: Class
subclass of: Saccharomycetales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

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

Bovinae
type: Class
subclass of: Bovidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Alphaproteobacteria
type: Class
subclass of: Proteobacteria
has_rank: NCBITaxon class
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11541974
database_cross_reference: PMID:11837318
database_cross_reference: PMID:16166687
database_cross_reference: PMID:16403855
database_cross_reference: PMID:19060069
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Alphabacteria
has_related_synonym: Proteobacteria alpha subdivision
has_related_synonym: Purple bacteria, alpha subdivision
has_related_synonym: a-proteobacteria
has_related_synonym: alpha proteobacteria
has_related_synonym: alpha subdivision
has_related_synonym: alpha subgroup

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: Alphabacteria
has_synonym_type: synonym

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: Proteobacteria alpha subdivision
has_synonym_type: synonym

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: Purple bacteria, alpha subdivision
has_synonym_type: synonym

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: a-proteobacteria
has_synonym_type: blast name

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: alpha proteobacteria
has_synonym_type: synonym

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: alpha subdivision
has_synonym_type: synonym

Axiom
annotated source: Alphaproteobacteria
annotated property: has_related_synonym
annotated target: alpha subgroup
has_synonym_type: synonym

Betaproteobacteria
type: Class
subclass of: Proteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Proteobacteria beta subdivision
alternative label: Purple bacteria, beta subdivision
alternative label: beta proteobacteria
alternative label: beta subdivision
alternative label: beta subgroup

Porcine epidemic diarrhea virus
type: Class
subclass of: Alphacoronavirus
alternative label: PEDV

Burkholderia pseudomallei
type: Class
subclass of: pseudomallei group
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1435366
has_alternative_id: NCBITaxon:1435368
has_alternative_id: NCBITaxon:1435988
has_alternative_id: NCBITaxon:1439853
has_alternative_id: NCBITaxon:1487954
has_alternative_id: NCBITaxon:1487955
database_cross_reference: GC_ID:11
database_cross_reference: PMID:12734250
database_cross_reference: PMID:1283774
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus pseudomallei
has_related_synonym: Bacterium whitmori
has_related_synonym: Burkholderia pseudomallai
has_related_synonym: Burkholderia pseudomallei MSHR4009
has_related_synonym: Burkholderia pseudomallei MSHR4018
has_related_synonym: Burkholderia pseudomallei MSHR44
has_related_synonym: Burkholderia pseudomallei MSHR7839
has_related_synonym: Burkholderia sp. MSHR7839
has_related_synonym: Loefflerella pseudomallei
has_related_synonym: Malleomyces pseudomallei
has_related_synonym: Pseudomonas pseudomallei

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Bacillus pseudomallei
has_synonym_type: synonym

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Bacterium whitmori
has_synonym_type: synonym

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Burkholderia pseudomallai
has_synonym_type: misspelling

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Burkholderia pseudomallei MSHR4009
has_synonym_type: misspelling

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Burkholderia pseudomallei MSHR4018
has_synonym_type: misspelling

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Burkholderia pseudomallei MSHR44
has_synonym_type: misspelling

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Burkholderia pseudomallei MSHR7839
has_synonym_type: misspelling

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Burkholderia sp. MSHR7839
has_synonym_type: misspelling

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Loefflerella pseudomallei
has_synonym_type: synonym

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Malleomyces pseudomallei
has_synonym_type: synonym

Axiom
annotated source: Burkholderia pseudomallei
annotated property: has_related_synonym
annotated target: Pseudomonas pseudomallei
has_synonym_type: synonym

Salmonella enterica
type: Class
subclass of: Salmonella
definition editor: Mirela L Vasconcelos
alternative label: Bacillus cholerae-suis
alternative label: Salmonella cholerae-suis
alternative label: Salmonella choleraesuis
alternative label: Salmonella enterica ser. choleraesuis

Hepeviridae
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Ancylostoma
type: Class
subclass of: Ancylostomatinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Ancylostoma caninum
type: Class
subclass of: Ancylostoma
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: dog hookworm
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Ancylostoma caninum
annotated property: has_exact_synonym
annotated target: dog hookworm
has_synonym_type: genbank common name

tick-borne encephalitis virus group
type: Class
subclass of: Flavivirus
has_rank: NCBITaxon subgenus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Tick-borne encephalitis viruses

Axiom
annotated source: tick-borne encephalitis virus group
annotated property: has_related_synonym
annotated target: Tick-borne encephalitis viruses
has_synonym_type: synonym

Brucella melitensis
type: Class
subclass of: Brucella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:8573514
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Micrococcus melitensis
has_related_synonym: Streptococcus Miletensis

Axiom
annotated source: Brucella melitensis
annotated property: has_related_synonym
annotated target: Micrococcus melitensis
has_synonym_type: synonym

Axiom
annotated source: Brucella melitensis
annotated property: has_related_synonym
annotated target: Streptococcus Miletensis
has_synonym_type: synonym

Brucella suis
type: Class
subclass of: Brucella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_exact_synonym: Brucella melitensis bv. Suis
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Brucella melitensis biovar Suis

Axiom
annotated source: Brucella suis
annotated property: has_exact_synonym
annotated target: Brucella melitensis bv. Suis
has_synonym_type: equivalent name

Axiom
annotated source: Brucella suis
annotated property: has_related_synonym
annotated target: Brucella melitensis biovar Suis
has_synonym_type: genbank synonym

Epsilonproteobacteria
type: Class
subclass of: delta/epsilon subdivisions
definition editor: Mirela L Vasconcelos
alternative label: Proteobacteria epsilon subdivision
alternative label: Purple bacteria, epsilon subdivision
alternative label: epsilon proteobacteria
alternative label: epsilon subdivision
alternative label: epsilon subgroup
alternative label: not Epsilobacteria

Spondweni virus group
type: Class
subclass of: Flavivirus
editor preferred term: Spondweni virus group

Schistosomatoidea
type: Class
subclass of: Strigeidida
definition editor: Mirela L Vasconcelos

Schistosomatidae
type: Class
subclass of: Schistosomatoidea
definition editor: Mirela L Vasconcelos
alternative label: blood flukes

Laurasiatheria
type: Class
subclass of: Boreoeutheria
has_rank: NCBITaxon superorder
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11214318
database_cross_reference: PMID:11214319
database_cross_reference: PMID:12878460
has_obo_namespace: ncbi_taxonomy

Euarchontoglires
type: Class
subclass of: Boreoeutheria

Simiiformes
type: Class
subclass of: Haplorrhini
alternative label: Anthropoidea

Cercopithecoidea
type: Class
subclass of: Catarrhini

Coxsackievirus A16
type: Class
subclass of: Enterovirus A
has_broad_synonym: CV-A16
has_broad_synonym: CVA-16
has_broad_synonym: CVA16
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Coxsackie A virus type 16
has_related_synonym: Human coxsackievirus A16
has_related_synonym: Human enterovirus CVA16

Axiom
annotated source: Coxsackievirus A16
annotated property: has_broad_synonym
annotated target: CV-A16
has_synonym_type: genbank acronym

Axiom
annotated source: Coxsackievirus A16
annotated property: has_broad_synonym
annotated target: CVA-16
has_synonym_type: acronym

Axiom
annotated source: Coxsackievirus A16
annotated property: has_broad_synonym
annotated target: CVA16
has_synonym_type: acronym

Axiom
annotated source: Coxsackievirus A16
annotated property: has_related_synonym
annotated target: Coxsackie A virus type 16
has_synonym_type: synonym

Axiom
annotated source: Coxsackievirus A16
annotated property: has_related_synonym
annotated target: Human coxsackievirus A16
has_synonym_type: synonym

Axiom
annotated source: Coxsackievirus A16
annotated property: has_related_synonym
annotated target: Human enterovirus CVA16
has_synonym_type: synonym

Embryophyta
type: Class
subclass of: Streptophytina
database_cross_reference: GC_ID:1
has_exact_synonym: higher plants
has_exact_synonym: land plants
has_exact_synonym: plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: land plants

Axiom
annotated source: Embryophyta
annotated property: has_exact_synonym
annotated target: higher plants
has_synonym_type: common name

Axiom
annotated source: Embryophyta
annotated property: has_exact_synonym
annotated target: land plants
has_synonym_type: common name

Axiom
annotated source: Embryophyta
annotated property: has_exact_synonym
annotated target: plants
has_synonym_type: common name

Axiom
annotated source: Embryophyta
annotated property: has_related_synonym
annotated target: land plants
has_synonym_type: blast name

Clostridiaceae
type: Class
subclass of: Clostridiales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy

Burkholderia
type: Class
subclass of: Burkholderiaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10555347
database_cross_reference: PMID:1283774
database_cross_reference: PMID:25566316
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Pseudomonas RNA homology group II

Axiom
annotated source: Burkholderia
annotated property: has_related_synonym
annotated target: Pseudomonas RNA homology group II
has_synonym_type: synonym

Tetrapoda
type: Class
subclass of: Dipnotetrapodomorpha
alternative label: tetrapods

Amniota
type: Class
subclass of: Tetrapoda
alternative label: amniotes
database_cross_reference: GC_ID:1
has_exact_synonym: amniotes
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Amniota
annotated property: has_exact_synonym
annotated target: amniotes
has_synonym_type: genbank common name

Theria
type: Class
subclass of: Mammalia
comment: authority: Theria Parker & Haswell, 1897

Sauria
type: Class
subclass of: Sauropsida
database_cross_reference: GC_ID:1
has_exact_synonym: diapsids
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Diapsida

Axiom
annotated source: Sauria
annotated property: has_exact_synonym
annotated target: diapsids
has_synonym_type: genbank common name

Axiom
annotated source: Sauria
annotated property: has_related_synonym
annotated target: Diapsida
has_synonym_type: synonym

Orthoretrovirinae
type: Class
subclass of: Retroviridae

H5N6 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H5N6 subtype of Influenza A virus

Entamoebidae
type: Class
subclass of: Archamoebae
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Entamoebida

Axiom
annotated source: Entamoebidae
annotated property: has_related_synonym
annotated target: Entamoebida
has_synonym_type: synonym

Viridiplantae
type: Class
subclass of: Eukaryota
has_rank: NCBITaxon kingdom
database_cross_reference: GC_ID:1
has_exact_synonym: green plants
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Chlorobionta
has_related_synonym: Chlorophyta/Embryophyta group
has_related_synonym: chlorophyte/embryophyte group
has_related_synonym: green plants

Axiom
annotated source: Viridiplantae
annotated property: has_exact_synonym
annotated target: green plants
has_synonym_type: common name

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: Chlorobionta
has_synonym_type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: Chlorophyta/Embryophyta group
has_synonym_type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: chlorophyte/embryophyte group
has_synonym_type: synonym

Axiom
annotated source: Viridiplantae
annotated property: has_related_synonym
annotated target: green plants
has_synonym_type: blast name

Opisthokonta
type: Class
subclass of: Eukaryota
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Fungi/Metazoa group
has_related_synonym: opisthokonts

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: Fungi/Metazoa group
has_synonym_type: synonym

Axiom
annotated source: Opisthokonta
annotated property: has_related_synonym
annotated target: opisthokonts
has_synonym_type: synonym

Onygenales
type: Class
subclass of: Eurotiomycetidae
has_rank: NCBITaxon order
has_alternative_id: NCBITaxon:259362
has_alternative_id: NCBITaxon:36053
has_alternative_id: NCBITaxon:5102
database_cross_reference: GC_ID:1
database_cross_reference: PMID:17486980
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Gymnoascales

Axiom
annotated source: Onygenales
annotated property: has_related_synonym
annotated target: Gymnoascales
has_synonym_type: synonym

Metazoa
type: Class
subclass of: Opisthokonta

Bilateria
type: Class
subclass of: Eumetazoa

Ancylostomatoidea
type: Class
subclass of: Strongylida
has_rank: NCBITaxon superfamily
database_cross_reference: GC_ID:1
has_exact_synonym: hookworms
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Ancylostomatoidea
annotated property: has_exact_synonym
annotated target: hookworms
has_synonym_type: genbank common name

Ancylostomatidae
type: Class
subclass of: Ancylostomatoidea
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Protostomia
type: Class
subclass of: Bilateria

H7N9 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H7N9 subtype of Influenza A virus

Neoptera
type: Class
subclass of: Pterygota

Endopterygota
type: Class
subclass of: Neoptera

Deuterostomia
type: Class
subclass of: Bilateria
alternative label: deuterostomes

Carnivora
type: Class
subclass of: Laurasiatheria
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_exact_synonym: carnivores
has_obo_namespace: ncbi_taxonomy
has_related_synonym: carnivores

Axiom
annotated source: Carnivora
annotated property: has_exact_synonym
annotated target: carnivores
has_synonym_type: genbank common name

Axiom
annotated source: Carnivora
annotated property: has_related_synonym
annotated target: carnivores
has_synonym_type: blast name

Alveolata
type: Class
subclass of: Eukaryota
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: alveolates

Euglenozoa
type: Class
subclass of: Eukaryota
definition editor: Mirela L Vasconcelos
alternative label: Euglenozoans

Rickettsieae
type: Class
subclass of: Rickettsiaceae
has_rank: NCBITaxon tribe
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11760958
database_cross_reference: PMID:8240958
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993

Axiom
annotated source: Rickettsieae
annotated property: has_related_synonym
annotated target: Rickettsieae Philip 1957 (Approved Lists 1980) emend. Brenner et al. 1993
has_synonym_type: synonym

Francisellaceae
type: Class
subclass of: Thiotrichales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16280474
database_cross_reference: PMID:22939414
database_cross_reference: PMID:26747442
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Francisella group

Axiom
annotated source: Francisellaceae
annotated property: has_related_synonym
annotated target: Francisella group
has_synonym_type: synonym

Cryptosporidiidae
type: Class
subclass of: Eimeriorina
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Cryptosporidae
has_related_synonym: Cryptosporiidae

Axiom
annotated source: Cryptosporidiidae
annotated property: has_related_synonym
annotated target: Cryptosporidae
has_synonym_type: misspelling

Axiom
annotated source: Cryptosporidiidae
annotated property: has_related_synonym
annotated target: Cryptosporiidae
has_synonym_type: misspelling

dsDNA viruses, no RNA stage
type: Class
subclass of: Viruses
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
label: dsDNA virus, no RNA stage

Retro-transcribing viruses
type: Class
subclass of: Viruses
alternative label: Retroid viruses

ssRNA positive-strand viruses, no DNA stage
type: Class
subclass of: ssRNA virus
editor preferred term: ssRNA positive-strand viruses, no DNA stage
imported from: http://purl.obolibrary.org/obo/obi.owl

ssRNA negative-strand virus
type: Class
subclass of: ssRNA virus

California encephalitis virus
type: Class
subclass of: California encephalitis orthobunyavirus
has_alternative_id: NCBITaxon:35512
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: California bunyavirus group
has_related_synonym: California encephalitis virus group
has_related_synonym: California serogroup
has_related_synonym: California virus

Axiom
annotated source: California encephalitis virus
annotated property: has_related_synonym
annotated target: California bunyavirus group
has_synonym_type: synonym

Axiom
annotated source: California encephalitis virus
annotated property: has_related_synonym
annotated target: California encephalitis virus group
has_synonym_type: synonym

Axiom
annotated source: California encephalitis virus
annotated property: has_related_synonym
annotated target: California serogroup
has_synonym_type: synonym

Axiom
annotated source: California encephalitis virus
annotated property: has_related_synonym
annotated target: California virus
has_synonym_type: synonym

dsRNA viruses
type: Class
subclass of: Viruses
definition editor: Mirela L Vasconcelos
alternative label: dsRNA nonenveloped viruses

Streptophyta
type: Class
subclass of: Viridiplantae
has_rank: NCBITaxon phylum
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Suina
type: Class
subclass of: Cetartiodactyla
has_rank: NCBITaxon infraorder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Artiodactyla
has_related_synonym: Suiformes

Axiom
annotated source: Suina
annotated property: has_related_synonym
annotated target: Artiodactyla
has_synonym_type: in part

Axiom
annotated source: Suina
annotated property: has_related_synonym
annotated target: Suiformes
has_synonym_type: in part

Pecora
type: Class
subclass of: Ruminantia
has_rank: NCBITaxon infraorder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Equus <subgenus>
type: Class
subclass of: Equus
has_rank: NCBITaxon subgenus
database_cross_reference: GC_ID:1
has_exact_synonym: Equus
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Equus subg. Equus

Axiom
annotated source: Equus <subgenus>
annotated property: has_exact_synonym
annotated target: Equus
has_synonym_type: scientific name

Axiom
annotated source: Equus <subgenus>
annotated property: has_related_synonym
annotated target: Equus subg. Equus
has_synonym_type: synonym

Jamestown Canyon virus
type: Class
subclass of: California encephalitis orthobunyavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Rhizobiales
type: Class
subclass of: Alphaproteobacteria
has_rank: NCBITaxon order
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16403855
database_cross_reference: PMID:1854635
has_exact_synonym: rhizobacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Rhizobiaceae group
has_related_synonym: alpha-2 proteobacteria

Axiom
annotated source: Rhizobiales
annotated property: has_exact_synonym
annotated target: rhizobacteria
has_synonym_type: genbank common name

Axiom
annotated source: Rhizobiales
annotated property: has_related_synonym
annotated target: Rhizobiaceae group
has_synonym_type: synonym

Axiom
annotated source: Rhizobiales
annotated property: has_related_synonym
annotated target: alpha-2 proteobacteria
has_synonym_type: in part

Plasmodium ovale
type: Class
subclass of: Plasmodium (Plasmodium)
definition editor: Matthew Diller
alternative label: malaria parasite p. ovale

Streptococcus sp. 'group A'
type: Class
subclass of: Streptococcus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Streptococcus sp. (group A)
has_related_synonym: group A streptococci
has_related_synonym: group A streptococcus

Axiom
annotated source: Streptococcus sp. 'group A'
annotated property: has_related_synonym
annotated target: Streptococcus sp. (group A)
has_synonym_type: synonym

Axiom
annotated source: Streptococcus sp. 'group A'
annotated property: has_related_synonym
annotated target: group A streptococci
has_synonym_type: synonym

Axiom
annotated source: Streptococcus sp. 'group A'
annotated property: has_related_synonym
annotated target: group A streptococcus
has_synonym_type: synonym

Brucella canis
type: Class
subclass of: Brucella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_exact_synonym: Brucella melitensis bv. Canis
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Brucella melitensis biovar Canis

Axiom
annotated source: Brucella canis
annotated property: has_exact_synonym
annotated target: Brucella melitensis bv. Canis
has_synonym_type: equivalent name

Axiom
annotated source: Brucella canis
annotated property: has_related_synonym
annotated target: Brucella melitensis biovar Canis
has_synonym_type: genbank synonym

Clavispora
type: Class
subclass of: Metschnikowiaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Chikungunya virus
type: Class
subclass of: SFV complex

Haplorrhini
type: Class
subclass of: Primates

Caniformia
type: Class
subclass of: Carnivora
has_rank: NCBITaxon suborder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Enterovirus A71
type: Class
subclass of: Enterovirus A
has_broad_synonym: EV-71
has_broad_synonym: EV-A71
has_broad_synonym: EV71
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Enterovirus 71
has_related_synonym: Enterovirus EV-A71
has_related_synonym: Human enterovirus 71
has_related_synonym: Human enterovirus A71
has_related_synonym: Human enterovirus type 71
has_related_synonym: enterovirus type 71

Axiom
annotated source: Enterovirus A71
annotated property: has_broad_synonym
annotated target: EV-71
has_synonym_type: acronym

Axiom
annotated source: Enterovirus A71
annotated property: has_broad_synonym
annotated target: EV-A71
has_synonym_type: genbank acronym

Axiom
annotated source: Enterovirus A71
annotated property: has_broad_synonym
annotated target: EV71
has_synonym_type: acronym

Axiom
annotated source: Enterovirus A71
annotated property: has_related_synonym
annotated target: Enterovirus 71
has_synonym_type: synonym

Axiom
annotated source: Enterovirus A71
annotated property: has_related_synonym
annotated target: Enterovirus EV-A71
has_synonym_type: synonym

Axiom
annotated source: Enterovirus A71
annotated property: has_related_synonym
annotated target: Human enterovirus 71
has_synonym_type: synonym

Axiom
annotated source: Enterovirus A71
annotated property: has_related_synonym
annotated target: Human enterovirus A71
has_synonym_type: synonym

Axiom
annotated source: Enterovirus A71
annotated property: has_related_synonym
annotated target: Human enterovirus type 71
has_synonym_type: synonym

Axiom
annotated source: Enterovirus A71
annotated property: has_related_synonym
annotated target: enterovirus type 71
has_synonym_type: synonym

Rubulavirus
type: Class
subclass of: Paramyxoviridae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Deltavirus
type: Class
subclass of: Viruses
definition editor: Mirela L Vasconcelos

Klebsiella granulomatis
type: Class
subclass of: Klebsiella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10555350
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Calymmatobacterium granulomatis
has_related_synonym: Donovania granulomatis
has_related_synonym: Encapsulatus inguinalis

Axiom
annotated source: Klebsiella granulomatis
annotated property: has_related_synonym
annotated target: Calymmatobacterium granulomatis
has_synonym_type: synonym

Axiom
annotated source: Klebsiella granulomatis
annotated property: has_related_synonym
annotated target: Donovania granulomatis
has_synonym_type: synonym

Axiom
annotated source: Klebsiella granulomatis
annotated property: has_related_synonym
annotated target: Encapsulatus inguinalis
has_synonym_type: synonym

Yellow fever virus group
type: Class
subclass of: Flavivirus
has_rank: NCBITaxon subgenus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Yellow fever viruses

Axiom
annotated source: Yellow fever virus group
annotated property: has_related_synonym
annotated target: Yellow fever viruses
has_synonym_type: synonym

Mammalia
type: Class
subclass of: Amniota
alternative label: mammals

Plasmodium (Plasmodium)
type: Class
subclass of: Plasmodium
definition editor: Matthew Diller
alternative label: plasmodium

Plasmodium (Laverania)
type: Class
subclass of: Plasmodium
definition editor: Matthew Diller
alternative label: laverania

Culicoidea
type: Class
subclass of: Culicomorpha

Aconoidasida
type: Class
subclass of: Apicomplexa
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: hematozoa

Eimeriorina
type: Class
subclass of: Eucoccidiorida
has_rank: NCBITaxon suborder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Enterovirus D68
type: Class
subclass of: Enterovirus D

Dinosauria
type: Class
subclass of: Archosauria
database_cross_reference: GC_ID:1
has_exact_synonym: dinosaur
has_exact_synonym: dinosaurs
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Dinosauria
annotated property: has_exact_synonym
annotated target: dinosaur
has_synonym_type: common name

Axiom
annotated source: Dinosauria
annotated property: has_exact_synonym
annotated target: dinosaurs
has_synonym_type: common name

Saurischia
type: Class
subclass of: Dinosauria
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Theropoda
type: Class
subclass of: Saurischia
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Coelurosauria
type: Class
subclass of: Theropoda
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Culicomorpha
type: Class
subclass of: Nematocera

Anophelinae
type: Class
subclass of: Culicidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Culicinae
type: Class
subclass of: Culicidae

ssRNA virus
type: Class
subclass of: Viruses

Koutango virus
type: Class
subclass of: Japanese encephalitis virus group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Legionellaceae
type: Class
subclass of: Legionellales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:434652
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Legionellaceae Brenner et al. 1979

Axiom
annotated source: Legionellaceae
annotated property: has_related_synonym
annotated target: Legionellaceae Brenner et al. 1979
has_synonym_type: synonym

Cyclospora
type: Class
subclass of: Eimeriidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Anopheles <subgenus>
type: Class
subclass of: Anopheles <genus>
has_rank: NCBITaxon subgenus
database_cross_reference: GC_ID:1
has_exact_synonym: Anopheles
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Anopheles <subgenus>
annotated property: has_exact_synonym
annotated target: Anopheles
has_synonym_type: scientific name

Legionella
type: Class
subclass of: Legionellaceae
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:29550
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16166707
database_cross_reference: PMID:434652
database_cross_reference: PMID:8573522
database_cross_reference: PMID:9734026
has_obo_namespace: ncbi_taxonomy

Dikarya
type: Class
subclass of: Fungi
has_rank: NCBITaxon subkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:15689432
database_cross_reference: PMID:16151185
database_cross_reference: PMID:17010206
database_cross_reference: PMID:17051209
database_cross_reference: PMID:17572334
has_obo_namespace: ncbi_taxonomy

Eurotiomycetidae
type: Class
subclass of: Eurotiomycetes
has_rank: NCBITaxon subclass
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Guanarito mammarenavirus
type: Class
subclass of: Mammarenavirus
has_rank: NCBITaxon species
has_broad_synonym: GTOV
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Guanarito arenavirus
has_related_synonym: Guanarito virus

Axiom
annotated source: Guanarito mammarenavirus
annotated property: has_broad_synonym
annotated target: GTOV
has_synonym_type: acronym

Axiom
annotated source: Guanarito mammarenavirus
annotated property: has_related_synonym
annotated target: Guanarito arenavirus
has_synonym_type: synonym

Axiom
annotated source: Guanarito mammarenavirus
annotated property: has_related_synonym
annotated target: Guanarito virus
has_synonym_type: synonym

Inkoo virus
type: Class
subclass of: California encephalitis orthobunyavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Tahyna virus
type: Class
subclass of: California encephalitis orthobunyavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Sabia mammarenavirus
type: Class
subclass of: Mammarenavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Sabi mammarenavirus
has_related_synonym: Sabia arenavirus
has_related_synonym: Sabia virus
has_related_synonym: Sabio virus

Axiom
annotated source: Sabia mammarenavirus
annotated property: has_related_synonym
annotated target: Sabi mammarenavirus
has_synonym_type: synonym

Axiom
annotated source: Sabia mammarenavirus
annotated property: has_related_synonym
annotated target: Sabia arenavirus
has_synonym_type: synonym

Axiom
annotated source: Sabia mammarenavirus
annotated property: has_related_synonym
annotated target: Sabia virus
has_synonym_type: synonym

Axiom
annotated source: Sabia mammarenavirus
annotated property: has_related_synonym
annotated target: Sabio virus
has_synonym_type: misspelling

Trichinella britovi
type: Class
subclass of: Trichinella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Picornavirales
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage

Perdicinae
type: Class
subclass of: Phasianidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Meleagridinae
type: Class
subclass of: Phasianidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Moraxellaceae
type: Class
subclass of: Pseudomonadales
definition editor: Mirela L Vasconcelos
alternative label: Acinetobacteraceae
alternative label: Branhamaceae

Acinetobacter
type: Class
subclass of: Moraxellaceae
definition editor: Mirela L Vasconcelos

Acinetobacter baumannii
type: Class
subclass of: Acinetobacter calcoaceticus/baumannii complex
definition editor: Mirela L Vasconcelos
alternative label: Acinetobacter genomosp. 2
alternative label: Acinetobacter genomospecies 2
alternative label: Bacterium anitratum

Sarcoptinae
type: Class
subclass of: Sarcoptidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Fungi
type: Class
subclass of: Opisthokonta
has_rank: NCBITaxon kingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11062127
database_cross_reference: PMID:12684019
has_exact_synonym: fungi
has_obo_namespace: ncbi_taxonomy
has_related_synonym: fungi

Axiom
annotated source: Fungi
annotated property: has_exact_synonym
annotated target: fungi
has_synonym_type: genbank common name

Axiom
annotated source: Fungi
annotated property: has_related_synonym
annotated target: fungi
has_synonym_type: blast name

Schizotrypanum
type: Class
subclass of: Trypanosoma
definition editor: Mirela L Vasconcelos

Mycobacterium lepromatosis
type: Class
subclass of: Mycobacterium
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:19019760
database_cross_reference: PMID:25831531
has_obo_namespace: ncbi_taxonomy

Neisseriaceae
type: Class
subclass of: Neisseriales
definition editor: Mirela L Vasconcelos

Neisseria
type: Class
subclass of: Neisseriaceae
definition editor: Mirela L Vasconcelos
alternative label: "Gonococcus" Lindau 1898
alternative label: "Merismopedia" Zopf 1885
alternative label: Gonococcus

Neisseria gonorrhoeae
type: Class
subclass of: Neisseria
definition editor: Mirela L Vasconcelos
alternative label: Diplococcus gonorrhoeae
alternative label: Gonococcus neisseri
alternative label: Merismopedia gonorrhoeae
alternative label: Micrococcus der gonorrhoe
alternative label: Micrococcus gonococcus
alternative label: Micrococcus gonorrhoeae

Neisseria meningitidis
type: Class
subclass of: Neisseria
definition editor: Mirela L Vasconcelos
alternative label: Diplokokkus intracellularis meningitidis
alternative label: Micrococcus intracellularis
alternative label: Micrococcus meningitidis
alternative label: Micrococcus meningitidis cerebrospinalis
alternative label: Neisseria weichselbaumii

Ascomycota
type: Class
subclass of: Dikarya
has_rank: NCBITaxon phylum
database_cross_reference: GC_ID:1
database_cross_reference: PMID:17572334
has_exact_synonym: ascomycetes
has_exact_synonym: sac fungi
has_obo_namespace: ncbi_taxonomy
has_related_synonym: ascomycetes

Axiom
annotated source: Ascomycota
annotated property: has_exact_synonym
annotated target: ascomycetes
has_synonym_type: genbank common name

Axiom
annotated source: Ascomycota
annotated property: has_exact_synonym
annotated target: sac fungi
has_synonym_type: common name

Axiom
annotated source: Ascomycota
annotated property: has_related_synonym
annotated target: ascomycetes
has_synonym_type: blast name

Saccharomycetes
type: Class
subclass of: Saccharomycotina
has_rank: NCBITaxon class
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Hemiascomycetes

Axiom
annotated source: Saccharomycetes
annotated property: has_related_synonym
annotated target: Hemiascomycetes
has_synonym_type: synonym

Saccharomycetales
type: Class
subclass of: Saccharomycetes
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_exact_synonym: budding yeasts
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Endomycetales

Axiom
annotated source: Saccharomycetales
annotated property: has_exact_synonym
annotated target: budding yeasts
has_synonym_type: genbank common name

Axiom
annotated source: Saccharomycetales
annotated property: has_related_synonym
annotated target: Endomycetales
has_synonym_type: synonym

Candida auris
type: Class
subclass of: Clavispora/Candida clade
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Insecta
type: Class
subclass of: Hexapoda

Alcaligenaceae
type: Class
subclass of: Burkholderiales
definition editor: Mirela L Vasconcelos

Ancylostoma duodenale
type: Class
subclass of: Ancylostoma
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Chlamydiales
type: Class
subclass of: Chlamydiia
definition editor: Mirela L Vasconcelos

Bordetella
type: Class
subclass of: Alcaligenaceae
definition editor: Mirela L Vasconcelos

Culex pipiens complex
type: Class
subclass of: Culex <subgenus>
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Bordetella pertussis
type: Class
subclass of: Bordetella
definition editor: Mirela L Vasconcelos
alternative label: Bacterium tussis-convulsivae
alternative label: Hemophilus pertussis
alternative label: Microbe de la coqueluche

Sarcoptidae
type: Class
subclass of: Sarcoptoidea
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Sarcoptes
type: Class
subclass of: Sarcoptinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Sarcoptes scabiei
type: Class
subclass of: Sarcoptes
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:197185
has_alternative_id: NCBITaxon:198574
has_alternative_id: NCBITaxon:268761
has_alternative_id: NCBITaxon:268762
has_alternative_id: NCBITaxon:268763
has_alternative_id: NCBITaxon:337908
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Sarcoptes scabiei type canis
has_related_synonym: Sarcoptes scabiei type chimp
has_related_synonym: Sarcoptes scabiei type hominis
has_related_synonym: Sarcoptes scabiei type suis
has_related_synonym: Sarcoptes scabiei type wallaby
has_related_synonym: Sarcoptes scabiei type wombati
has_related_synonym: Sarcoptes scabiei var. canis
has_related_synonym: Sarcoptes scabiei var. chimp
has_related_synonym: Sarcoptes scabiei var. hominis
has_related_synonym: Sarcoptes scabiei var. nyctereutis
has_related_synonym: Sarcoptes scabiei var. suis
has_related_synonym: Sarcoptes scabiei var. wallaby
has_related_synonym: Sarcoptes scabiei var. wombati

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei type canis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei type chimp
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei type hominis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei type suis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei type wallaby
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei type wombati
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. canis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. chimp
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. hominis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. nyctereutis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. suis
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. wallaby
has_synonym_type: synonym

Axiom
annotated source: Sarcoptes scabiei
annotated property: has_related_synonym
annotated target: Sarcoptes scabiei var. wombati
has_synonym_type: synonym

Ancylostomatinae
type: Class
subclass of: Ancylostomatidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Culex <subgenus>
type: Class
subclass of: Culex <genus>
has_rank: NCBITaxon subgenus
database_cross_reference: GC_ID:1
has_exact_synonym: Culex
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Culex <subgenus>
annotated property: has_exact_synonym
annotated target: Culex
has_synonym_type: scientific name

Stegomyia
type: Class
subclass of: Aedes

Culicini
type: Class
subclass of: Culicinae
has_rank: NCBITaxon tribe
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Enterobacteriaceae
type: Class
subclass of: Enterobacterales
definition editor: Mirela L Vasconcelos
alternative label: Enterobacteraceae

Salmonella enterica subsp. enterica serovar Paratyphi A
type: Class
subclass of: Salmonella enterica subsp. enterica
definition editor: Mirela L Vasconcelos
alternative label: Bacterium paratyphi
alternative label: Bacterium paratyphi typhus A
alternative label: Salmonella choleraesuis choleraesuis (serotype paratyphi A)
alternative label: Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A
alternative label: Salmonella paratyphi
alternative label: Salmonella paratyphi A
alternative label: Salmonella paratyphi-a

Salmonella bongori
type: Class
subclass of: Salmonella
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:59206
database_cross_reference: GC_ID:11
database_cross_reference: PMID:15653929
database_cross_reference: PMID:15653930
database_cross_reference: PMID:2915026
database_cross_reference: PMID:4011990
database_cross_reference: PMID:7149525
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Salmonella cholerae-suis subsp. bongori
has_related_synonym: Salmonella choleraesuis subsp. bongori
has_related_synonym: Salmonella enterica V
has_related_synonym: Salmonella enterica subsp. V
has_related_synonym: Salmonella enterica subsp. bongori

Axiom
annotated source: Salmonella bongori
annotated property: has_related_synonym
annotated target: Salmonella cholerae-suis subsp. bongori
has_synonym_type: synonym

Axiom
annotated source: Salmonella bongori
annotated property: has_related_synonym
annotated target: Salmonella choleraesuis subsp. bongori
has_synonym_type: synonym

Axiom
annotated source: Salmonella bongori
annotated property: has_related_synonym
annotated target: Salmonella enterica V
has_synonym_type: synonym

Axiom
annotated source: Salmonella bongori
annotated property: has_related_synonym
annotated target: Salmonella enterica subsp. V
has_synonym_type: synonym

Axiom
annotated source: Salmonella bongori
annotated property: has_related_synonym
annotated target: Salmonella enterica subsp. bongori
has_synonym_type: synonym

Herpesvirales
type: Class
subclass of: dsDNA viruses, no RNA stage
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Coccidioides
type: Class
subclass of: Onygenales incertae sedis
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Coccidioides immitis
type: Class
subclass of: Coccidioides
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Amoebozoa
type: Class
subclass of: Eukaryota
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
has_obo_namespace: ncbi_taxonomy

Archamoebae
type: Class
subclass of: Amoebozoa
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
has_obo_namespace: ncbi_taxonomy

Escherichia
type: Class
subclass of: Enterobacteriaceae
definition editor: Mirela L Vasconcelos

Escherichia coli
type: Class
subclass of: Escherichia
definition editor: Mirela L Vasconcelos
alternative label: Bacillus coli
alternative label: Bacterium coli
alternative label: Bacterium coli commune
alternative label: E. coli
alternative label: Enterococcus coli

Kinetoplastida
type: Class
subclass of: Euglenozoa
definition editor: Mirela L Vasconcelos
alternative label: Kinetoplastea
alternative label: Protomonadida
alternative label: kinetoplasts

Trypanosomatidae
type: Class
subclass of: Kinetoplastida
definition editor: Mirela L Vasconcelos

Bundibugyo ebolavirus
type: Class
subclass of: Ebolavirus
alternative label: Ebolavirus bundibugyo

Trypanosoma
type: Class
subclass of: Trypanosomatidae
definition editor: Mirela L Vasconcelos

Trypanosoma cruzi
type: Class
subclass of: Schizotrypanum
definition editor: Mirela L Vasconcelos

Klebsiella
type: Class
subclass of: Enterobacteriaceae
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:39823
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10555350
database_cross_reference: PMID:11411716
database_cross_reference: PMID:12635932
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Hyalococcus

Axiom
annotated source: Klebsiella
annotated property: has_related_synonym
annotated target: Hyalococcus
has_synonym_type: synonym

Diplomonadida
type: Class
subclass of: Fornicata
database_cross_reference: GC_ID:1
has_exact_synonym: diplomonads
has_obo_namespace: ncbi_taxonomy
has_related_synonym: diplomonads

Axiom
annotated source: Diplomonadida
annotated property: has_exact_synonym
annotated target: diplomonads
has_synonym_type: common name

Axiom
annotated source: Diplomonadida
annotated property: has_related_synonym
annotated target: diplomonads
has_synonym_type: blast name

Hexamitidae
type: Class
subclass of: Diplomonadida
has_rank: NCBITaxon family
database_cross_reference: GC_ID:6
has_obo_namespace: ncbi_taxonomy

Giardia
type: Class
subclass of: Giardiinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Giardia intestinalis
type: Class
subclass of: Giardia
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
database_cross_reference: PMID:11432808
database_cross_reference: PMID:19135417
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Giardia duodenalis
has_related_synonym: Giardia lamblia
has_related_synonym: Lamblia intestinalis

Axiom
annotated source: Giardia intestinalis
annotated property: has_related_synonym
annotated target: Giardia duodenalis
has_synonym_type: synonym

Axiom
annotated source: Giardia intestinalis
annotated property: has_related_synonym
annotated target: Giardia lamblia
has_synonym_type: genbank synonym

Axiom
annotated source: Giardia intestinalis
annotated property: has_related_synonym
annotated target: Lamblia intestinalis
has_synonym_type: synonym

Entamoeba
type: Class
subclass of: Entamoebidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Apicomplexa
type: Class
subclass of: Alveolata
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: apicomplexans

Coccidia
type: Class
subclass of: Conoidasida
has_rank: NCBITaxon class
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: coccidians

Axiom
annotated source: Coccidia
annotated property: has_related_synonym
annotated target: coccidians
has_synonym_type: synonym

Eimeriidae
type: Class
subclass of: Eimeriorina
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eimeriids

Axiom
annotated source: Eimeriidae
annotated property: has_related_synonym
annotated target: Eimeriids
has_synonym_type: synonym

Cryptosporidium
type: Class
subclass of: Cryptosporidiidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Cryptosporidium parvum
type: Class
subclass of: Cryptosporidium
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Haemosporida
type: Class
subclass of: Aconoidasida
definition editor: Matthew Diller
definition editor: William R. Hogan
alternative label: haemosporidians
alternative label: haemosporina

Plasmodium
type: Class
subclass of: Plasmodiidae
definition editor: Matthew Diller

Plasmodium falciparum
type: Class
subclass of: Plasmodium (Laverania)
definition editor: Matthew Diller
definition editor: Mirela L Vasconcelos
alternative label: malaria parasite P. falciparum
alternative label: plasmodium (laverania) falciparum

Plasmodium vivax
type: Class
subclass of: Plasmodium (Plasmodium)
definition editor: Matthew Diller
alternative label: malaria parasite p. vivax

Plasmodium malariae
type: Class
subclass of: Plasmodium (Plasmodium)
definition editor: Matthew Diller

Salmonella
type: Class
subclass of: Enterobacteriaceae
definition editor: Mirela L Vasconcelos

Salmonella enterica subsp. enterica
type: Class
subclass of: Salmonella enterica
definition editor: Mirela L Vasconcelos
alternative label: Salmonella cholerae-suis subsp. cholerae-suis
alternative label: Salmonella choleraesuis subsp. choleraesuis
alternative label: Salmonella enterica I
alternative label: Salmonella enterica subsp. I

Eumetazoa
type: Class
subclass of: Metazoa

Platyhelminthes
type: Class
subclass of: Bilateria
definition editor: Mirela L Vasconcelos
alternative label: flatworms

Trematoda
type: Class
subclass of: Platyhelminthes
definition editor: Mirela L Vasconcelos

Digenea
type: Class
subclass of: Trematoda
definition editor: Mirela L Vasconcelos
alternative label: flukes

Strigeidida
type: Class
subclass of: Digenea
definition editor: Mirela L Vasconcelos

Schistosoma
type: Class
subclass of: Schistosomatidae
definition editor: Mirela L Vasconcelos

Schistosoma mansoni
type: Class
subclass of: Schistosoma
definition editor: Mirela L Vasconcelos

Schistosoma haematobium
type: Class
subclass of: Schistosoma
definition editor: Mirela L Vasconcelos

Shigella
type: Class
subclass of: Enterobacteriaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:26834722
has_obo_namespace: ncbi_taxonomy

Shigella dysenteriae
type: Class
subclass of: Shigella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:12054222
has_exact_synonym: Escherichia/Shigella dysenteriae
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus dysenteriae
has_related_synonym: Bacillus dysentericus
has_related_synonym: Bacillus shigae
has_related_synonym: Eberthella dysenteriae
has_related_synonym: Shigella shigae

Axiom
annotated source: Shigella dysenteriae
annotated property: has_exact_synonym
annotated target: Escherichia/Shigella dysenteriae
has_synonym_type: equivalent name

Axiom
annotated source: Shigella dysenteriae
annotated property: has_related_synonym
annotated target: Bacillus dysenteriae
has_synonym_type: synonym

Axiom
annotated source: Shigella dysenteriae
annotated property: has_related_synonym
annotated target: Bacillus dysentericus
has_synonym_type: synonym

Axiom
annotated source: Shigella dysenteriae
annotated property: has_related_synonym
annotated target: Bacillus shigae
has_synonym_type: synonym

Axiom
annotated source: Shigella dysenteriae
annotated property: has_related_synonym
annotated target: Eberthella dysenteriae
has_synonym_type: synonym

Axiom
annotated source: Shigella dysenteriae
annotated property: has_related_synonym
annotated target: Shigella shigae
has_synonym_type: synonym

Shigella flexneri
type: Class
subclass of: Shigella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_exact_synonym: Escherichia/Shigella flexneri
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Shigella paradysenteriae

Axiom
annotated source: Shigella flexneri
annotated property: has_exact_synonym
annotated target: Escherichia/Shigella flexneri
has_synonym_type: equivalent name

Axiom
annotated source: Shigella flexneri
annotated property: has_related_synonym
annotated target: Shigella paradysenteriae
has_synonym_type: synonym

Nematoda
type: Class
subclass of: Ecdysozoa
has_rank: NCBITaxon phylum
database_cross_reference: GC_ID:1
has_exact_synonym: nematode
has_exact_synonym: nematodes
has_exact_synonym: roundworm
has_exact_synonym: roundworms
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Nemata
has_related_synonym: nematodes

Axiom
annotated source: Nematoda
annotated property: has_exact_synonym
annotated target: nematode
has_synonym_type: common name

Axiom
annotated source: Nematoda
annotated property: has_exact_synonym
annotated target: nematodes
has_synonym_type: common name

Axiom
annotated source: Nematoda
annotated property: has_exact_synonym
annotated target: roundworm
has_synonym_type: common name

Axiom
annotated source: Nematoda
annotated property: has_exact_synonym
annotated target: roundworms
has_synonym_type: genbank common name

Axiom
annotated source: Nematoda
annotated property: has_related_synonym
annotated target: Nemata
has_synonym_type: synonym

Axiom
annotated source: Nematoda
annotated property: has_related_synonym
annotated target: nematodes
has_synonym_type: blast name

Rhabditida
type: Class
subclass of: Chromadorea
has_rank: NCBITaxon order
has_alternative_id: NCBITaxon:33251
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Shigella sonnei
type: Class
subclass of: Shigella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacterium sonnei

Axiom
annotated source: Shigella sonnei
annotated property: has_related_synonym
annotated target: Bacterium sonnei
has_synonym_type: synonym

Yersinia <bacteria>
type: Class
subclass of: Yersiniaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
has_exact_synonym: Yersinia
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Yersinia <bacteria>
annotated property: has_exact_synonym
annotated target: Yersinia
has_synonym_type: scientific name

Yersinia enterocolitica
type: Class
subclass of: Yersinia <bacteria>
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacterium enterocoliticum

Axiom
annotated source: Yersinia enterocolitica
annotated property: has_related_synonym
annotated target: Bacterium enterocoliticum
has_synonym_type: synonym

Strongylida
type: Class
subclass of: Rhabditida
has_rank: NCBITaxon suborder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Yersinia pestis
type: Class
subclass of: Yersinia pseudotuberculosis complex
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:15084509
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus pestis
has_related_synonym: Bacterium pestis
has_related_synonym: Pasteurella pestis
has_related_synonym: Pestisella pestis
has_related_synonym: Yersinia pseudotuberculosis subsp. pestis

Axiom
annotated source: Yersinia pestis
annotated property: has_related_synonym
annotated target: Bacillus pestis
has_synonym_type: synonym

Axiom
annotated source: Yersinia pestis
annotated property: has_related_synonym
annotated target: Bacterium pestis
has_synonym_type: synonym

Axiom
annotated source: Yersinia pestis
annotated property: has_related_synonym
annotated target: Pasteurella pestis
has_synonym_type: synonym

Axiom
annotated source: Yersinia pestis
annotated property: has_related_synonym
annotated target: Pestisella pestis
has_synonym_type: synonym

Axiom
annotated source: Yersinia pestis
annotated property: has_related_synonym
annotated target: Yersinia pseudotuberculosis subsp. pestis
has_synonym_type: synonym

Trichocephalida
type: Class
subclass of: Dorylaimia
has_rank: NCBITaxon order
has_alternative_id: NCBITaxon:36085
has_alternative_id: NCBITaxon:6331
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Trichinellidae
type: Class
subclass of: Trichocephalida
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Trichinella
type: Class
subclass of: Trichinellidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Trichinella spiralis
type: Class
subclass of: Trichinella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Trichinella nativa
type: Class
subclass of: Trichinella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Trichinella nelsoni
type: Class
subclass of: Trichinella
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Vibrionaceae
type: Class
subclass of: Vibrionales
definition editor: Mirela L Vasconcelos

Zika virus
type: Class
subclass of: Spondweni virus group
editor preferred term: Zika virus

Lujo mammarenavirus
type: Class
subclass of: Mammarenavirus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Lujo virus

Axiom
annotated source: Lujo mammarenavirus
annotated property: has_related_synonym
annotated target: Lujo virus
has_synonym_type: synonym

Vibrio
type: Class
subclass of: Vibrionaceae
definition editor: Mirela L Vasconcelos
alternative label: Beneckea
alternative label: Listonella
alternative label: Microspira
alternative label: Pacinia

Arthropoda
type: Class
subclass of: Panarthropoda

Vibrio cholerae
type: Class
subclass of: Vibrio
definition editor: Mirela L Vasconcelos
alternative label: Bacillo virgola del Koch
alternative label: Bacillus cholerae
alternative label: Bacillus cholerae-asiaticae
alternative label: Kommabacillus
alternative label: Liquidivibrio cholerae
alternative label: Microspira comma
alternative label: Pacinia cholerae-asiaticae
alternative label: Spirillum cholerae
alternative label: Spirillum cholerae-asiaticae
alternative label: Vibrio cholera
alternative label: Vibrio cholerae Pacini 1854
alternative label: Vibrio cholerae-asiaticae
alternative label: Vibrio comma

Vibrio parahaemolyticus
type: Class
subclass of: Vibrio harveyi group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:14071901
database_cross_reference: PMID:4935323
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Beneckea parahaemolytica
has_related_synonym: Oceanomonas parahaemolytica
has_related_synonym: Pasteurella parahaemolytica
has_related_synonym: Vibrio parahemolyticus

Axiom
annotated source: Vibrio parahaemolyticus
annotated property: has_related_synonym
annotated target: Beneckea parahaemolytica
has_synonym_type: synonym

Axiom
annotated source: Vibrio parahaemolyticus
annotated property: has_related_synonym
annotated target: Oceanomonas parahaemolytica
has_synonym_type: synonym

Axiom
annotated source: Vibrio parahaemolyticus
annotated property: has_related_synonym
annotated target: Pasteurella parahaemolytica
has_synonym_type: synonym

Axiom
annotated source: Vibrio parahaemolyticus
annotated property: has_related_synonym
annotated target: Vibrio parahemolyticus
has_synonym_type: misspelling

Vibrio vulnificus
type: Class
subclass of: Vibrio
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1015934
database_cross_reference: PMID:8186099
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Beneckea vulnifica

Axiom
annotated source: Vibrio vulnificus
annotated property: has_related_synonym
annotated target: Beneckea vulnifica
has_synonym_type: synonym

Chelicerata
type: Class
subclass of: Arthropoda
has_rank: NCBITaxon subphylum
database_cross_reference: GC_ID:1
has_exact_synonym: chelicerates
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Chelicerata
annotated property: has_exact_synonym
annotated target: chelicerates
has_synonym_type: common name

Giardiinae
type: Class
subclass of: Hexamitidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:6
has_obo_namespace: ncbi_taxonomy

delta/epsilon subdivisions
type: Class
subclass of: Proteobacteria
definition editor: Mirela L Vasconcelos
alternative label: not Thiobacteria

Arachnida
type: Class
subclass of: Chelicerata
has_rank: NCBITaxon class
database_cross_reference: GC_ID:1
has_exact_synonym: arachnids
has_obo_namespace: ncbi_taxonomy
has_related_synonym: arachnids

Axiom
annotated source: Arachnida
annotated property: has_exact_synonym
annotated target: arachnids
has_synonym_type: genbank common name

Axiom
annotated source: Arachnida
annotated property: has_related_synonym
annotated target: arachnids
has_synonym_type: blast name

Sedoreovirinae
type: Class
subclass of: Reoviridae
definition editor: Mirela L Vasconcelos

Acari
type: Class
subclass of: Arachnida
has_rank: NCBITaxon subclass
database_cross_reference: GC_ID:1
has_exact_synonym: mites and ticks
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Acarina
has_related_synonym: mites & ticks

Axiom
annotated source: Acari
annotated property: has_exact_synonym
annotated target: mites and ticks
has_synonym_type: genbank common name

Axiom
annotated source: Acari
annotated property: has_related_synonym
annotated target: Acarina
has_synonym_type: synonym

Axiom
annotated source: Acari
annotated property: has_related_synonym
annotated target: mites & ticks
has_synonym_type: blast name

Coronavirinae
type: Class
subclass of: Coronaviridae

Alphacoronavirus
type: Class
subclass of: Coronavirinae
alternative label: Coronavirus group 1
alternative label: Group 1 species

Betacoronavirus
type: Class
subclass of: Coronavirinae

Acariformes
type: Class
subclass of: Acari
has_rank: NCBITaxon superorder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Astigmata
type: Class
subclass of: Sarcoptiformes
has_rank: NCBITaxon suborder
has_alternative_id: NCBITaxon:41437
has_alternative_id: NCBITaxon:41440
has_alternative_id: NCBITaxon:41441
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Hexapoda
type: Class
subclass of: Pancrustacea

Pasteurellaceae
type: Class
subclass of: Pasteurellales
definition editor: Mirela L Vasconcelos

Diptera
type: Class
subclass of: Endopterygota

Nematocera
type: Class
subclass of: Diptera

Culicidae
type: Class
subclass of: Culicoidea
alternative label: mosquitos

Aedes
type: Class
subclass of: Aedini

Aedes aegypti
type: Class
subclass of: Stegomyia
alternative label: Stegomyia aegypti

Anopheles <genus>
type: Class
subclass of: Anophelinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_exact_synonym: Anopheles
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Anopheles <genus>
annotated property: has_exact_synonym
annotated target: Anopheles
has_synonym_type: scientific name

saccharomyceta
type: Class
subclass of: Ascomycota
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

leotiomyceta
type: Class
subclass of: Pezizomycotina
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Culex <genus>
type: Class
subclass of: Culicini
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:44555
database_cross_reference: GC_ID:1
has_exact_synonym: Culex
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Culex <genus>
annotated property: has_exact_synonym
annotated target: Culex
has_synonym_type: scientific name

Culex quinquefasciatus
type: Class
subclass of: Culex pipiens complex
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
database_cross_reference: PMID:12597651
has_exact_synonym: southern house mosquito
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Culex fatigan
has_related_synonym: Culex fatigans
has_related_synonym: Culex pipiens fatigans
has_related_synonym: Culex pipiens quinquefasciatus
has_related_synonym: Culex pipiens quiquefasciatus
has_related_synonym: Culex quinquifasciatus
has_related_synonym: Culex quinquifasiatus
has_related_synonym: Culex quiquefasciatus

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_exact_synonym
annotated target: southern house mosquito
has_synonym_type: genbank common name

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex fatigan
has_synonym_type: misspelling

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex fatigans
has_synonym_type: synonym

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex pipiens fatigans
has_synonym_type: synonym

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex pipiens quinquefasciatus
has_synonym_type: synonym

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex pipiens quiquefasciatus
has_synonym_type: misspelling

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex quinquifasciatus
has_synonym_type: misspelling

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex quinquifasiatus
has_synonym_type: misspelling

Axiom
annotated source: Culex quinquefasciatus
annotated property: has_related_synonym
annotated target: Culex quiquefasciatus
has_synonym_type: misspelling

Vibrio harveyi group
type: Class
subclass of: Vibrio
has_rank: NCBITaxon species group
database_cross_reference: GC_ID:11
database_cross_reference: PMID:17704223
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Vibrio harveyi clade

Axiom
annotated source: Vibrio harveyi group
annotated property: has_related_synonym
annotated target: Vibrio harveyi clade
has_synonym_type: synonym

Thiotrichales
type: Class
subclass of: Gammaproteobacteria
has_rank: NCBITaxon order
database_cross_reference: GC_ID:11
database_cross_reference: PMID:16280474
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Thiomicrospira group
has_related_synonym: Thiothrix/Francisella group

Axiom
annotated source: Thiotrichales
annotated property: has_related_synonym
annotated target: Thiomicrospira group
has_synonym_type: synonym

Axiom
annotated source: Thiotrichales
annotated property: has_related_synonym
annotated target: Thiothrix/Francisella group
has_synonym_type: synonym

Pseudomonadales
type: Class
subclass of: Gammaproteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Pseudomonaceae/Moraxellaceae group

Helicobacteraceae
type: Class
subclass of: Campylobacterales
definition editor: Mirela L Vasconcelos
alternative label: Helicobacter group

Campylobacteraceae
type: Class
subclass of: Campylobacterales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Campylobacter group
has_related_synonym: Campylobacteraceae Vandamme and De Ley 1991

Axiom
annotated source: Campylobacteraceae
annotated property: has_related_synonym
annotated target: Campylobacter group
has_synonym_type: synonym

Axiom
annotated source: Campylobacteraceae
annotated property: has_related_synonym
annotated target: Campylobacteraceae Vandamme and De Ley 1991
has_synonym_type: synonym

Haemophilus
type: Class
subclass of: Pasteurellaceae
definition editor: Mirela L Vasconcelos

Haemophilus influenzae
type: Class
subclass of: Haemophilus
definition editor: Mirela L Vasconcelos
alternative label: Bacterium influenzae
alternative label: Coccobacillus pfeifferi
alternative label: Haemophilus meningitidis
alternative label: Influenza-bacillus
alternative label: Mycobacterium influenzae

[Haemophilus] ducreyi
type: Class
subclass of: Haemophilus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_exact_synonym: Haemophilus ducreyi
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus ulceris cancrosi
has_related_synonym: Coccobacillus ducreyi

Axiom
annotated source: [Haemophilus] ducreyi
annotated property: has_exact_synonym
annotated target: Haemophilus ducreyi
has_synonym_type: equivalent name

Axiom
annotated source: [Haemophilus] ducreyi
annotated property: has_related_synonym
annotated target: Bacillus ulceris cancrosi
has_synonym_type: synonym

Axiom
annotated source: [Haemophilus] ducreyi
annotated property: has_related_synonym
annotated target: Coccobacillus ducreyi
has_synonym_type: synonym

Pterygota
type: Class
subclass of: Dicondylia

Eucoccidiorida
type: Class
subclass of: Coccidia
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucoccidiida

Axiom
annotated source: Eucoccidiorida
annotated property: has_related_synonym
annotated target: Eucoccidiida
has_synonym_type: synonym

Rickettsiales
type: Class
subclass of: Alphaproteobacteria
has_rank: NCBITaxon order
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11760958
database_cross_reference: PMID:8240958
has_exact_synonym: rickettsias
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993
has_related_synonym: Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001
has_related_synonym: alpha-1 proteobacteria

Axiom
annotated source: Rickettsiales
annotated property: has_exact_synonym
annotated target: rickettsias
has_synonym_type: genbank common name

Axiom
annotated source: Rickettsiales
annotated property: has_related_synonym
annotated target: Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Brenner et al. 1993
has_synonym_type: synonym

Axiom
annotated source: Rickettsiales
annotated property: has_related_synonym
annotated target: Rickettsiales Gieszczykiewicz 1939 (Approved Lists 1980) emend. Dumler et al. 2001
has_synonym_type: synonym

Axiom
annotated source: Rickettsiales
annotated property: has_related_synonym
annotated target: alpha-1 proteobacteria
has_synonym_type: in part

Anaplasma
type: Class
subclass of: Anaplasmataceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11760958
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001

Axiom
annotated source: Anaplasma
annotated property: has_related_synonym
annotated target: Anaplasma Theiler 1910 (Approved Lists 1980) emend. Dumler et al. 2001
has_synonym_type: synonym

Nidovirales
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage
editor preferred term: Nidovirales
imported from: http://purl.obolibrary.org/obo/obi.owl

Chordata
type: Class
subclass of: Deuterostomia
alternative label: chordates

Vertebrata
type: Class
subclass of: Craniata
alternative label: vertebrates
comment: authority: Vertebrata Cuvier, 1812

Rickettsiaceae
type: Class
subclass of: Rickettsiales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11760958
database_cross_reference: PMID:2592342
database_cross_reference: PMID:8240958
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993
has_related_synonym: Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001

Axiom
annotated source: Rickettsiaceae
annotated property: has_related_synonym
annotated target: Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Brenner et al. 1993
has_synonym_type: synonym

Axiom
annotated source: Rickettsiaceae
annotated property: has_related_synonym
annotated target: Rickettsiaceae Pinkerton 1936 (Approved Lists 1980) emend. Dumler et al. 2001
has_synonym_type: synonym

Coxiella <Bacteria>
type: Class
subclass of: Coxiellaceae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
has_exact_synonym: Coxiella
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Burnetia

Axiom
annotated source: Coxiella <Bacteria>
annotated property: has_exact_synonym
annotated target: Coxiella
has_synonym_type: scientific name

Axiom
annotated source: Coxiella <Bacteria>
annotated property: has_related_synonym
annotated target: Burnetia
has_synonym_type: synonym

Mycobacterium tuberculosis complex
type: Class
subclass of: Mycobacterium

Coxiella burnetii
type: Class
subclass of: Coxiella <Bacteria>
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:9226923
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Coxiella burnetii8
has_related_synonym: Rickettsia burneti
has_related_synonym: Rickettsia diaporica

Axiom
annotated source: Coxiella burnetii
annotated property: has_related_synonym
annotated target: Coxiella burnetii8
has_synonym_type: misspelling

Axiom
annotated source: Coxiella burnetii
annotated property: has_related_synonym
annotated target: Rickettsia burneti
has_synonym_type: synonym

Axiom
annotated source: Coxiella burnetii
annotated property: has_related_synonym
annotated target: Rickettsia diaporica
has_synonym_type: synonym

Gnathostomata
type: Class
subclass of: Vertebrata
alternative label: jawed vertebrates

Rickettsia
type: Class
subclass of: Rickettsieae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10939649
database_cross_reference: PMID:11491333
database_cross_reference: PMID:9103608
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Rickettsia da Rocha-Lima 1916

Axiom
annotated source: Rickettsia
annotated property: has_related_synonym
annotated target: Rickettsia da Rocha-Lima 1916
has_synonym_type: synonym

Rickettsia prowazekii
type: Class
subclass of: typhus group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:15879256
has_obo_namespace: ncbi_taxonomy

Rickettsia rickettsii
type: Class
subclass of: spotted fever group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: "Dermacentroxenus rickettsii" Wolbach 1919
has_related_synonym: Dermacentroxenus rickettsii
has_related_synonym: Rickettsia rickettsii (Wolbach 1919) Brumpt 1922

Axiom
annotated source: Rickettsia rickettsii
annotated property: has_related_synonym
annotated target: "Dermacentroxenus rickettsii" Wolbach 1919
has_synonym_type: synonym

Axiom
annotated source: Rickettsia rickettsii
annotated property: has_related_synonym
annotated target: Dermacentroxenus rickettsii
has_synonym_type: synonym

Axiom
annotated source: Rickettsia rickettsii
annotated property: has_related_synonym
annotated target: Rickettsia rickettsii (Wolbach 1919) Brumpt 1922
has_synonym_type: synonym

Rickettsia typhi
type: Class
subclass of: typhus group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Dermacentroxenus typhi
has_related_synonym: Rickettsia mooseri

Axiom
annotated source: Rickettsia typhi
annotated property: has_related_synonym
annotated target: Dermacentroxenus typhi
has_synonym_type: synonym

Axiom
annotated source: Rickettsia typhi
annotated property: has_related_synonym
annotated target: Rickettsia mooseri
has_synonym_type: synonym

Burkholderiales
type: Class
subclass of: Betaproteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Burkholderia/Oxalobacter/Ralstonia group

Chlamydiaceae
type: Class
subclass of: Chlamydiales
definition editor: Mirela L Vasconcelos

Guaroa virus
type: Class
subclass of: Guaroa orthobunyavirus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Chlamydia
type: Class
subclass of: Chlamydia/Chlamydophila group
definition editor: Mirela L Vasconcelos
alternative label: Bedsonia
alternative label: Chlamydophila
alternative label: Miyagawanella
alternative label: Rakeia
alternative label: Rickettsiaformis

Chlamydia trachomatis
type: Class
subclass of: Chlamydia
definition editor: Mirela L Vasconcelos
alternative label: Chlamydozoon trachomatis
alternative label: Rickettsia trachomae
alternative label: Rickettsia trachomatis

Sarcopterygii
type: Class
subclass of: Euteleostomi

Sarcoptiformes
type: Class
subclass of: Acariformes
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Sarcoptoidea
type: Class
subclass of: Psoroptidia
has_rank: NCBITaxon superfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Listrophoroidea
has_related_synonym: Psoroptoidea

Axiom
annotated source: Sarcoptoidea
annotated property: has_related_synonym
annotated target: Listrophoroidea
has_synonym_type: synonym

Axiom
annotated source: Sarcoptoidea
annotated property: has_related_synonym
annotated target: Psoroptoidea
has_synonym_type: synonym

Chlamydia psittaci
type: Class
subclass of: Chlamydia
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:812
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10319462
database_cross_reference: PMID:12807198
database_cross_reference: PMID:8102247
database_cross_reference: PMID:8347519
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Chlamydia psitacci
has_related_synonym: Chlamydophila psittaci
has_related_synonym: Chlamydozoon psittaci
has_related_synonym: Ehrlichia psittaci
has_related_synonym: Rickettsia psittaci
has_related_synonym: Rickettsiaformis psittacosis

Axiom
annotated source: Chlamydia psittaci
annotated property: has_related_synonym
annotated target: Chlamydia psitacci
has_synonym_type: misspelling

Axiom
annotated source: Chlamydia psittaci
annotated property: has_related_synonym
annotated target: Chlamydophila psittaci
has_synonym_type: genbank synonym

Axiom
annotated source: Chlamydia psittaci
annotated property: has_related_synonym
annotated target: Chlamydozoon psittaci
has_synonym_type: synonym

Axiom
annotated source: Chlamydia psittaci
annotated property: has_related_synonym
annotated target: Ehrlichia psittaci
has_synonym_type: synonym

Axiom
annotated source: Chlamydia psittaci
annotated property: has_related_synonym
annotated target: Rickettsia psittaci
has_synonym_type: synonym

Axiom
annotated source: Chlamydia psittaci
annotated property: has_related_synonym
annotated target: Rickettsiaformis psittacosis
has_synonym_type: synonym

Sauropsida
type: Class
subclass of: Amniota
database_cross_reference: GC_ID:1
has_exact_synonym: sauropsids
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Sauropsida
annotated property: has_exact_synonym
annotated target: sauropsids
has_synonym_type: genbank common name

Archosauria
type: Class
subclass of: Archelosauria
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Corynebacteriales
type: Class
subclass of: Actinobacteria <class>
alternative label: Corynebacterineae

Dicondylia
type: Class
subclass of: Insecta

Bacillus cereus group
type: Class
subclass of: Bacillus

Aves
type: Class
subclass of: Coelurosauria
has_rank: NCBITaxon class
database_cross_reference: GC_ID:1
has_exact_synonym: birds
has_obo_namespace: ncbi_taxonomy
has_related_synonym: birds

Axiom
annotated source: Aves
annotated property: has_exact_synonym
annotated target: birds
has_synonym_type: genbank common name

Axiom
annotated source: Aves
annotated property: has_related_synonym
annotated target: birds
has_synonym_type: blast name

Neognathae
type: Class
subclass of: Aves
has_rank: NCBITaxon superorder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Anseriformes
type: Class
subclass of: Galloanserae
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Anatidae
type: Class
subclass of: Anseriformes
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_exact_synonym: waterfowl
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Anatidae
annotated property: has_exact_synonym
annotated target: waterfowl
has_synonym_type: genbank common name

Cyclospora cayetanensis
type: Class
subclass of: Cyclospora
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Panarthropoda
type: Class
subclass of: Ecdysozoa

Craniata
type: Class
subclass of: Chordata

Galliformes
type: Class
subclass of: Galloanserae
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_exact_synonym: fowls
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Galliformes
annotated property: has_exact_synonym
annotated target: fowls
has_synonym_type: genbank common name

Phasianidae
type: Class
subclass of: Galliformes
has_rank: NCBITaxon family
has_alternative_id: NCBITaxon:9099
database_cross_reference: GC_ID:1
has_exact_synonym: turkeys
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Phasianidae
annotated property: has_exact_synonym
annotated target: turkeys
has_synonym_type: genbank common name

Gallus
type: Class
subclass of: Phasianinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Gallus gallus
type: Class
subclass of: Gallus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: bantam
has_exact_synonym: chicken
has_exact_synonym: chickens
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Gallus domesticus
has_related_synonym: Gallus gallus domesticus

Axiom
annotated source: Gallus gallus
annotated property: has_exact_synonym
annotated target: bantam
has_synonym_type: common name

Axiom
annotated source: Gallus gallus
annotated property: has_exact_synonym
annotated target: chicken
has_synonym_type: genbank common name

Axiom
annotated source: Gallus gallus
annotated property: has_exact_synonym
annotated target: chickens
has_synonym_type: common name

Axiom
annotated source: Gallus gallus
annotated property: has_related_synonym
annotated target: Gallus domesticus
has_synonym_type: misnomer

Axiom
annotated source: Gallus gallus
annotated property: has_related_synonym
annotated target: Gallus gallus domesticus
has_synonym_type: misnomer

Salmonella enterica subsp. enterica serovar Typhi
type: Class
subclass of: Salmonella enterica subsp. enterica
definition editor: Mirela L Vasconcelos
alternative label: Bacillus typhi
alternative label: Bacterium (subgen. Eberthella) typhi
alternative label: Salmonella choleraesuis serovar Typhi
alternative label: Salmonella choleraesuis typhi
alternative label: Salmonella enterica ser. typhi
alternative label: Salmonella enterica serotype Typhi
alternative label: Salmonella enterica serovar Typhi
alternative label: Salmonella typhi

Phasianinae
type: Class
subclass of: Phasianidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Coturnix
type: Class
subclass of: Perdicinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Staphylococcaceae
type: Class
subclass of: Bacillales
editor preferred term: Staphylococcaceae
alternative label: Staphylococcus group

Acinetobacter calcoaceticus/baumannii complex
type: Class
subclass of: Acinetobacter
definition editor: Mirela L Vasconcelos

Meleagris
type: Class
subclass of: Meleagridinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Meleagris gallopavo
type: Class
subclass of: Meleagris
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: common turkey
has_exact_synonym: turkey
has_exact_synonym: wild turkey
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Meleagris gallopavo
annotated property: has_exact_synonym
annotated target: common turkey
has_synonym_type: common name

Axiom
annotated source: Meleagris gallopavo
annotated property: has_exact_synonym
annotated target: turkey
has_synonym_type: genbank common name

Axiom
annotated source: Meleagris gallopavo
annotated property: has_exact_synonym
annotated target: wild turkey
has_synonym_type: common name

Bacilli
type: Class
subclass of: Firmicutes
definition editor: Mirela L Vasconcelos
alternative label: Bacillus/Lactobacillus/Strptococcus group
alternative label: Firmibacteria

Enterobacterales
type: Class
subclass of: Gammaproteobacteria
definition editor: Mirela L Vasconcelos
alternative label: Enterobacteriaceae and related endosymbionts
alternative label: Enterobacteriaceae group
alternative label: Enterobacteriales

Cetartiodactyla
type: Class
subclass of: Laurasiatheria
database_cross_reference: GC_ID:1
has_exact_synonym: whales, hippos, ruminants, pigs, camels etc.
has_obo_namespace: ncbi_taxonomy
has_related_synonym: even-toed ungulates

Axiom
annotated source: Cetartiodactyla
annotated property: has_exact_synonym
annotated target: whales, hippos, ruminants, pigs, camels etc.
has_synonym_type: genbank common name

Axiom
annotated source: Cetartiodactyla
annotated property: has_related_synonym
annotated target: even-toed ungulates
has_synonym_type: blast name

Eutheria
type: Class
subclass of: Theria
alternative label: Placentalia
alternative label: eutherian mammals
alternative label: placental mammals
alternative label: placentals

Coturnix japonica
type: Class
subclass of: Coturnix
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: Japanese quail
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Coturnix coturnix Japonicus
has_related_synonym: Coturnix coturnix japanica
has_related_synonym: Coturnix coturnix japonica
has_related_synonym: Coturnix japonica japonica

Axiom
annotated source: Coturnix japonica
annotated property: has_exact_synonym
annotated target: Japanese quail
has_synonym_type: genbank common name

Axiom
annotated source: Coturnix japonica
annotated property: has_related_synonym
annotated target: Coturnix coturnix Japonicus
has_synonym_type: synonym

Axiom
annotated source: Coturnix japonica
annotated property: has_related_synonym
annotated target: Coturnix coturnix japanica
has_synonym_type: synonym

Axiom
annotated source: Coturnix japonica
annotated property: has_related_synonym
annotated target: Coturnix coturnix japonica
has_synonym_type: synonym

Axiom
annotated source: Coturnix japonica
annotated property: has_related_synonym
annotated target: Coturnix japonica japonica
has_synonym_type: synonym

Anaplasmataceae
type: Class
subclass of: Rickettsiales
has_rank: NCBITaxon family
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11760958
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001
has_related_synonym: Ehrlichiae

Axiom
annotated source: Anaplasmataceae
annotated property: has_related_synonym
annotated target: Anaplasmataceae Philip 1957 (Approved Lists 1980) emend. Dumler et al. 2001
has_synonym_type: synonym

Axiom
annotated source: Anaplasmataceae
annotated property: has_related_synonym
annotated target: Ehrlichiae
has_synonym_type: misspelling

Ehrlichia
type: Class
subclass of: Anaplasmataceae
has_rank: NCBITaxon genus
has_alternative_id: NCBITaxon:778
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11414267
database_cross_reference: PMID:11760958
has_obo_namespace: ncbi_taxonomy
has_related_synonym: "Ehrlichia (subgen. Cowdria)" Moshkovski 1945
has_related_synonym: "Kurlovia" Zhdanov 1953
has_related_synonym: "Nicollea" (in part) Macchiavello 1947
has_related_synonym: "Nicollea" Macchiavello 1947
has_related_synonym: "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937
has_related_synonym: Cowdria
has_related_synonym: Cowdria Moshkovski 1947
has_related_synonym: Ehrlichia (subgen. Cowdria)
has_related_synonym: Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001
has_related_synonym: Kurlovia
has_related_synonym: Nicollea
has_related_synonym: Rickettsia (subgen. Ehrlichia)
has_related_synonym: possibly "Donatienella" Rousselot 1948

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: "Ehrlichia (subgen. Cowdria)" Moshkovski 1945
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: "Kurlovia" Zhdanov 1953
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: "Nicollea" (in part) Macchiavello 1947
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: "Nicollea" Macchiavello 1947
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: "Rickettsia (subgen. Ehrlichia)" Moshkovski 1937
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Cowdria
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Cowdria Moshkovski 1947
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Ehrlichia (subgen. Cowdria)
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Ehrlichia Moshkovski 1945 (Approved Lists 1980) emend. Dumler et al. 2001
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Kurlovia
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Nicollea
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: Rickettsia (subgen. Ehrlichia)
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia
annotated property: has_related_synonym
annotated target: possibly "Donatienella" Rousselot 1948
has_synonym_type: synonym

Primates
type: Class
subclass of: Euarchontoglires
alternative label: Primata
alternative label: primate
alternative label: primates

Ehrlichia chaffeensis
type: Class
subclass of: canis group
has_rank: NCBITaxon species
database_cross_reference: GC_ID:11
database_cross_reference: PMID:11760958
database_cross_reference: PMID:1757557
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001
has_related_synonym: Ehrlichia chaffensis

Axiom
annotated source: Ehrlichia chaffeensis
annotated property: has_related_synonym
annotated target: Ehrlichia chaffeensis Anderson et al. 1992 emend. Dumler et al. 2001
has_synonym_type: synonym

Axiom
annotated source: Ehrlichia chaffeensis
annotated property: has_related_synonym
annotated target: Ehrlichia chaffensis
has_synonym_type: misspelling

Anaplasma phagocytophilum
type: Class
subclass of: phagocytophilum group
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:59888
has_alternative_id: NCBITaxon:75053
has_alternative_id: NCBITaxon:75115
has_alternative_id: NCBITaxon:946
database_cross_reference: GC_ID:11
database_cross_reference: PMID:1115421
database_cross_reference: PMID:11760958
database_cross_reference: PMID:8195363
has_exact_synonym: agent of human granulocytic ehrlichiosis
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Anaplasma phagocytophila
has_related_synonym: Cytoecetes bovis
has_related_synonym: Cytoecetes phagocytophila
has_related_synonym: Ehrlichia equi
has_related_synonym: Ehrlichia phagocytophila
has_related_synonym: Ehrlichia sp. 'HGE agent'
has_related_synonym: HGE agent
has_related_synonym: Rickettsia phagocytophila
has_related_synonym: Rickettsia phagocytophila ovis
has_related_synonym: human granulocytic Ehrlichia

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_exact_synonym
annotated target: agent of human granulocytic ehrlichiosis
has_synonym_type: common name

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Anaplasma phagocytophila
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Cytoecetes bovis
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Cytoecetes phagocytophila
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Ehrlichia equi
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Ehrlichia phagocytophila
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Ehrlichia sp. 'HGE agent'
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: HGE agent
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Rickettsia phagocytophila
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: Rickettsia phagocytophila ovis
has_synonym_type: synonym

Axiom
annotated source: Anaplasma phagocytophilum
annotated property: has_related_synonym
annotated target: human granulocytic Ehrlichia
has_synonym_type: synonym

Catarrhini
type: Class
subclass of: Simiiformes

Cercopithecidae
type: Class
subclass of: Cercopithecoidea
alternative label: Old World monkeys
alternative label: monkey
alternative label: monkeys

Cercopithecinae
type: Class
subclass of: Cercopithecidae

Macaca
type: Class
subclass of: Cercopithecinae
alternative label: macaque
alternative label: macaques

Macaca fascicularis
type: Class
subclass of: Macaca
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:36519
database_cross_reference: GC_ID:1
has_exact_synonym: crab eating macaque
has_exact_synonym: crab-eating macaque
has_exact_synonym: cynomolgus monkey
has_exact_synonym: cynomolgus monkeys
has_exact_synonym: long-tailed macaque
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Macaca cynomolgus
has_related_synonym: Macaca irus
has_related_synonym: cynomolgus macaque

Axiom
annotated source: Macaca fascicularis
annotated property: has_exact_synonym
annotated target: crab eating macaque
has_synonym_type: common name

Axiom
annotated source: Macaca fascicularis
annotated property: has_exact_synonym
annotated target: crab-eating macaque
has_synonym_type: genbank common name

Axiom
annotated source: Macaca fascicularis
annotated property: has_exact_synonym
annotated target: cynomolgus monkey
has_synonym_type: common name

Axiom
annotated source: Macaca fascicularis
annotated property: has_exact_synonym
annotated target: cynomolgus monkeys
has_synonym_type: common name

Axiom
annotated source: Macaca fascicularis
annotated property: has_exact_synonym
annotated target: long-tailed macaque
has_synonym_type: common name

Axiom
annotated source: Macaca fascicularis
annotated property: has_related_synonym
annotated target: Macaca cynomolgus
has_synonym_type: synonym

Axiom
annotated source: Macaca fascicularis
annotated property: has_related_synonym
annotated target: Macaca irus
has_synonym_type: synonym

Axiom
annotated source: Macaca fascicularis
annotated property: has_related_synonym
annotated target: cynomolgus macaque
has_synonym_type: synonym

Macaca mulatta
type: Class
subclass of: Macaca
alternative label: Rhesus monkey
alternative label: rhesus macaque
alternative label: rhesus macaques
alternative label: rhesus monkeys

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

Canidae
type: Class
subclass of: Caniformia
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_exact_synonym: dog, coyote, wolf, fox
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Canidae
annotated property: has_exact_synonym
annotated target: dog, coyote, wolf, fox
has_synonym_type: genbank common name

Canis
type: Class
subclass of: Canidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Canis lupus
type: Class
subclass of: Canis
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: gray wolf
has_exact_synonym: grey wolf
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Canis lupus
annotated property: has_exact_synonym
annotated target: gray wolf
has_synonym_type: genbank common name

Axiom
annotated source: Canis lupus
annotated property: has_exact_synonym
annotated target: grey wolf
has_synonym_type: common name

Canis lupus familiaris
type: Class
subclass of: Canis lupus
has_rank: NCBITaxon subspecies
database_cross_reference: GC_ID:1
has_exact_synonym: dog
has_exact_synonym: dogs
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Canis canis
has_related_synonym: Canis domesticus
has_related_synonym: Canis familiaris

Axiom
annotated source: Canis lupus familiaris
annotated property: has_exact_synonym
annotated target: dog
has_synonym_type: genbank common name

Axiom
annotated source: Canis lupus familiaris
annotated property: has_exact_synonym
annotated target: dogs
has_synonym_type: common name

Axiom
annotated source: Canis lupus familiaris
annotated property: has_related_synonym
annotated target: Canis canis
has_synonym_type: synonym

Axiom
annotated source: Canis lupus familiaris
annotated property: has_related_synonym
annotated target: Canis domesticus
has_synonym_type: synonym

Axiom
annotated source: Canis lupus familiaris
annotated property: has_related_synonym
annotated target: Canis familiaris
has_synonym_type: synonym

Perissodactyla
type: Class
subclass of: Laurasiatheria
has_rank: NCBITaxon order
database_cross_reference: GC_ID:1
has_exact_synonym: odd-toed ungulates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: odd-toed ungulates

Axiom
annotated source: Perissodactyla
annotated property: has_exact_synonym
annotated target: odd-toed ungulates
has_synonym_type: genbank common name

Axiom
annotated source: Perissodactyla
annotated property: has_related_synonym
annotated target: odd-toed ungulates
has_synonym_type: blast name

Equidae
type: Class
subclass of: Perissodactyla
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_exact_synonym: horses
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Equidae
annotated property: has_exact_synonym
annotated target: horses
has_synonym_type: genbank common name

Equus
type: Class
subclass of: Equidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Equus caballus
type: Class
subclass of: Equus <subgenus>
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: domestic horse
has_exact_synonym: equine
has_exact_synonym: horse
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Equus ferus caballus
has_related_synonym: Equus przewalskii f. caballus
has_related_synonym: Equus przewalskii forma caballus

Axiom
annotated source: Equus caballus
annotated property: has_exact_synonym
annotated target: domestic horse
has_synonym_type: common name

Axiom
annotated source: Equus caballus
annotated property: has_exact_synonym
annotated target: equine
has_synonym_type: common name

Axiom
annotated source: Equus caballus
annotated property: has_exact_synonym
annotated target: horse
has_synonym_type: genbank common name

Axiom
annotated source: Equus caballus
annotated property: has_related_synonym
annotated target: Equus ferus caballus
has_synonym_type: synonym

Axiom
annotated source: Equus caballus
annotated property: has_related_synonym
annotated target: Equus przewalskii f. caballus
has_synonym_type: synonym

Axiom
annotated source: Equus caballus
annotated property: has_related_synonym
annotated target: Equus przewalskii forma caballus
has_synonym_type: synonym

Suidae
type: Class
subclass of: Suina
has_rank: NCBITaxon family
has_alternative_id: NCBITaxon:39423
database_cross_reference: GC_ID:1
has_exact_synonym: boars
has_exact_synonym: pigs
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Suidae
annotated property: has_exact_synonym
annotated target: boars
has_synonym_type: common name

Axiom
annotated source: Suidae
annotated property: has_exact_synonym
annotated target: pigs
has_synonym_type: genbank common name

Sus
type: Class
subclass of: Suidae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Sus scrofa
type: Class
subclass of: Sus
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: pig
has_exact_synonym: pigs
has_exact_synonym: swine
has_exact_synonym: wild boar
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Sus scrofus

Axiom
annotated source: Sus scrofa
annotated property: has_exact_synonym
annotated target: pig
has_synonym_type: genbank common name

Axiom
annotated source: Sus scrofa
annotated property: has_exact_synonym
annotated target: pigs
has_synonym_type: common name

Axiom
annotated source: Sus scrofa
annotated property: has_exact_synonym
annotated target: swine
has_synonym_type: common name

Axiom
annotated source: Sus scrofa
annotated property: has_exact_synonym
annotated target: wild boar
has_synonym_type: common name

Axiom
annotated source: Sus scrofa
annotated property: has_related_synonym
annotated target: Sus scrofus
has_synonym_type: misspelling

Ruminantia
type: Class
subclass of: Cetartiodactyla
has_rank: NCBITaxon suborder
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Artiodactyla

Axiom
annotated source: Ruminantia
annotated property: has_related_synonym
annotated target: Artiodactyla
has_synonym_type: in part

Bovidae
type: Class
subclass of: Pecora
has_rank: NCBITaxon family
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Bos
type: Class
subclass of: Bovinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_exact_synonym: oxen, cattle
has_obo_namespace: ncbi_taxonomy

Axiom
annotated source: Bos
annotated property: has_exact_synonym
annotated target: oxen, cattle
has_synonym_type: genbank common name

Bos taurus
type: Class
subclass of: Bos
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:272461
database_cross_reference: GC_ID:1
has_exact_synonym: bovine
has_exact_synonym: cattle
has_exact_synonym: cow
has_exact_synonym: domestic cattle
has_exact_synonym: domestic cow
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bos Tauurus
has_related_synonym: Bos bovis
has_related_synonym: Bos primigenius taurus

Axiom
annotated source: Bos taurus
annotated property: has_exact_synonym
annotated target: bovine
has_synonym_type: common name

Axiom
annotated source: Bos taurus
annotated property: has_exact_synonym
annotated target: cattle
has_synonym_type: genbank common name

Axiom
annotated source: Bos taurus
annotated property: has_exact_synonym
annotated target: cow
has_synonym_type: common name

Axiom
annotated source: Bos taurus
annotated property: has_exact_synonym
annotated target: domestic cattle
has_synonym_type: common name

Axiom
annotated source: Bos taurus
annotated property: has_exact_synonym
annotated target: domestic cow
has_synonym_type: common name

Axiom
annotated source: Bos taurus
annotated property: has_related_synonym
annotated target: Bos Tauurus
has_synonym_type: misspelling

Axiom
annotated source: Bos taurus
annotated property: has_related_synonym
annotated target: Bos bovis
has_synonym_type: synonym

Axiom
annotated source: Bos taurus
annotated property: has_related_synonym
annotated target: Bos primigenius taurus
has_synonym_type: synonym

Capra
type: Class
subclass of: Caprinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Capra hircus
type: Class
subclass of: Capra
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:57076
database_cross_reference: GC_ID:1
has_exact_synonym: domestic goat
has_exact_synonym: goat
has_exact_synonym: goats
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Capra aegagrus hircus
has_related_synonym: Carpa hircus
has_related_synonym: South African angora goat

Axiom
annotated source: Capra hircus
annotated property: has_exact_synonym
annotated target: domestic goat
has_synonym_type: common name

Axiom
annotated source: Capra hircus
annotated property: has_exact_synonym
annotated target: goat
has_synonym_type: genbank common name

Axiom
annotated source: Capra hircus
annotated property: has_exact_synonym
annotated target: goats
has_synonym_type: common name

Axiom
annotated source: Capra hircus
annotated property: has_related_synonym
annotated target: Capra aegagrus hircus
has_synonym_type: synonym

Axiom
annotated source: Capra hircus
annotated property: has_related_synonym
annotated target: Carpa hircus
has_synonym_type: misspelling

Axiom
annotated source: Capra hircus
annotated property: has_related_synonym
annotated target: South African angora goat
has_synonym_type: misspelling

Ovis
type: Class
subclass of: Caprinae
has_rank: NCBITaxon genus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

Ovis aries
type: Class
subclass of: Ovis
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:9936
database_cross_reference: GC_ID:1
has_exact_synonym: domestic sheep
has_exact_synonym: lambs
has_exact_synonym: sheep
has_exact_synonym: wild sheep
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Ovis ammon aries
has_related_synonym: Ovis orientalis aries
has_related_synonym: Ovis ovis

Axiom
annotated source: Ovis aries
annotated property: has_exact_synonym
annotated target: domestic sheep
has_synonym_type: common name

Axiom
annotated source: Ovis aries
annotated property: has_exact_synonym
annotated target: lambs
has_synonym_type: common name

Axiom
annotated source: Ovis aries
annotated property: has_exact_synonym
annotated target: sheep
has_synonym_type: genbank common name

Axiom
annotated source: Ovis aries
annotated property: has_exact_synonym
annotated target: wild sheep
has_synonym_type: common name

Axiom
annotated source: Ovis aries
annotated property: has_related_synonym
annotated target: Ovis ammon aries
has_synonym_type: synonym

Axiom
annotated source: Ovis aries
annotated property: has_related_synonym
annotated target: Ovis orientalis aries
has_synonym_type: synonym

Axiom
annotated source: Ovis aries
annotated property: has_related_synonym
annotated target: Ovis ovis
has_synonym_type: synonym

Caprinae
type: Class
subclass of: Bovidae
has_rank: NCBITaxon subfamily
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy

contraindication
type: Class
subclass of: disposition
definition: A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment.
definition source: http://en.wikipedia.org/wiki/Contraindication
imported from: http://purl.obolibrary.org/obo/dideo/dev/dideo.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: has part
        some values from: objective specification
editor preferred term: 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.
definition: A processual entity 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: obi.owl

processed material
type: Class
subclass of: material entity
editor preferred term: 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

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

intervention design
type: Class
subclass of: study design
editor preferred term: intervention design
example of usage: PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
has curation status: pending final vetting
definition: An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
definition editor: Philppe Rocca-Serra
definition source: OBI branch derived
imported from: http://purl.obolibrary.org/obo/obi.owl

data encoding
type: Class
subclass of: documenting
editor preferred term: data encoding
example of usage: storage of measurement results from an assay into a text file, such as
has curation status: metadata complete
definition: a documenting process to encode an information entity into a digital document
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
imported from: http://purl.obolibrary.org/obo/obi.owl

organization
type: Class
subclass of: material entity
editor preferred term: 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

averaging objective
type: Class
subclass of: data transformation objective
editor preferred term: averaging objective
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
has curation status: ready for release
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
definition editor: Elisabetta Manduchi
definition editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: http://purl.obolibrary.org/obo/obi.owl

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

scattered molecular aggregate
type: Class
subclass of: object_aggregate
editor preferred term: scattered molecular aggregate
example of usage: the sodium and chloride ions in a glass of salt water
has curation status: metadata incomplete
definition: a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
definition editor: PERSON: Alan Ruttenberg
alternative label: Collective
definition source: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: http://purl.obolibrary.org/obo/obi.owl

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

center value
type: Class
subclass of: data item
editor preferred term: center value
has curation status: pending final vetting
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
definition editor: PERSON: James Malone
definition editor: PERSON: Monnie McGee
alternative label: median
imported from: http://purl.obolibrary.org/obo/obi.owl
Unique Apollo Label: median

average value
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: averaging data transformation
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
editor preferred term: average value
has curation status: pending final vetting
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
definition editor: PERSON: James Malone
definition editor: PERSON: Monnie McGee
alternative label: arithmetic mean
alternative label: false
imported from: http://purl.obolibrary.org/obo/obi.owl
elucidation: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
Unique Apollo Label: mean

graph of vertices
type: Class
subclass of: graph
editor preferred term: graph of vertices
example of usage: For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
has curation status: metadata incomplete
definition: A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.
definition editor: Bjoern Peters
definition editor: Chris Stoeckert
definition editor: James Malone
definition source: WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
imported from: http://purl.obolibrary.org/obo/obi.owl

device
type: Class
subclass of: processed material
editor preferred term: 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
has curation status: metadata incomplete
definition: A device is a processed material which is designed to perform some function or functions
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…
editor note: food should not classify as a device - counter example for using manufacturer and not device. macroscopic only
editor note: if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition.
definition editor: PERSON: Helen Parkinson
alternative label: instrument
definition source: OBI Vancouver workshop 2010
definition source: OBI development call 2012-12-17.
comment: would include reagents

computer cluster
type: Class
subclass of: computer
editor preferred term: computer cluster
has curation status: metadata complete
definition: A group of linked computers, working together closely so that in many respects they form a single computer.
definition editor: PERSON: Erik Segerdell
definition source: http://en.wikipedia.org/wiki/Cluster_(computing)
imported from: http://purl.obolibrary.org/obo/obi.owl

service
type: Class
subclass of: planned process
editor preferred term: service
example of usage: providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
has curation status: metadata complete
definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
definition editor: Carlo; Matt
definition source: OBI workshop San Diego 2011
imported from: http://purl.obolibrary.org/obo/obi.owl

environmental history design
type: Class
subclass of: study design
editor preferred term: environmental history design
has curation status: metadata complete
definition: A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_698 environmental_history_design
imported from: http://purl.obolibrary.org/obo/obi.owl

disease state design
type: Class
subclass of: study design
editor preferred term: disease state design
has curation status: metadata complete
definition: A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_902 disease_state_design
imported from: http://purl.obolibrary.org/obo/obi.owl

pathogenicity design
type: Class
subclass of: study design
editor preferred term: pathogenicity design
has curation status: metadata complete
definition: A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_807 pathogenicity_design
imported from: http://purl.obolibrary.org/obo/obi.owl

data service
type: Class
equivalent class: Class
  intersection of: service
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: Class
      union of: data service software
      union of: Restriction
        on property: is_specified_output_of
        some values from: Class
subclass of: service
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    union of: data service software
    union of: Restriction
      on property: is_specified_output_of
      some values from: Class
        intersection of: compiling software
        intersection of: Restriction
editor preferred term: data service
example of usage: Data analysis service such statistical abalysis or storage service such data backup.
has curation status: pending final vetting
definition: A service that has some information content entity as input and output.
definition editor: PERSON: Carlo Torniai
definition editor: PERSON: Matthew Brush
definition source: PERSON: Carlo Torniai
imported from: http://purl.obolibrary.org/obo/obi.owl
comment: Information content entity was used as specified input and output since it was more appropriate then data item or dataset.

rate measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred term: rate measurement datum
example of usage: The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
has curation status: metadata complete
definition: A scalar measurement datum that represents the number of events occuring over a time interval
definition editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: http://purl.obolibrary.org/obo/obi.owl

investigation description
type: Class
subclass of: textual entity
editor preferred term: investigation description
has curation status: metadata complete
definition: A textual entity that describes an investigation.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: http://purl.obolibrary.org/obo/obi.owl
ISA alternative term: study description
NIAID GSCID-BRC alternative term: project description
Unique Apollo Label: investigationDescription
Source: NIAID GSCID-BRC

latitude coordinate measurement datum
type: Class
subclass of: geodetic coordinate measurement datum
editor preferred term: latitude coordinate measurement datum
has curation status: metadata complete
definition: A measurement datum that is the measure of the latitude coordinate of a site.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative label: latitude
definition source: NIAID GSCID-BRC metadata working group
imported from: http://purl.obolibrary.org/obo/obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Location - Latitude
Source: NIAID GSCID-BRC

longitude coordinate measurement datum
type: Class
subclass of: geodetic coordinate measurement datum
editor preferred term: longitude coordinate measurement datum
has curation status: metadata complete
definition: A measurement datum that is the measure of the longitude coordinate of a site.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative label: longitude
definition source: NIAID GSCID-BRC metadata working group
imported from: http://purl.obolibrary.org/obo/obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Location - Longitude
Source: NIAID GSCID-BRC

investigation identifier
type: Class
subclass of: centrally registered identifier symbol
editor preferred term: investigation identifier
has curation status: metadata complete
definition: A CRID symbol used to identify an investigation.
definition editor: Person: Chris Stoeckert, Jie Zhneg
definition source: NIAID GSCID-BRC metadata working group
imported from: http://purl.obolibrary.org/obo/obi.owl
NIAID GSCID-BRC alternative term: project ID
Unique Apollo Label: investigationLabel
Source: NIAID GSCID-BRC

grant identifier
type: Class
subclass of: identifier
editor preferred term: grant identifier
has curation status: metadata complete
definition: A CRID symbol used to identify a grant.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: http://purl.obolibrary.org/obo/obi.owl
NIAID GSCID-BRC alternative term: grant ID
Source: NIAID GSCID-BRC

scalar value specification
type: Class
subclass of: value specification
editor preferred term: scalar value specification
has curation status: metadata incomplete
definition: A value specification that consists of two parts: a numeral and a unit label
definition editor: PERSON:Bjoern Peters
imported from: http://purl.obolibrary.org/obo/obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred term: 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: http://purl.obolibrary.org/obo/obi.owl

systematic review study design
type: Class
subclass of: study design
editor preferred term: systematic review study design
example of usage: Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/ar\ ticles/PMC4090399/
example of usage: The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic re\ view. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/
has curation status: metadata complete
definition: A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according \ to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were no\ t justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed.
definition editor: PERSON: Bill Hogan

digital object identifier
type: Class
subclass of: identifier
editor preferred term: digital object identifier
example of usage: The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
has curation status: metadata complete
definition: A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles.
editor note: Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/
definition editor: OBI developers
alternative label: DOI
definition source: https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/
imported from: http://purl.obolibrary.org/obo/obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
disjoint with: disorder
editor preferred term: 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: obi.owl
Unique Apollo Label: Individual

data transformation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
editor preferred term: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: ready for release
has curation status: pending final vetting
definition: A data transformation is a process which produces output data from input data
definition: A planned process that produces output data from input data.
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Philippe Rocca-Serra
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative label: data analysis
alternative label: data processing
definition source: Branch editors
imported from: obi.owl

data transformation objective
type: Class
subclass of: objective specification
editor preferred term: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
definition editor: James Malone
definition source: PERSON: James Malone
imported from: http://purl.obolibrary.org/obo/obi.owl

averaging data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: average value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: data transformation
editor preferred term: averaging data transformation
has curation status: metadata incomplete
definition: An averaging data transformation is a data transformation that has objective averaging.
definition editor: James Malone
definition source: PERSON: James Malone
imported from: http://purl.obolibrary.org/obo/obi.owl

observation design
type: Class
subclass of: study design
editor preferred term: observation design
example of usage: PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
has curation status: pending final vetting
definition: observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
definition editor: Philippe Rocca-Serra
definition source: OBI branch derived
imported from: http://purl.obolibrary.org/obo/obi.owl

calculated datum
type: Class
subclass of: measurement datum
editor preferred term: predicted data item
has curation status: metadata complete
definition: A data item that was generated on the basis of a calculation or logical reasoning
editor note: BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted.
definition editor: Philippe Rocca-Serra; Bjoern Peters
imported from: http://purl.obolibrary.org/obo/obi.owl
comment: APOLLO DEVELOPERS: We need to check whether OBI changes the label and the hierarchical place of this class.
label: predicted data item

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

computer
type: Class
subclass of: device
editor preferred term: computer
example of usage: Apple PowerBook, Dell OptiPlex
has curation status: ready for release
definition: A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
definition editor: Melanie Courtot
definition editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Computer

study design
type: Class
subclass of: plan specification
editor preferred term: 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 label: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

time series design
type: Class
subclass of: study design
editor preferred term: time series design
example of usage: PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limite…
has curation status: pending final vetting
definition: Groups of assays that are related as part of a time series.
definition editor: Philippe Rocca-Serra on behalf of MO
definition source: MO_887
imported from: http://purl.obolibrary.org/obo/obi.owl

software execution
type: Class
subclass of: planned process
definition: A planned process that realizes the concretization of a software.
definition editor: ITPPR
alternative label: operation
definition source: ITPPR
imported from: http://purl.obolibrary.org/obo/OBIws.owl

web service execution
type: Class
subclass of: software execution
definition: A software execution that is provided by the web service, and involves invoking software execution over network.
definition editor: ITPPR
alternative label: web service operation
definition source: ITPPR
imported from: http://purl.obolibrary.org/obo/OBIws.owl

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: http://purl.obolibrary.org/obo/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: http://purl.obolibrary.org/obo/ogms.owl
Unique Apollo Label: result

phenotype
type: Class
subclass of: quality
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T11:13:49Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

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

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

homeostasis
type: Class
subclass of: disposition
definition: A disposition of the whole organism (or of some causally relatively isolated part of the organism, such as a single cell) to regulate its bodily processes in such a way as (1) to maintain bodily qualities within a certain range or profile and (2) to respond successfully to departures from this range caused by internal influences or environmental influences such as poisoning.
definition editor: Albert Goldfain
definition editor: Barry Smith
definition editor: Richard H. Scheuermann
definition editor: Werner Ceusters
definition source: Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on translational bioinformatics. 2009;2009:116. Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/
curator note: creation date: 2009-06-23T11:22:01Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

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

bodily process
type: Class
subclass of: process
subclass of: Restriction
  on property: has participant at all times
  some values from: extended organism
definition: A process in which at least one bodily component of an organsim participates.
definition source: http://www.jbiomedsem.com/content/1/1/10
comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060

disease course
type: Class
subclass of: process
editor preferred term: disease course
definition: The totality of all processes through which a given disease instance is realized.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:55:44Z
imported from: ogms.owl
imported from: http://purl.obolibrary.org/obo/ido.owl

extended organism
type: Class
subclass of: object_aggregate
definition: An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-01-25T04:51:11Z
imported from: ogms.owl
comment: From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087

treatment
type: Class
subclass of: planned process
definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
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: http://purl.obolibrary.org/obo/ogms.owl
Unique Apollo Label: Treatment
comment: Apollo-SV currently defines two subclasses of treatment. See vaccination and antiviral treatment.

life course
type: Class
subclass of: history
definition: A processual entity which has as parts all the processes in which a given organism is participant.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z
imported from: http://purl.obolibrary.org/obo/ogms.owl
elucidation: A processual entity which has as parts all the processes in which a given organism is participant.
Unique Apollo Label: LifeCycle

health care process
type: Class
subclass of: process
definition: A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

health care encounter
type: Class
subclass of: planned process
subclass of: health care process
definition: A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

hospitalization
type: Class
subclass of: health care encounter
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: http://purl.obolibrary.org/obo/ogms.owl
Unique Apollo Label: hospitalization

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

inpatient encounter
type: Class
subclass of: health care encounter
definition: A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night.
definition editor: Albert Goldfain
definition source: http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
curator note: creation date: 2011-02-21T09:57:44Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

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

relapse
type: Class
subclass of: process
definition: A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
imported from: http://purl.obolibrary.org/obo/ogms.owl

unique resource locator
type: Class
subclass of: identifier
definition: A CRID that constitutes a reference to an Internet resource.
definition editor: Mathias Brochhausen
alternative label: uri
definition source: http://en.wikipedia.org/wiki/Uniform_resource_locator
imported from: http://purl.obolibrary.org/obo/omiabis.owl
Unique Apollo Label: url

human social role
type: Class
subclass of: organism social role
subclass of: Homo sapiens role
definition: A social role inhering in a human being.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan

human health care role
type: Class
subclass of: role in human social processes
subclass of: Restriction
  on property: is realized by
  some values from: health care encounter
definition: A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
definition editor: Mathias Brochhausen
definition editor: William R. Hogan
alternative label: health care role

patient role
type: Class
subclass of: human health care role
subclass of: organism role
definition: A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
definition editor: Amanda Hicks
definition editor: Mathias Brochhausen
alternative label: patient
definition source: CAFE domain expert working group.
comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.

health care provider organization role
type: Class
subclass of: organization health care role
subclass of: Restriction
  on property: is realized by
  some values from: health care encounter
definition: A role that inheres in an organization and that is realized by the providing of services in a health care encounter.
contributor: Mathias Brochhausen
creator: Amanda Hicks

aggregate of objectual organisms
type: Class
subclass of: object_aggregate
subclass of: Restriction
  on property: has member
  all values from: Class
    intersection of: object
    intersection of: organism
definition: An object aggregate of objectual organisms.
comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class.

collection of humans
type: Class
subclass of: aggregate of objectual organisms
subclass of: Restriction
  on property: has member
  all values from: Homo sapiens
definition: An object aggregate all of whose components are human beings.

organization social role
type: Class
subclass of: organization role
subclass of: role in human social processes
definition: A role in human social processes that inheres in an organization.
definition editor: William R. Hogan
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.

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

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
comment: Previous definition: An organization social role played by an organization in health care processes.

human patient role
type: Class
equivalent class: Class
  intersection of: patient role
  intersection of: Restriction
    on property: characteristic of
    some values from: Homo sapiens
subclass of: patient role
subclass of: Homo sapiens role
definition: A patient role that inheres in a human being.

aggregate of organizations
type: Class
equivalent class: Class
  intersection of: Class
    complement of: organization
  intersection of: Restriction
    on property: has member
    all values from: organization
  intersection of: Restriction
    on property: has member
    min qualified cardinality: 2
    on class: organization
subclass of: material entity
subclass of: Restriction
  on property: has member
  some values from: organization
definition: An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
definition editor: William R. Hogan Amanda Hicks
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

material entity role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: material entity
subclass of: role
subclass of: Restriction
  on property: characteristic of
  some values from: material entity
subclass of: Restriction
  on property: characteristic of
  all values from: material entity

organism role
type: Class
equivalent class: Class
  intersection of: material entity role
  intersection of: Restriction
    on property: characteristic of
    some values from: organism
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: organism
subclass of: Restriction
  on property: characteristic of
  all values from: organism

Homo sapiens role
type: Class
equivalent class: Class
  intersection of: organism role
  intersection of: Restriction
    on property: characteristic of
    some values from: Homo sapiens
subclass of: organism role
subclass of: Restriction
  on property: characteristic of
  some values from: Homo sapiens
subclass of: Restriction
  on property: characteristic of
  all values from: Homo sapiens

organization role
type: Class
equivalent class: Class
  intersection of: role
  intersection of: Restriction
    on property: characteristic of
    some values from: organization
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  some values from: organization
subclass of: Restriction
  on property: characteristic of
  all values from: organization

school function
type: Class
subclass of: function
definition: A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population.
definition editor: Mathias Brochhausen

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

school role
type: Class
subclass of: organization social role
definition editor: An organization social role that inheres in an organization and is realized by providing formal education to students.
definition editor: Mathias Brochhausen

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
subclass of: Restriction
  on property: bearer of
  some values from: hospital role
definition: An organization that is the bearer of a hospital role.
definition editor: Mathias Brochhausen

school organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: bearer of
    some values from: school role
subclass of: organization
subclass of: Restriction
  on property: bearer of
  some values from: school role
definition: An organization that is the bearer of a school role.
definition editor: Mathias Brochhausen

student role
type: Class
subclass of: Class
  intersection of: human role within an organization
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: deontic declaration
      intersection of: Restriction
        on property: process has causal agent
        some values from: school organization
definition: A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.
definition editor: Mathias Brochhausen

nursery school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen

primary school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen

architectural structure
type: Class
subclass of: material entity
definition: A material entity that is a human made strcuture with firm connection between its foundation and the ground.
definition editor: Mathias Brochhausen
definition source: http://de.wikipedia.org/wiki/Bauwerk
comment: "Building" is a subclass of this.
comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".

facility
type: Class
equivalent class: Class
  intersection of: architectural structure
  intersection of: Restriction
    on property: bearer of
    some values from: function
subclass of: architectural structure
subclass of: Restriction
subclass of: Restriction
  on property: bearer of
  some values from: function
definition: An architectural structure that bears some function.
definition editor: Mathias Brochhausen

Axiom
annotated source: facility
annotated property: subClassOf
annotated target: Restriction
version info: 09/09/2017

school facility
type: Class
equivalent class: Class
  intersection of: facility
  intersection of: Class
    union of: Restriction
      on property: is owned by
      some values from: school organization
    union of: Restriction
      on property: is administered by
      some values from: school organization
  intersection of: Restriction
    on property: bearer of
    some values from: school function
subclass of: facility
subclass of: Restriction
  on property: bearer of
  some values from: school function
definition: A facility that is run by a school organization and is the bearer of a school function.
definition editor: Mathias Brochhausen

secondary school role
type: Class
subclass of: school role
definition editor: Mathias Brochhausen

human role within an organization
type: Class
subclass of: Class
  intersection of: human social role
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: deontic declaration
      intersection of: Restriction
        on property: process has causal agent
        some values from: Class
definition: A human social role that is created by a deontic declaration performed by an organization.
definition editor: Amanda Hicks
alternative label: human organizational role

human traveling information
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: is about
    some values from: human travel
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: human travel
definition: An information content entity that is about human travel.
definition source: https://github.com/ufbmi/OMRSE/issues/79
contributor: Jie Zheng
creator: Amanda Hicks

health care function
type: Class
equivalent class: Class
  intersection of: function
  intersection of: Restriction
    on property: is realized by
    some values from: health care encounter
subclass of: function
subclass of: Restriction
  on property: is realized by
  some values from: health care encounter

role in human social processes
type: Class
subclass of: material entity role
subclass of: Restriction
  on property: characteristic of
  all values from: material entity
definition: A role that inheres in some entity that is realized in a social act.
definition editor: Matthew Diller
contributor: Mathias Brochhausen
comment: Previous definition: A role played by an entity in human social processes.

quality
type: Class
subclass of: characteristic
definition: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
id: PATO:0000001

Axiom
annotated source: quality
annotated property: definition
annotated target: A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
database_cross_reference: PATOC:GVG

distance
type: Class
subclass of: physical quality
definition: A quality that is the extent of space between two entities.
imported from: http://purl.obolibrary.org/obo/pato.owl
Unique Apollo Label: Distance
has_obo_namespace: quality
id: PATO:0000040
in_subset: attribute slim
in_subset: relational slim
in_subset: scalar slim

biological sex
type: Class
subclass of: quality
editor preferred term: biological sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
imported from: http://purl.obolibrary.org/obo/obi.owl
Unique Apollo Label: biologicalSex

morphology
type: Class
subclass of: physical object quality
editor preferred term: 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
has_obo_namespace: quality
id: PATO:0000051
in_subset: attribute slim

size
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000117
in_subset: attribute slim
in_subset: scalar slim

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

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

structure
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_alternative_id: PATO:0001452
has_broad_synonym: conformation
has_exact_synonym: relational structural quality
has_obo_namespace: quality
id: PATO:0000141
in_subset: attribute slim

temperature
type: Class
subclass of: physical quality
definition: A physical quality of the thermal energy of a system.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000146
in_subset: attribute slim
in_subset: scalar slim

female
type: Class
subclass of: biological sex
editor preferred term: female
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
imported from: http://purl.obolibrary.org/obo/obi.owl

male
type: Class
subclass of: biological sex
editor preferred term: male
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
imported from: http://purl.obolibrary.org/obo/obi.owl

physical quality
type: Class
subclass of: physical object quality
editor preferred term: 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: pato.owl
has_alternative_id: PATO:0002079
database_cross_reference: Wikipedia:Physical_property
has_exact_synonym: relational physical quality
has_obo_namespace: quality
id: PATO:0001018
in_subset: attribute slim

physical object quality
type: Class
subclass of: quality
editor preferred term: physical object quality
definition: A quality which inheres in a continuant.
imported from: pato.owl
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
database_cross_reference: snap:Quality
has_exact_synonym: monadic quality of a continuant
has_exact_synonym: multiply inhering quality of a physical entity
has_exact_synonym: quality of a continuant
has_exact_synonym: quality of a single physical entity
has_exact_synonym: quality of an object
has_exact_synonym: quality of continuant
has_narrow_synonym: monadic quality of an object
has_narrow_synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

area
type: Class
subclass of: 2-D extent
definition: A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0001323
in_subset: attribute slim
in_subset: mpath slim
in_subset: scalar slim
comment: MIREOT'd into GEO to represent the area quality of a geographical region, including land area and water area.

1-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_exact_synonym: 1-D size
has_obo_namespace: quality
id: PATO:0001708
in_subset: attribute slim

2-D extent
type: Class
subclass of: size
definition: A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_exact_synonym: 2-D size
has_obo_namespace: quality
id: PATO:0001709
in_subset: attribute slim

in contact with
type: Class
subclass of: structure
definition: A structural quality inhering in a bearer by virtue of the bearer's touching another entity.
imported from: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
has_related_synonym: contiguous
id: PATO:0001961
in_subset: relational slim
in_subset: value slim

radius
type: Class
subclass of: length
definition: A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter.
imported from: http://purl.obolibrary.org/obo/pato.owl
Unique Apollo Label: radius
created by: gkoutos
creation date: 2012-11-15T05:17:15Z
has_obo_namespace: quality
id: PATO:0002390
in_subset: attribute slim
in_subset: scalar slim

PCO:collection of organisms
type: Class
subclass of: object_aggregate
example of usage: Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative label: group of organisms
alternative label: organism collection
comment: May be of the same or different species.

population
type: Class
subclass of: collection of organisms of the same species
subclass of: Restriction
  on property: part of continuant at all times
  some values from: biotic ecosystem
definition: A collection of organisms, all of the same species, that live in the same place.
editor note: Still uncertain if this should include every organism of a species living in an area or any subset of them. For now make this a general term (unspecified) and then subclasses can be more specific.
definition source: ISBN:0878932739
Unique Apollo Label: Population
comment: It is sometimes difficult to define the physical boundaries of a population. In the case of sexually reproducing organisms, the individuals within a population have the potential to reproduce with one another during the course of their lifetimes. 'Community', as often used to describe a group of humans, is a type of population. Classes for population already exist in IDO ('organism population', IDO_0000509) and OBI ('population', OBI_0000181). The definitions should be standardized across ontologies and only one term used.

collection of organisms of the same species
type: Class
subclass of: PCO:collection of organisms
definition: A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.

effect size estimate
type: Class
subclass of: measurement datum
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
has curation status: ready for release
definition: effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: AGB,PRS
imported from: http://purl.obolibrary.org/obo/stato.owl
STATO alternative term: effect size

study group population size
type: Class
subclass of: count
has curation status: ready for release
definition: statistical sample size is a count evaluating the number of individual experimental units
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: AGB-PRS
imported from: http://purl.obolibrary.org/obo/stato.owl
STATO alternative term: statistical sample size
Unique Apollo Label: sampleSize

true negative rate
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
alternative label: specificity

true positive rate
type: Class
subclass of: measurement datum
has curation status: ready for release
definition: sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
alternative label: recall
alternative label: sensitivity
definition source: adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html

relative risk
type: Class
subclass of: effect size estimate
definition: Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
alternative label: risk ratio
definition source: ready for release
imported from: http://purl.obolibrary.org/obo/stato.owl

categorical variable
type: Class
subclass of: variable
has curation status: ready for release
definition: a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
alternative label: discrete variable
alternative label: nominal variable
alternative label: qualitative factor
definition source: http://udel.edu/~mcdonald/statvartypes.html
imported from: http://purl.obolibrary.org/obo/stato.owl
Unique Apollo Label: categoricalVariable
Source: https://onlinecourses.science.psu.edu/stat503/node/7

variable
type: Class
subclass of: data item
has curation status: ready for release
definition: a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: STATO
definition source: adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1
imported from: http://purl.obolibrary.org/obo/stato.owl
Unique Apollo Label: variable

non-parametric distribution
type: Class
subclass of: unconditional probability distribution
has curation status: metadata incomplete
definition: Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.
definition editor: Camille Maumet
definition editor: Karl Helmer
definition editor: Philippe Rocca-Serra
definition editor: Thomas Nichols
imported from: http://purl.obolibrary.org/obo/stato.owl
Unique Apollo Label: NonparametricProbabilityDistribution
comment: Initially discussed at https://github.com/incf-nidash/nidm/pull/191

weighted arithmetic mean
type: Class
subclass of: average value
has curation status: metadata incomplete
definition: The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value. The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others. The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes.
definition editor: Alejandra Gonzalez-Beltran
definition editor: Matthew Diller
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Weighted_arithmetic_mean
STATO_0000391: https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html np.average(range(1,11), weights=range(10,0,-1))
bug-database: https://github.com/ISA-tools/stato/issues/59

transmission process
type: Class
subclass of: process
definition: A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
editor note: Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species.
editor note: Suggested label: pathogen transmission process
imported from: trans.owl
imported from: Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: http://purl.obolibrary.org/obo/uberon.owl
RO_0002175: Viridiplantae
RO_0002175: Fungi
database_cross_reference: AAO:0010825
database_cross_reference: AEO:0000003
database_cross_reference: BILA:0000003
database_cross_reference: CARO:0000003
database_cross_reference: EHDAA2:0003003
database_cross_reference: EMAPA:0
database_cross_reference: FBbt:00007001
database_cross_reference: FMA:305751
database_cross_reference: FMA:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:A13
database_cross_reference: MESH:D000825
database_cross_reference: SCTID:362889002
database_cross_reference: TAO:0000037
database_cross_reference: TGMA:0001823
database_cross_reference: VHOG:0001759
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0003000
database_cross_reference: ZFA:0000037
database_cross_reference: http://dbpedia.org/ontology/AnatomicalStructure
has_exact_synonym: biological structure
has_exact_synonym: connected biological structure
has_obo_namespace: uberon
id: UBERON:0000061
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: CARO:0000003

Axiom
annotated source: anatomical structure
annotated property: has_exact_synonym
annotated target: connected biological structure
database_cross_reference: CARO:0000003

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
definition: Anatomical entity that has mass.
imported from: http://purl.obolibrary.org/obo/uberon.owl
RO_0002175: Viridiplantae
RO_0002175: Fungi
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FBbt:00007016
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: Anatomical entity that has mass.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

anatomical system
type: Class
subclass of: anatomical group
definition: Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia].
imported from: http://purl.obolibrary.org/obo/uberon.owl
external_definition: Anatomical group that has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[TAO]
external_definition: Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[AAO]
external_definition: Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity.[CARO]
has_broad_synonym: system
database_cross_reference: AAO:0000007
database_cross_reference: AEO:0000011
database_cross_reference: BILA:0000011
database_cross_reference: BSA:0000049
database_cross_reference: CALOHA:TS-2088
database_cross_reference: CARO:0000011
database_cross_reference: EHDAA2:0003011
database_cross_reference: EHDAA:392
database_cross_reference: EMAPA:16103
database_cross_reference: EV:0100000
database_cross_reference: FBbt:00004856
database_cross_reference: FMA:7149
database_cross_reference: HAO:0000011
database_cross_reference: MA:0000003
database_cross_reference: NIF_GrossAnatomy:birnlex_14
database_cross_reference: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
database_cross_reference: SCTID:278195005
database_cross_reference: TAO:0001439
database_cross_reference: TGMA:0001831
database_cross_reference: UMLS:C0460002
database_cross_reference: VHOG:0001725
database_cross_reference: WBbt:0005746
database_cross_reference: WBbt:0005763
database_cross_reference: Wikipedia:Organ_system
database_cross_reference: XAO:0003002
database_cross_reference: ZFA:0001439
database_cross_reference: galen:AnatomicalSystem
database_cross_reference: ncithesaurus:Organ_System
has_exact_synonym: body system
has_exact_synonym: organ system
has_obo_namespace: uberon
id: UBERON:0000467
in_subset: uberon slim
in_subset: upper level

tissue
type: Class
subclass of: multicellular anatomical structure
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: http://purl.obolibrary.org/obo/uberon.owl
database_cross_reference: AAO:0000607
database_cross_reference: AAO:0010054
database_cross_reference: AEO:0000043
database_cross_reference: BILA:0000043
database_cross_reference: CALOHA:TS-2090
database_cross_reference: CARO:0000043
database_cross_reference: EHDAA2:0003043
database_cross_reference: FBbt:00007003
database_cross_reference: FMA:9637
database_cross_reference: HAO:0000043
database_cross_reference: MA:0003002
database_cross_reference: MESH:A10
database_cross_reference: NIF_GrossAnatomy:birnlex_19
database_cross_reference: TAO:0001477
database_cross_reference: TGMA:0001844
database_cross_reference: UMLS:C0040300
database_cross_reference: VHOG:0001757
database_cross_reference: WBbt:0005729
database_cross_reference: XAO:0003040
database_cross_reference: ZFA:0001477
database_cross_reference: galen:Tissue
database_cross_reference: ncithesaurus:Tissue
has_exact_synonym: portion of tissue
has_exact_synonym: tissue portion
has_narrow_synonym: simple tissue
has_obo_namespace: uberon
id: UBERON:0000479
in_subset: upper level
comment: Editor note: changed label and definition to reflect CARO2

anatomical group
type: Class
subclass of: anatomical structure
definition: Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue.
imported from: http://purl.obolibrary.org/obo/uberon.owl
database_cross_reference: AAO:0010008
database_cross_reference: AEO:0000054
database_cross_reference: BILA:0000054
database_cross_reference: CARO:0000054
database_cross_reference: EHDAA2:0003054
database_cross_reference: HAO:0000054
database_cross_reference: TAO:0001512
database_cross_reference: TGMA:0001846
database_cross_reference: VHOG:0001724
database_cross_reference: XAO:0003001
database_cross_reference: ZFA:0001512
has_obo_namespace: uberon
id: UBERON:0000480
in_subset: upper level

anatomical entity
type: Class
subclass of: independent continuant
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
RO_0002175: Viridiplantae
RO_0002175: Fungi
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BFO:0000004
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
id: UBERON:0001062
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
database_cross_reference: FMA:62955
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: database_cross_reference
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

immune system
type: Class
subclass of: anatomical system
definition: Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
imported from: http://purl.obolibrary.org/obo/uberon.owl
homology_notes: The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
database_cross_reference: AAO:0011003
database_cross_reference: BILA:0000104
database_cross_reference: FMA:9825
database_cross_reference: GAID:328
database_cross_reference: MA:0002711
database_cross_reference: MESH:A15.382
database_cross_reference: OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA
database_cross_reference: SCTID:362590003
database_cross_reference: TAO:0001159
database_cross_reference: UMLS:C0020962
database_cross_reference: VHOG:0001247
database_cross_reference: Wikipedia:Immune_system
database_cross_reference: XAO:0003152
database_cross_reference: ZFA:0001159
database_cross_reference: ncithesaurus:Immune_System
has_obo_namespace: uberon
id: UBERON:0002405
in_subset: uberon slim
in_subset: vertebrate core
comment: This class was created automatically from a combination of ontologies

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
imported from: http://purl.obolibrary.org/obo/uberon.owl
RO_0002175: Viridiplantae
RO_0002175: Fungi
database_cross_reference: CARO:0010000
database_cross_reference: FBbt:00100313
has_exact_synonym: multicellular structure
has_obo_namespace: uberon
id: UBERON:0010000
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: multicellular anatomical structure
annotated property: definition
annotated target: An anatomical structure that has more than one cell as a part.
database_cross_reference: CARO:0010000

Axiom
annotated source: multicellular anatomical structure
annotated property: has_exact_synonym
annotated target: multicellular structure
database_cross_reference: FBbt:00100313

life cycle temporal boundary
type: Class
subclass of: process
definition: A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
imported from: http://purl.obolibrary.org/obo/uberon.owl
has_obo_namespace: uberon
id: UBERON:0035943
in_subset: upper level

life-death temporal boundary
type: Class
subclass of: life cycle temporal boundary
definition: A life cycle temporal boundary that marks the end of the life cycle of the organism.
imported from: uberon.owl
has_exact_synonym: end of life cycle
has_exact_synonym: moment of death
has_exact_synonym: time of death
has_obo_namespace: uberon
has_related_synonym: death
has_related_synonym: end of life
id: UBERON:0035944

unit
type: Class
subclass of: information content entity
imported from: http://purl.org/obo/owl/unit
has_obo_namespace: unit.ontology

length unit
type: Class
subclass of: measurement unit label
editor preferred term: length unit
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred term: mass unit
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred term: time unit
imported from: uo.owl
imported from: UO
Unique Apollo Label: unitOfTime

area unit
type: Class
subclass of: measurement unit label
definition: A unit which is a standard measure of the amount of a 2-dimensional flat surface.
imported from: http://purl.obolibrary.org/obo/uo.owl
created by: george gkoutos
has_obo_namespace: unit.ontology
id: UO:0000047
in_subset: unit group slim

dimensionless unit
type: Class
subclass of: measurement unit label
definition: A unit which is a standard measure of physical quantity consisting of only a numerical number without any units.
imported from: http://purl.org/obo/owl/unit
Unique Apollo Label: DimensionlessUnit
has_obo_namespace: unit.ontology
in_subset: unit group slim

percent
type: Class
subclass of: ratio
definition: A dimensionless ratio unit which denotes numbers as fractions of 100.
imported from: http://purl.org/obo/owl/unit
Unique Apollo Label: Percent
has_obo_namespace: unit.ontology
in_subset: unit slim

ratio
type: Class
subclass of: dimensionless unit
definition: A dimensionless unit which denotes an amount or magnitude of one quantity relative to another.
imported from: http://purl.org/obo/owl/unit
Unique Apollo Label: Ratio
has_obo_namespace: unit.ontology
in_subset: unit group slim

fraction
type: Class
subclass of: ratio
definition: A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator).
imported from: http://purl.org/obo/owl/unit
Unique Apollo Label: Fraction
has_obo_namespace: unit.ontology
in_subset: unit slim

rate unit
type: Class
subclass of: measurement unit label
definition: A unit which represents a standard measurement occurrence of a process per unit time.
imported from: http://purl.org/obo/owl/unit
Unique Apollo Label: Rate
has_obo_namespace: unit.ontology
in_subset: unit group slim

vaccine
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: vaccine preparation
  intersection of: Restriction
    on property: bearer of
    some values from: Class
      intersection of: vaccine function
      intersection of: Restriction
        on property: is realized by
        some values from: vaccination
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: vaccine preparation
subclass of: Restriction
  on property: bearer of
  some values from: Class
    intersection of: vaccine function
    intersection of: Restriction
      on property: is realized by
      some values from: vaccination
definition: A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
editor note: Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy.
definition editor: YH, BP, BS, MC, LC, XZ, RS
definition editor: a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo.
imported from: http://purl.obolibrary.org/obo/vo.owl
Unique Apollo Label: Vaccine
see also: MeSH: D014612

vaccine contraindication
type: Class
subclass of: contraindication
definition: A vaccine contraindication is a contraindication that increases the risks of a vaccination.
definition editor: YH
alternative label: contraindication for vaccination
imported from: http://purl.obolibrary.org/obo/vo.owl
Unique Apollo Label: VaccineContraindications

vaccine function
type: Class
subclass of: function
definition: vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host.
editor note: PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term.
definition editor: YH, MC, XZ, and AR
imported from: http://purl.obolibrary.org/obo/vo.owl

vaccine preparation
type: Class
subclass of: planned process
definition: vaccine preparation is a manufacturing process to produce a vaccine.
definition editor: YH, BP
alternative label: vaccine generation
alternative label: vaccine production
imported from: http://purl.obolibrary.org/obo/vo.owl

obsolete specificity of case detection
type: Class
definition: The specificity of a system that classifies organisms into the binary categories of individual who meets the criteria of a particular case definition and individual who does NOT meet the criteria of a particular type of disease X.
definition editor: William R. Hogan
elucidation: The specificity of a process or system that detects organisms who satisfy a case definition.
Unique Apollo Label: specificityOfCaseDetection
comment: deprecated due to malformed URI and created anew.
deprecated: true

obsolete specificity of treatment detection
type: Class
definition: the specificity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment
definition editor: William R. Hogan
elucidation: the specificity of the process or system that detects organisms that have undergone a particular treatment
Unique Apollo Label: specificityOfTreatmentDetection
comment: Deprecated due to malformed URI and created anew.
deprecated: true

obsolete sensitivity of treatment detection
type: Class
definition: the sensitivity of a system that classifies organisms into the binary categories of having received a particular treatment and not having received a particular treatment
definition editor: William R. Hogan
elucidation: the sensitivity of the process or system that detects organisms that have undergone a particular treatment
Unique Apollo Label: sensitivityOfTreatmentDetection
comment: Deprecated due to malformed URI and created anew.
deprecated: true

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

news article
type: Class
subclass of: document
imported from: http://purl.org/obo/owl/flybase_vocab
has_obo_namespace: pub_type
in_subset: camcur
comment: Originally imported into Apollo-SV for purpose of indexing in OBC.ide news articles relevant to infectious disease epidemiology.

genomic data
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: organism
definition: Genomic data is data about the genomes of an organism.
definition editor: James Malone

Obsolete Class
type: Class
imported from: http://www.geneontology.org/formats/oboInOwl
label: obsolete_class

organism population universal
type: NamedIndividual

atmosphere of the Earth
type: NamedIndividual
type: atmosphere

angular degree
type: NamedIndividual
type: plane angle measurement unit label
editor preferred term: angular degree
label: °

rad
type: NamedIndividual
type: plane angle measurement unit label
editor preferred term: radian
definition: A unit of measurement of planar angles where a full circle is 2π. Specifically the angle is the length of the arc subtended by the angle divided by the circumference of the circle.
definition editor: Josh Hanna
definition editor: William R. Hogan
comment: Technically in the S.I. system it is a derived unit m•m^-1.
label: radian

square mile
type: NamedIndividual
type: area unit
editor preferred term: square mile
comment: An area unit which is equal to the area enclosed by a square in a flat plane which is one mile on every side.

example to be eventually removed
type: NamedIndividual
type: curation status specification
editor preferred term: example to be eventually removed

failed exploratory term
type: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: 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: NamedIndividual
type: curation status specification
editor preferred term: 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: NamedIndividual
type: curation status specification
editor preferred term: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
editor preferred term: ready for release
has curation status: pending final vetting
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

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

pending final vetting
type: NamedIndividual
type: curation status specification
editor preferred term: 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.

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
label: obsolete_core
deprecated: true

placeholder removed
type: Thing
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor preferred term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: 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 term: requires discussion
has curation status: pending final vetting
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
definition editor: Alan Ruttenberg
definition source: group:OBI

out of scope
type: NamedIndividual
type: obsolescence reason specification
definition: The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
editor note: This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/77
ontology term requester: https://orcid.org/0000-0001-5208-3432

week
type: NamedIndividual
type: time unit
comment: "A time unit which is equal to 7 days." [Wikipedia:Wikipedia]

square meter
type: NamedIndividual
type: area unit
comment: "An area unit which is equal to an area enclosed by a square with sides each 1 meter long." [NIST:NIST]

axiom holds for all times
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: x
head: ClassAtom
  class predicate: Nothing
  argument1: y

Class
intersection of: one-dimensional temporal region
intersection of: Restriction
  on property: has temporal occupant
  qualified cardinality: 1
  on class: history