Apollo Structured Vocabulary (Apollo-SV)
type: Ontology
version IRI: apollo sv.owl
imports: classes-only.owl
imports: geo.owl
imports: pno.owl
imports: core.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
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: 2022-11-25

NLM ID
type: AnnotationProperty
alternative term: 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 label: linking ISSN
alternative term: 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 term: 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
textual definition: The date on which a URI annotated with this property was created.
term 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 label: author list
term 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 label: source code version control repository URL
term 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 label: human readable synopsis
textual definition: A comment that summarizes the most relevant or salient features and history of the entity for human readers.
term editor: William R. Hogan
sub property of: comment

BFO OWL specification label
type: AnnotationProperty

BFO CLIF specification label
type: AnnotationProperty

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.

editor preferred label
type: AnnotationProperty
has curation status: IAO_0000122
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
has curation status: IAO_0000122

has curation status
type: AnnotationProperty

textual definition
type: AnnotationProperty
has curation status: IAO_0000122
label: definition

editor note
type: AnnotationProperty
has curation status: IAO_0000122

term editor
type: AnnotationProperty
has curation status: IAO_0000122
label: definition editor

alternative term
type: AnnotationProperty
has curation status: IAO_0000125

definition source
type: AnnotationProperty
has curation status: IAO_0000122

has obsolescence reason
type: AnnotationProperty

curator note
type: AnnotationProperty
has curation status: IAO_0000122

imported from
type: AnnotationProperty
has curation status: IAO_0000125

expand expression to

OBO foundry unique label
type: AnnotationProperty
has curation status: IAO_0000125

elucidation
type: AnnotationProperty

has associated axiom(nl)
type: AnnotationProperty

has associated axiom(fol)
type: AnnotationProperty

ISA alternative term
type: AnnotationProperty

NIAID GSCID-BRC alternative term
type: AnnotationProperty

temporal interpretation

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

external_definition
type: AnnotationProperty

homology_notes
type: AnnotationProperty

Unique Apollo Label
type: AnnotationProperty
textual 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 term: UAL

has_rank
type: AnnotationProperty
textual 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

Creator
type: AnnotationProperty

Source
type: AnnotationProperty

dc:type

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

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

ontology version IUI
type: AnnotationProperty
editor preferred label: 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: NCBITaxon 9606
  union of: organization
range: Class
  union of: BFO_0000004
  union of: BFO_0000015
  union of: information content entity
textual 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: BFO_0000001
textual 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: BFO_0000001
textual 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
term editor: Mathias Brochhausen
deprecated: true

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

has basis in
type: ObjectProperty
domain: BFO_0000016
range: BFO_0000019
editor preferred label: has basis in quality
textual 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.

is realized by
type: ObjectProperty
sub property of: topObjectProperty
inverse of: realizes
domain: BFO_0000017
range: BFO_0000015
editor preferred label: obsolete_is_realized_by
has curation status: IAO_0000122
textual 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'
term editor: GROUP:OBI:<http://obi.sourceforge.net>
term editor: PERSON: Chris Mungall
alternative term: executed_during
alternative term: has_realization
alternative term: is_realized_as
alternative term: realized by
alternative term: realized_by
has obsolescence reason: IAO_0000228
imported from: http://purl.obolibrary.org/obo/obi.owl

realizes
type: ObjectProperty
editor preferred label: realizes

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

precedes
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: precedes
textual 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: ro-eco

occurs in
type: ObjectProperty
alternative term: occurs_in
imported from: http://purl.obolibrary.org/obo/ido.owl
imported from: http://purl.obolibrary.org/obo/obi.owl
has_obo_namespace: relationship
comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
label: unfolds_in

contains process
type: ObjectProperty
sub property of: topObjectProperty
BFO OWL specification label: contains-process
BFO CLIF specification label: containsProcess
textual 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

is aggregate of
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: is aggregate of
alternative term: aggregate of
alternative term: aggregate_of
imported from: http://purl.obolibrary.org/obo/obi.owl

exists at
type: ObjectProperty

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
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.
textual 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
BFO OWL specification label: o-has-ppart
BFO CLIF specification label: hasProperOccurrentPart
textual 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])
textual 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
textual 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])
textual 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

part of occurrent
type: ObjectProperty
sub property of: topObjectProperty
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.
textual 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 occurrent
type: ObjectProperty
sub property of: part of occurrent
BFO OWL specification label: o-ppart-of
BFO CLIF specification label: properOccurrentPartOf
textual definition: [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
textual 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
textual definition: b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
textual 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: BFO_0000003
range: BFO_0000008
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: BFO_0000008
range: BFO_0000003
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

specifically depends on at some time
type: ObjectProperty
domain: Class
  union of: BFO_0000015
  union of: BFO_0000020
range: Class
  union of: BFO_0000015
  union of: BFO_0000020
  union of: Class
    intersection of: BFO_0000004
    intersection of: Class
      complement of: BFO_0000006
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]

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: BFO_0000015
range: BFO_0000040

has history
type: ObjectProperty
domain: BFO_0000040
range: BFO_0000015

has measurement unit label
type: ObjectProperty
sub property of: BFO_0000051
type: FunctionalProperty
range: measurement unit label

is about
type: ObjectProperty
has curation status: IAO_0000125

is duration of
type: ObjectProperty
has curation status: IAO_0000120
textual definition: relates a process to a time-measurement-datum that represents the duration of the process
term editor: Person:Alan Ruttenberg

has time stamp
type: ObjectProperty
sub property of: BFO_0000051
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
has curation status: IAO_0000123
textual definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
term editor: Alan Ruttenberg

has measurement datum
type: ObjectProperty
sub property of: BFO_0000051
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
has curation status: IAO_0000123
textual definition: relates a time stamped measurement datum to the measurement datum that was measured
term editor: Alan Ruttenberg

IAO_0020012
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

IAO_0020018
type: ObjectProperty
sub property of: ObsoleteProperty
deprecated: true

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

achieves_planned_objective
type: ObjectProperty
sub property of: topObjectProperty
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
textual 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.
term 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

owns
type: ObjectProperty
sub property of: topObjectProperty
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.

is owned by
type: ObjectProperty
sub property of: topObjectProperty
textual 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.
imported from: http://purl.obolibrary.org/obo/omrse.owl

is enrolled in school
type: ObjectProperty
sub property of: topObjectProperty
imported from: http://purl.obolibrary.org/obo/omrse.owl

is admitted to hospital
type: ObjectProperty
sub property of: topObjectProperty
imported from: http://purl.obolibrary.org/obo/omrse.owl

is bearer of
type: ObjectProperty
sub property of: topObjectProperty
alternative term: bearer of
alternative term: bearer_of
imported from: http://purl.obolibrary.org/obo/omrse.owl

has_participant
type: ObjectProperty
editor preferred label: has_participant

RO_0000059
type: ObjectProperty
editor preferred label: is_concretization_of

immediately_preceded_by
type: ObjectProperty
sub property of: preceded by
textual definition: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
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

immediately_precedes
type: ObjectProperty
sub property of: precedes

ends during
type: ObjectProperty
sub property of: temporal relation
term editor: David Osumi-Sutherland
alternative term: o
alternative term: overlaps
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

spatially disjoint from
type: ObjectProperty
sub property of: topObjectProperty
has curation status: IAO_0000125
textual 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.
term 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: RO_0001901
in_subset: ro-eco

negatively regulates
type: ObjectProperty
sub property of: topObjectProperty
has curation status: IAO_0000125
textual definition: x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
term 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)

has active participant
type: ObjectProperty
sub property of: has_participant
example of usage: 'heart development' has active participant some Shh protein
has curation status: IAO_0000125
textual 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
term editor: Chris Mungall
alternative term: has agent
imported from: http://purl.obolibrary.org/obo/ro.owl
in_subset: ro-eco

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
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: IAO_0000125
textual 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
term editor: Chris Mungall
imported from: http://purl.obolibrary.org/obo/ro/releases/2019-02-02/ro.owl
temporal interpretation: RO_0001901

temporal relation
type: ObjectProperty
sub property of: topObjectProperty
domain: BFO_0000003
range: BFO_0000003
has curation status: IAO_0000125
editor note: move to BFO?
definition source: Allen
imported from: http://purl.obolibrary.org/obo/obi.owl
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 with
type: ObjectProperty
sub property of: temporal relation
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: IAO_0000125
textual 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.
alternative term: started by
imported from: http://purl.obolibrary.org/obo/obi.owl

ends
type: ObjectProperty
sub property of: temporal relation
has curation status: IAO_0000125
textual definition: inverse of ends with
Source: http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl

ends with
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
has curation status: IAO_0000125
textual 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.
alternative term: finished with
Source: http://purl.obolibrary.org/obo/ro/release/2013-04-28/ro.owl

colocalizes with
type: ObjectProperty
sub property of: topObjectProperty
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)
textual definition: a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
term 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

causally downstream of
type: ObjectProperty
sub property of: causal relation between processes
has curation status: IAO_0000428
textual definition: inverse of upstream of
term editor: Chris Mungall
imported from: http://purl.obolibrary.org/obo/ro.owl

causally upstream of
type: ObjectProperty
sub property of: causal relation between processes
has curation status: IAO_0000428
textual definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
term editor: Chris Mungall
imported from: http://purl.obolibrary.org/obo/ro.owl

causal relation between processes
type: ObjectProperty
sub property of: topObjectProperty
textual 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.
term 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

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
textual 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: BFO_0000031

has measurement value
type: DatatypeProperty
type: FunctionalProperty

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

purely intentional entity
type: Class
subclass of: BFO_0000031
textual 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
textual definition: A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic.
term 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: reproduction number
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
textual definition: The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population.
term 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
textual definition: A population survey that assesses the level of immunity against a particular pathogen in a specified population.
term 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
textual 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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: Class
      intersection of: Class
        union of: NCBITaxon 9606
        union of: organization
      intersection of: Restriction
        on property: commissions
        some values from: simulating of process of type X
subclass of: IAO_0020000
textual 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: IAO_0000594
textual 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: OBI_0000299
    some values from: software
subclass of: planned process
textual definition: A planned process resulting in a software product involving the creation of source code.
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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: Class
      intersection of: Class
        union of: NCBITaxon 9606
        union of: organization
      intersection of: Restriction
        on property: RO_0000056
        some values from: Class
subclass of: software developer identifier
textual 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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: simulation software application
subclass of: IAO_0020000
subclass of: Restriction
  on property: BFO_0000050
  some values from: complete simulator identifier
textual 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
subclass of: control strategy start time information
textual definition: A control strategy start time information item that is based on a condition that triggers the control strategy.
term 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: IAO_0000029
textual 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: IAO_0020000
subclass of: Restriction
  on property: BFO_0000050
  some values from: complete simulator identifier
textual 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: UO_0000003
textual 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: BFO_0000051
  some values from: simulation time step action specification
textual 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: BFO_0000038
    intersection of: Restriction
      on property: has temporal occupant
      some values from: infectious period
textual definition: A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts.
term 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: BFO_0000038
    intersection of: Restriction
      on property: has temporal occupant
      some values from: latent period
textual 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.
term 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: count
term editor: Mathias Brochhausen

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

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

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

count of simulated population
type: Class
subclass of: count
subclass of: Class
  intersection of: count
  intersection of: Restriction
    on property: is about
    some values from: simulated population
textual definition: The count of (simulated organisms) in a simulated population.
term 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
textual 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
textual 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
textual 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
textual 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: OBI_0000312
    some values from: facility survey
  intersection of: Restriction
    on property: OBI_0000312
    all values from: facility survey
subclass of: census
term 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: RO_0000059
      some values from: Class
        intersection of: plan specification
        intersection of: Restriction
subclass of: planned process
textual 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: RO_0002351
    all values from: Class
      intersection of: NCBITaxon 9606
      intersection of: Restriction
        on property: is 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
term 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: RO_0000056
    some values from: simulating of process of type X
subclass of: simulation
textual 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.
term 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
label: simulation of population

count
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: OBI_0000312
    some values from: counting
subclass of: measurement datum
textual definition: A measurement datum that is the output of counting.
term editor: Mathias Brochhausen
elucidation: A measurement datum that is the output of counting.
Unique Apollo Label: count

counting
type: Class
textual definition: The planned process of finding the number of elements in a finite set of objects.
term 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: RO_0000056
    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
textual 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
textual 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: IAO_0020000
textual definition: An identifier that refers to a geographical location to be used as location of a population in a simulation.
term 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
textual 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: RO_0000056
    some values from: simulating of process of type X
subclass of: simulation of organism
textual 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: BFO_0000051
  some values from: Class
    intersection of: IAO_0020000
    intersection of: Restriction
      on property: IAO_0000219
      some values from: disease
textual 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.
term editor: Mathias Brochhausen
elucidation: The disease being simulated.
Unique Apollo Label: disease

reproduction number
type: Class
subclass of: average value
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
textual definition: The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection.
term 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: RO_0002351
    all values from: Class
      intersection of: NCBITaxon 9606
      intersection of: Restriction
        on property: is 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
term editor: Mathias Brochhausen
comment: Key motivating use case was Synthia synthetic population data.

obsolete_asymptomatic infection fraction
type: Class
subclass of: Obsolete Class
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: epidemic model
subclass of: IAO_0020000
textual definition: An identifier that refers to a specific simulator.
term 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: simulating of process of type X
subclass of: Class
  intersection of: simulating of process of type X
  intersection of: Restriction
    on property: has_participant
    some values from: epidemic model
textual definition: A simulating of a disease epidemic or pandemic.
term 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
term 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: RO_0000056
      some values from: infectious disease control strategy execution
textual 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
textual 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
textual 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
textual 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: RO_0002351
    all values from: Class
      intersection of: NCBITaxon 9606
      intersection of: Restriction
        on property: is 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: RO_0000056
        some values from: infectious disease control strategy execution
  intersection of: Restriction
    on property: RO_0000056
    some values from: simulating of process of type X
subclass of: simulation of organism
textual 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
textual 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: IAO_0000029
  intersection of: Restriction
    on property: IAO_0000219
    some values from: simulating of process of type X
  intersection of: Restriction
    on property: OBI_0000312
    all values from: IAO_0020010
subclass of: IAO_0000029
textual 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: BFO_0000038
  intersection of: Restriction
    on property: RO_0000056
    all values from: simulating of process of type X
textual 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: BFO_0000050
    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: OBI_0001938
    some values from: OBI_0001931
textual definition: An action specification that specifies the length of the time steps interval assumed in a simulation.
term 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: IAO_0000029
  intersection of: Restriction
    on property: IAO_0000219
    some values from: simulation of time step
  intersection of: Restriction
    on property: OBI_0000312
    all values from: IAO_0020010
subclass of: IAO_0000029
textual 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: BFO_0000001
subclass of: purely intentional entity
textual 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
textual 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: is bearer of
        some values from: susceptibility
  intersection of: Restriction
    on property: RO_0000056
    some values from: simulating of process of type X
subclass of: simulation of organism
textual 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
textual 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: RO_0000056
    some values from: simulating of process of type X
subclass of: simulation of organism
textual 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
textual 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 in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation
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: BFO_0000050
  some values from: infectious disease control strategy
textual 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: BFO_0000051
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: Class
editor preferred label: age structure data set
textual 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: BFO_0000051
    some values from: infectious disease control objective specification
subclass of: plan specification
textual 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: count
textual 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: count
textual 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: RO_0002351
        all values from: Class
textual 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: OBI_0000471
  intersection of: Restriction
    on property: BFO_0000051
    some values from: vaccination
  intersection of: Restriction
    on property: OBI_0000299
    some values from: measured vaccination efficacy
subclass of: OBI_0000471
textual 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: RO_0002351
    some values from: population
  intersection of: Restriction
    on property: RO_0002351
    all values from: population
textual 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
subclass of: information content entity
elucidation: The increments of measurement for a measurable thing
deprecated: true

ecosystem
type: Class
subclass of: BFO_0000040
textual 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: count
textual 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: count
textual 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: BFO_0000040
textual 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
textual 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: IAO_0000055
subclass of: Restriction
  on property: BFO_0000050
  some values from: infectious disease control strategy
textual 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: BFO_0000040
textual 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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: Class
      intersection of: Class
        union of: NCBITaxon 9606
        union of: organization
      intersection of: Restriction
        on property: RO_0000056
        some values from: software development
subclass of: IAO_0020000
textual 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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    qualified cardinality: 1
    on class: IAO_0000594
subclass of: IAO_0020000
textual 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: BFO_0000024
textual 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: IAO_0020000
subclass of: Restriction
  on property: BFO_0000050
  some values from: complete software identifier
textual 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: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: software
subclass of: IAO_0020000
subclass of: Restriction
  on property: BFO_0000050
  some values from: complete software identifier
textual 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: GEO_000000371
  intersection of: Restriction
    on property: BFO_0000050
    has value: atmosphere of the Earth
subclass of: GEO_000000371

obsolete_educational institution
type: Class
subclass of: Obsolete Class
textual 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: BFO_0000050
      some values from: school closure control strategy
    intersection of: Restriction
      on property: BFO_0000050
      some values from: action specification
  intersection of: Restriction
    on property: is about
    some values from: school organization
textual 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: BFO_0000050
        some values from: organism
subclass of: reproduction
subclass of: Restriction
  on property: immediately_preceded_by
  some values from: infection acquisition
textual definition: A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon.
term editor: William R. Hogan
alternative term: infection process
alternative term: 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: is 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
        intersection of: Restriction
  intersection of: Restriction
    on property: causally upstream of
    some values from: infection
subclass of: entry into host
textual 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
term 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: IAO_0020000
subclass of: Restriction
  on property: IAO_0000219
  some values from: BFO_0000040
textual 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
      intersection of: Class
        complement of: Restriction
subclass of: BFO_0000015
term editor: Mathias Brochhausen

vaccination identifier
type: Class
subclass of: IAO_0020000
subclass of: Restriction
  on property: IAO_0000219
  some values from: directive information entity
textual 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: IAO_0020000
subclass of: Restriction
  on property: IAO_0000219
  some values from: BFO_0000040
textual 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
textual 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
subclass of: information content entity
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
textual 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: IAO_0000001
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
textual 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: RO_0002351
    all values from: Class
      intersection of: NCBITaxon 9606
      intersection of: Restriction
        on property: is 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
textual 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
textual 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
textual 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: RO_0000056
        some values from: infectious disease control strategy execution
textual 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
      intersection of: Restriction
        on property: is bearer of
        some values from: contagiousness
  intersection of: Restriction
    on property: immediately_preceded_by
    some values from: latent period
subclass of: BFO_0000015
term editor: Mathias Brochhausen

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

vaccination
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: RO_0000059
      some values from: Class
        intersection of: plan specification
        intersection of: Restriction
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: BFO_0000040
      intersection of: Restriction
        on property: is 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: is bearer of
        some values from: susceptibility
subclass of: treatment
textual 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.
term 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
subclass of: BFO_0000016
term 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: BFO_0000016
  intersection of: Class
    intersection of: Restriction
      on property: RO_0000052
      some values from: BFO_0000040
    intersection of: Restriction
      on property: is realized by
      all values from: contamination acquisition
subclass of: BFO_0000016
term editor: Mathias Brochhausen

resistance to infection
type: Class
subclass of: BFO_0000016
textual 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
term editor: Mathias Brochhausen @de
term 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
subclass of: action specification
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
subclass of: directive information entity
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
textual definition: Resistance to infection that is conferred by immune system/immune mechansisms.
term 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: BFO_0000051
    some values from: Class
      intersection of: counting
      intersection of: Restriction
        on property: OBI_0000299
        some values from: Class
subclass of: planned process
textual definition: A planned process involving counting numbers of a organism population, possibly including counting sub-populations fulfilling specific criteria.
term 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: OBI_0000312
    some values from: population survey
  intersection of: Restriction
    on property: OBI_0000312
    all values from: population survey
subclass of: census
textual 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: RO_0002351
    all values from: Class
      intersection of: host
      intersection of: Class
        complement of: Restriction
subclass of: host population
textual 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: BFO_0000051
    some values from: Class
      intersection of: counting
      intersection of: Restriction
        on property: OBI_0000299
        some values from: Class
      intersection of: Restriction
        on property: OBI_0000299
        some values from: Class
subclass of: population survey
textual definition: A population survey that counts the number of individuals in the population who are infected with a particular pathogen.
term 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
textual 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: OBI_0000312
      some values from: population immunity survey
    intersection of: Restriction
      on property: OBI_0000312
      some values from: population infection survey
  intersection of: Class
    intersection of: Restriction
      on property: OBI_0000312
      some values from: population immunity survey
    intersection of: Restriction
      on property: OBI_0000312
      all values from: population infection survey
subclass of: census
textual definition: A census that is the result of a population infection survey and a population immunity survey.
term editor: Mathias Brochhausen
alternative term: 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: OBI_0000312
    some values from: population demographic survey
  intersection of: Restriction
    on property: OBI_0000312
    all values from: population demographic survey
subclass of: census
textual definition: A census that is the specific outcome of a population demographic survey.
term editor: Mathias Brochhausen
elucidation: A census that is the specific outcome of a population demographic survey.

obsolete_contamination
type: Class
subclass of: Obsolete Class
term editor: Mathias Brochhausen
deprecated: true

MIDAS scenario
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: BFO_0000111
        some values from: Class
subclass of: information content entity
textual definition: An ecosystem in which a population of hosts is undergoing at least one infection.
term 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: BFO_0000111
        some values from: Class
subclass of: information content entity
textual definition: An information content entity that is about a MIDAS scenario and contains population disease census data.
term 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
term editor: A population of organisms that have been infected, but are no longer able to transmit the disease and to acquire the infection again.
term editor: Mathias Brochhausen

agent-level ecosystem data generation
type: Class
subclass of: dataset creating
editor preferred label: synthetic ecosystem constructing
textual definition: A planned process that has one or more synthetic ecosystem datasets as output.
term editor: Mathias Brochhausen
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: creating a synthetic ecosystem dataset
alternative term: 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: OBI_0000312
    some values from: Class
      intersection of: agent-level ecosystem data generation
      intersection of: Restriction
        on property: OBI_0000293
        some values from: population census
subclass of: census
textual definition: A census that is the specified output of a agent-level ecosystem data generation that had census data as an input.
term 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: BFO_0000004
  intersection of: Restriction
    on property: RO_0001015
    some values from: Class
      intersection of: pathogen
      intersection of: Class
        complement of: Restriction
subclass of: BFO_0000004
textual definition: An independent continuant that is the localization of a pathogen, but is not undergoing an infection.
term 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: OBI_0000293
    some values from: pathogen
  intersection of: Restriction
    on property: OBI_0000293
    some values from: Class
      union of: Class
        complement of: contaminated thing
      union of: Class
        complement of: pathogen
  intersection of: Restriction
    on property: OBI_0000299
    some values from: contaminated thing
subclass of: entry into host
textual 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.
term editor: Mathias Brochhausen
term 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
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
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
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: OBI_0000293
    some values from: antiviral drug
subclass of: drug treatment
textual 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: BFO_0000016
  intersection of: Restriction
    on property: is realized by
    all values from: infection acquisition
  intersection of: Restriction
    on property: RO_0000052
    all values from: Class
      intersection of: organism
      intersection of: Class
        complement of: host
subclass of: BFO_0000016
textual definition: The ability to participate in infection acquisition as a host.
term editor: Mathias Brochhausen
elucidation: The ability to participate in infection acquisition as a host.

census
type: Class
subclass of: data set
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: Class
textual definition: A data set of a specific entity in a specified region at a specified time.
term 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
textual 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
textual definition: An organization created with the purpose of providing education to those of its members that are bearer of student role.
term 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
term 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: RO_0002351
    all values from: Class
      intersection of: NCBITaxon 9606
      intersection of: Restriction
        on property: is 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
textual definition: The collection of students administrated by exaclty one school organization.
term 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: BFO_0000051
  some values from: Restriction
    on property: is about
    some values from: ecosystem
textual 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
textual definition: A human social role that is realized by attending a school to receive formal education.
term 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
textual definition: An anti-infective individual treatment control strategy that has as part an action specification that is realized in antiviral treatment.
term 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: BFO_0000016

simulator time specification
type: Class
subclass of: epidemic simulator action specification
subclass of: Class
  intersection of: Restriction
    on property: BFO_0000051
    some values from: simulation run length
  intersection of: Restriction
    on property: BFO_0000051
    some values from: simulation time step action specification
textual 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
textual 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.
term 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: IAO_0020000
textual 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: BFO_0000040
        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: BFO_0000040
subclass of: biological process
editor preferred label: biological contamination
textual 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.
term 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
textual 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
textual 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
textual 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
  intersection of: Restriction
    on property: is bearer of
    some values from: contagiousness
subclass of: host
textual 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
textual 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
subclass of: data item
textual 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
textual 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: BFO_0000051
    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
textual definition: An infectious disease control strategy that immediately targets individuals.
term editor: Mathias Brochhausen
elucidation: An infectious disease control strategy that immediately targets individuals.
Unique Apollo Label: IndividualTreatmentControlMeasure

target population
type: Class
subclass of: population
textual 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
subclass of: information content entity
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
subclass of: census
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
textual 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
textual 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: BFO_0000015
subclass of: Class
  union of: Restriction
    on property: BFO_0000050
    some values from: disease course
  union of: Restriction
    on property: immediately_preceded_by
    some values from: disease course
textual definition: A processual entity that is either the outcome of a disease course or a part of a disease course and has etiological relevance.
term 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: is bearer of
    some values from: susceptibility
subclass of: organism
textual definition: An organism that is the bearer of a susceptibility disposition.
term 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: is bearer of
    some values from: immune resistance to infection
subclass of: organism
textual definition: An organism that is the bearer of an immune resistance disposition.
term 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: is bearer of
    some values from: resistance to infection
subclass of: organism
textual definition: an organism that is the bearer of resistance to infection
term 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
textual 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
  intersection of: Class
    complement of: Restriction
      on property: RO_0000091
      some values from: contagiousness
subclass of: host
editor preferred label: organism in latent period of infection
textual definition: An infectious agent host who is NOT able to transmit the infection to another organism of the same species.
term 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
textual definition: A simulator configuration that start an Apollo simulator.
term editor: Mathias Brochhausen
elucidation: A simulator configuration that start an Apollo simulator.
Unique Apollo Label: RunSimulationMessage

transmission probability
type: Class
subclass of: probability
textual 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
textual 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
textual definition: A schedule that specifies the availability of a particular drug over a specific temporal interval in a specified geographical region.
term 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
textual definition: An information content entity that specifies the vaccination efficacy that is part of a simulator configuration.
term 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
textual 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
textual 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
textual 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.
term 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
textual definition: An objective specification that specifies the disease outcome a vaccination seeks to prevent.
term 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: IAO_0020000
textual definition: An information content entity that designates a biological taxon and optionally a clade of pathogens.
term 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: BFO_0000040
    intersection of: Class
      complement of: organism
  intersection of: Restriction
    on property: BFO_0000050
    some values from: abiotic ecosystem
subclass of: BFO_0000040
textual definition: A material entity that is part of an abiotic ecosystem.
term 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
textual definition: An immune population that acts as the members know they are immune (do not seek vaccination/antiviral treatment, etc.).
term 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
textual definition: An immune population that acts as the members assume they are not immune (e.g. seek vaccination/antiviral treatment).
term 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
textual definition: The process of an organism stopping to experience any symptoms caused by a disease.
term 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
textual definition: The process of an organism beginning to experience symptoms caused by a disease.
term 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
textual definition: The process of an organism beginning to experience severe symptoms caused by a disease.
term 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: BFO_0000144
textual definition: A process profile that specifies the degree to which a host is likely to pass on an infection to a susceptible organism.
term 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: BFO_0000016
textual 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.
term 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
textual definition: A travel-related infectious disease control strategy that has an action specification that is realized in restricting movement of organisms across international borders.
term 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
textual 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.
term 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
textual definition: an infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious.
term 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
textual definition: A travel-related infectious disease control strategy whose action specification is realized in restricting travel of organims from one ecosystem to another ecosystem
term 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
textual definition: A taxonomy identifier that denotes a group of organisms or groups of organisms based on common ancestors.
term 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: RO_0002351
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: contains process
        some values from: infection
subclass of: host population
textual 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: RO_0002351
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: is bearer of
        some values from: susceptibility
subclass of: host population
textual 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
textual 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

pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: is bearer of
    some values from: infectiousness
subclass of: organism
textual 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
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: contains process
    some values from: reproduction
subclass of: organism
textual 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: RO_0000052
    all values from: host
subclass of: disease
textual 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
textual definition: A information content entity that specifies the date of a census.
term 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: OBI_0001931
textual definition: An information content entity specifying the upper and lower limit of a range of ages of continuants.
term 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: BFO_0000051
  some values from: UO_0000003
textual definition: A name of temporal region that specifies a time span on a specified time scale by giving a start time and a duration.
term 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: BFO_0000038
    intersection of: Restriction
      on property: has temporal occupant
      some values from: BFO_0000015
textual definition: A measurement datum that quantifies a temporal region that is occupied by a processual entity.
term 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
textual definition: a unique identifier that refers to a disease.
term 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
textual definition: A probability distribution of two jointly distributed random variables X and Y, where Y is know to be a particular value.
term 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
textual 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.
term 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
textual 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.
term 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
subclass of: unconditional probability distribution
term editor: Mathias Brochhausen
Unique Apollo Label: ParametricProbabilityDistribution
deprecated: true

nonparametric probability distribution
type: Class
subclass of: unconditional probability distribution
term editor: Mathias Brochhausen
IAO_0100001: non-parametric distribution
Unique Apollo Label: NonparametricProbabilityDistribution
deprecated: true

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

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

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

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

log normal distribution
type: Class
subclass of: continuous parametric probability distribution
textual definition: A continuous parametric probability distribution that takes as its input a normally-distributed logarithmic function with mean μ and standard deviation σ.
term 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
textual definition: the gamma distribution is a two-parameter family of continuous probability distributions
term 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
textual 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."
term 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
textual 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.
term 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
textual definition: The duration between the appearance of symptoms of a disease and the start of a treatment.
term 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: IAO_0020000
textual 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
textual 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: IAO_0000055
textual 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
textual 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
textual 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: is 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: entry into host
textual definition: An infection acquisition whereby a susceptible host acquires an infection from a contaminated thing.
term 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: is bearer of
        some values from: susceptibility
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: host
      intersection of: Restriction
        on property: is bearer of
        some values from: contagiousness
  intersection of: Restriction
    on property: causally upstream of
    some values from: infection
subclass of: entry into host
textual definition: An infection acquisition whereby a susceptible host acquires an infection from an infectious host.
term 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: BFO_0000016
textual 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.
term 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
textual 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
term 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: IAO_0020000
textual definition: An identifier that designates a scale according to which time is measured (e.g., Gregorian Calendar).
term 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
textual definition: An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance.
term 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
textual definition: An infectious disease control trigger definition for a reactive control measure based on the outcome of disease surveillance.
term 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
textual 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
textual definition: the duration of time that has elapsed from the zero reference point to a later time on the time scale
term 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
textual 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
textual definition: The probability that entry is denied as part of a border control strategy.
term 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
textual definition: The probability that exit is denied as part of a border control strategy.
term 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: BFO_0000038
    intersection of: Restriction
      on property: has temporal occupant
      some values from: treatment
textual definition: A duration that measures the temporal interval occupied by a treatment course.
term 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
textual definition: The count of the number of doses that are part of a treatment course.
term 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
textual definition: An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a school.
term editor: Matthew Diller
term 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
textual definition: An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a household.
term editor: Matthew Diller
term 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
textual definition: An epidemic simulator action specification that specifies the factor by which to multiply the transmission coefficient for contacts that occur in a workplace.
term editor: Matthew Diller
term 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
textual 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
textual definition: The duration from the closure of a place until the time when it is reopened.
term 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
textual definition: An objective specification that specifies the disease outcome that a treatment seeks to prevent.
term 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
textual 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
term 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
textual definition: The unit of measure for the supply schedule of an individual treatment.
term 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
term 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
term 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
textual definition: A unit of measure for a threshold in a reactive infectious disease control strategy.
term 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
textual definition: An information content entity that specifies the criteria that an organism must meet to be considered to be in some abnormal state.
term 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
subclass of: duration
term 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
subclass of: Class
  intersection of: Restriction
    on property: has proper occurrent part
    some values from: infection
  intersection of: Restriction
    on property: has proper occurrent part
    some values from: infection acquisition
textual 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.
term editor: William R. Hogan
alternative term: 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
textual definition: An immune organism that acts as if it is immune (i.e., it does not seek vaccination or avoid contact with infectious organisms).
term 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
textual definition: An immune organism that acts as if it is NOT immune (i.e., it seeks vaccination and/or avoids contact with infectious organisms).
term 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
textual 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.
term 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: is bearer of
    some values from: naturally-acquired active immune resistance
subclass of: organism
textual definition: An organism that is the bearer of a naturally-acquired, active immune resistance to infection.
term 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
textual definition: An individual treatment control strategy that has as part an action specification that is realized in anti-infective treatment.
term 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
textual definition: An anti-infective individual treatment control strategy that has as part an action specification that is realized in antibacterial treatment.
term 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: BFO_0000015
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 label: infection in an ecosystem
textual definition: A process comprised of numerous infections and infection acquisitions with a particular pathogen in one or more populations of hosts.
term 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: BFO_0000051
    some values from: vector control action specification
subclass of: infectious disease control strategy
textual definition: An infectious disease control strategy that has a vector control action specification as part.
term 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: BFO_0000051
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: Class
subclass of: census
textual definition: A census of entities of a certain type or types in the abiotic ecosystem.
term 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
textual 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".
term 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
textual 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.
term 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: multicellular organism reproduction
  intersection of: Restriction
    on property: has active participant
    some values from: Culicidae
subclass of: multicellular organism reproduction
textual definition: A multicellular organism reproduction that has as its agent a mosquito (taxon Culicidae, ID 7157)
term 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: BFO_0000038
    intersection of: Restriction
      on property: has temporal occupant
      some values from: gonotrophic cycle
subclass of: duration
textual definition: The duration of the temporal interval occupied by a gonotropic period.
term editor: Matthew Diller
term 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
textual definition: The process in a female mosquito of taking a blood meal, developing eggs, and laying the eggs (oviposition).
term 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
textual definition: An abiotic ecosystem census of the locations where pregnant female mosquitos lay their eggs.
term 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
subclass of: average value
term 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: BFO_0000015
subclass of: Restriction
  on property: temporal part of
  some values from: Class
    intersection of: BFO_0000015
    intersection of: Restriction
      on property: realizes
      some values from: infectious disease
textual 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.
term 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: OBI_0000293
    some values from: drug product
subclass of: treatment
textual definition: A treatment with a drug product.
term 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
textual definition: An infectious disease control strategy whereby the household members of infectious indivduals voluntarily stay at home to avoid further potentially infectious contacts.
term 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
textual 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.
term 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 label: epidemic investigation study design
term 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 label: quarantine control strategy
term 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
textual 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.
term editor: Matthew Diller
term 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: BFO_0000050
        some values from: organism
subclass of: reproduction
editor preferred label: biological colonization
textual 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.
term 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 label: infection in a population
textual definition: an infection in an ecosystem occurring in one population of organisms
term 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 label: colonization acquisition
textual 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
term 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 label: decolonization control strategy
textual 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
term 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
editor preferred label: establishment of infection from self colonization
textual 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.
term 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: resistance to infection
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 label: chemical resistance to infection
textual 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.
term editor: William R. Hogan
alternative term: chemoprotection
alternative term: chemoprotective resistance
alternative term: 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
equivalent class: Class
  intersection of: resistance to infection
  intersection of: Restriction
    on property: RO_0000052
    some values from: organism
  intersection of: Restriction
    on property: negatively regulates
    some values from: Class
      intersection of: Class
        union of: infection
        union of: infection acquisition
      intersection of: Restriction
        on property: has_participant
        some values from: Class
subclass of: resistance to infection
editor preferred label: resistance to malaria infection
textual definition: A resistance to infection by P. vivax, P. ovale, P. malariae, and/or P. falciparum.
term editor: William R. Hogan
alternative term: malaria resistance
alternative term: 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
textual definition: A symbiosis where the organisms that are interacting remain physically external to one another.
term editor: Matthew Diller
term 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
equivalent class: Class
  intersection of: symbiosis
  intersection of: Class
    intersection of: Restriction
      on property: has occurrent part
      some values from: bodily harm
    intersection of: Restriction
      on property: has_participant
      min qualified cardinality: 2
      on class: organism
subclass of: ectosymbiosis
textual definition: An ectosymbiosis that results in harm to all participating organisms.
term editor: Matthew Diller
term 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: RO_0000056
        some values from: bodily harm
subclass of: ectosymbiosis
textual definition: An ectosymbiosis that results in harm to one of the participating organisms but neither harms nor benefits the other participating organisms.
term editor: Matthew Diller
term 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: RO_0000056
        some values from: bodily harm
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: RO_0000056
        some values from: bodily benefit
subclass of: ectosymbiosis
textual definition: An ectosymbiosis that results in harm to one of the participating organisms and benefit to another participating organism.
term editor: Matthew Diller
term 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
equivalent class: Class
  intersection of: agonism
  intersection of: Restriction
    on property: has_participant
    min qualified cardinality: 2
    on class: Class
      intersection of: organism
      intersection of: Restriction
        on property: adjacent to
        some values from: organism
equivalent class: Class
  intersection of: intimate agonism
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: bodily harm
      intersection of: Restriction
        on property: BFO_0000051
        some values from: life-death temporal boundary
subclass of: agonism
textual 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.
term editor: Matthew Diller
term 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: BFO_0000051
    some values from: Class
      intersection of: bodily harm
      intersection of: Class
        complement of: Restriction
subclass of: intimate agonism
textual definition: An intimate agonism in which the harm is not fatal to the host.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0000052
        some values from: organism
subclass of: ectosymbiotic parasitism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic parasitism
textual definition: An ectosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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
equivalent class: Class
  intersection of: ectosymbiotic 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: RO_0000052
        some values from: organism
subclass of: intimate agonism
textual definition: An intimate agonism in which the harm is fatal to the host.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: ectoparasitoidism
elucidation: An intimate agonism in which the harm is fatal to the host.

facultative ectosymbiotic parasitoidism
type: Class
equivalent class: Class
  intersection of: ectosymbiotic 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: RO_0000052
        some values from: organism
subclass of: ectosymbiotic parasitoidism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic parasitoidism
textual definition: An ectosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000051
    some values from: bodily benefit
subclass of: ectosymbiosis
textual definition: An ectosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0000052
        some values from: organism
subclass of: ectosymbiotic commensalism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic commensalism
textual definition: An ectosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000051
    some values from: bodily benefit
  intersection of: Restriction
    on property: BFO_0000051
    all values from: bodily benefit
subclass of: ectosymbiosis
textual definition: An ectosymbiosis that results in benefit to all participating organisms.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0000052
        some values from: organism
subclass of: ectosymbiotic mutualism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: ectosymbiotic mutualism
textual definition: An ectosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0001025
        some values from: organism
subclass of: symbiosis
textual definition: A symbiosis where one organism is physically contained within another organism (called the 'host').
term editor: Matthew Diller
term 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: BFO_0000051
    some values from: Class
      intersection of: bodily harm
      intersection of: Class
        complement of: Restriction
subclass of: endosymbiosis
textual definition: An endosymbiosis that results in benefit to the parasite and harm to the host.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: endoparasitism
elucidation: An endosymbiosis that results in benefit to the parasite and harm to the host.

transient agonism
type: Class
equivalent class: Class
  intersection of: agonism
  intersection of: Restriction
    on property: has_participant
    min qualified cardinality: 2
    on class: Class
      intersection of: organism
      intersection of: Restriction
        on property: colocalizes with
        some values from: organism
subclass of: agonism
textual definition: An agonism where the participating organisms maintain significant physical separation from one another through most or all of the interaction.
term editor: Matthew Diller
term 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: BFO_0000051
    some values from: Class
      intersection of: bodily harm
      intersection of: Restriction
        on property: BFO_0000051
        some values from: Class
subclass of: transient agonism
textual definition: A non-intimate agonism in which the harm is fatal.
term editor: Matthew Diller
term 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: BFO_0000051
    some values from: Class
      intersection of: bodily harm
      intersection of: Class
        complement of: Restriction
subclass of: transient agonism
textual definition: A non-intimate agonism in which the harm is not fatal.
term editor: Matthew Diller
term 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: RO_0000052
        some values from: organism
subclass of: endosymbiotic parasitism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic parasitism
textual definition: An endosymbiotic parasitism that realizes a biological function that inheres in some proper part of the parasite.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000051
    some values from: Class
      intersection of: bodily harm
      intersection of: Restriction
        on property: BFO_0000051
        some values from: life-death temporal boundary
subclass of: endosymbiosis
textual definition: An endosymbiosis that results in benefit to the parasitoid and is fatal to the host.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0000052
        some values from: organism
subclass of: endosymbiotic parasitoidism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic parasitoidism
textual definition: An endosymbiotic parasitoidism that realizes a biological function that inheres in some proper part of the parasitoid.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000051
    some values from: bodily benefit
subclass of: endosymbiosis
textual definition: An endosymbiosis that results in benefit to one participating organism and neither harm nor benefit to the other participating organisms.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0000052
        some values from: organism
subclass of: endosymbiotic commensalism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic commensalism
textual definition: An endosymbiotic commensalism that realizes a biological function that inheres in some proper part of the commensal organism that benefits.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000051
    some values from: bodily benefit
  intersection of: Restriction
    on property: BFO_0000051
    all values from: bodily benefit
subclass of: endosymbiosis
textual definition: An endosymbiosis that results in benefit to all participating organisms.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: RO_0000052
        some values from: organism
subclass of: endosymbiotic mutualism
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: BFO_0000034
      intersection of: Class
        intersection of: Restriction
subclass of: endosymbiotic mutualism
textual definition: An endosymbiotic mutualism that realizes a biological function that inheres in some proper part of at least one of the organisms participating.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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
subclass of: BFO_0000016
textual 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.
term editor: Matthew Diller
term 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: BFO_0000015
textual definition: A process that has as output a material entity that is the material basis for an abnormal homeostasis dispostion.
term editor: Matthew Diller
term 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: BFO_0000015
textual 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.
term editor: Matthew Diller
term 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
textual definition: An organism participating in an ectosymbiotic or endosymbiotic parasitism as the organism that benefits.
term editor: Matthew Diller
term 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
textual definition: An organism participating in an ectosymbiotic or endosymbiotic parasitoidism as the organism that benefits.
term editor: Matthew Diller
term 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
textual 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
textual definition: A name of temporal region that designates a temporal boundary
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A contraindication that increases the risk of a treatment.
term editor: Matthew Diller
term 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
textual definition: A duration that is specified as a probability distribution over a range of numbers.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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 label: specificity of case detection
textual 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.
term 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
textual 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.
term 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
textual 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.
term 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
textual 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
textual definition: 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.
term editor: Matthew Diller
term 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.

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

census taking
type: Class
subclass of: planned process
textual definition: A planned process that realizes a census plan specification.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A vector control strategy that is realized by spraying chemicals in a place to kill individuals of the vector population.
term editor: Matthew Diller
term 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
textual definition: A vector control strategy for mosquitoes that is realized by reducing the number of water-containing vessels in which mosquitoes can lay eggs.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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: BFO_0000016
textual definition: A disposition of a treatment surveillance infrastructure to detect individuals who have received treatment in the geographical region the infrastructure aims to cover.
term editor: Matthew Diller
term 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: IAO_0020000

population serology survey
type: Class
subclass of: population survey
textual definition: A population survey that assesses the presence (plus or minus quantity) of antibody to a particular antigen in individuals in a population.
term editor: Matthew Diller
term 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
textual definition: A data set that is a collection of case records.
term editor: Matthew Diller
term 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: RO_0000056
      some values from: infection
subclass of: data set
textual 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.
term editor: Matthew Diller
term 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
subclass of: data item
textual definition: A count of individuals in a population who meet an infection case definition during a particular time interval.
term editor: Matthew Diller
term 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: BFO_0000038
textual definition: The temporal interval occupied by an epidemic.
term editor: Matthew Diller
alternative term: epidemic period
elucidation: The temporal interval occupied by an epidemic.
Unique Apollo Label: EpidemicPeriod

individual mosquito behavior
type: Class
subclass of: behavior
textual definition: An individual behavior of a mosquito (organism of family Culicidae).
term editor: Matthew Diller
term 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
textual definition: An individual behavior of a human being.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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: BFO_0000016
  intersection of: Restriction
    on property: RO_0000052
    some values from: organism
  intersection of: Restriction
    on property: is realized by
    all values from: infection
subclass of: BFO_0000016
editor preferred label: infectious disposition
textual 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.
term 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 label: potentially infectious contact process
textual 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.
term editor: William R. Hogan
alternative term: 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: BFO_0000023
  intersection of: Restriction
    on property: is realized by
    some values from: potentially infectious contacting
subclass of: BFO_0000023
editor preferred label: potentially infectous contact role
textual definition: A role borne by an organism that is realized in a potentially infectious contact process.
term editor: William R. Hogan
alternative term: contact role
alternative term: 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: is bearer of
    some values from: potentially infectious contact role
subclass of: organism
editor preferred label: potentially infectious contact organism
textual definition: An organism that is the bearer of a potentially infectious contact role during a potentially infectious contact process.
term 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 label: potentially infectious contact definition
textual 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.
term 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
textual definition: An individual treatment control strategy that immediately targets individuals in the population who are at the perimeter of an epidemic.
term editor: Matthew Diller
term 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
textual definition: A seed site for a Wolbachia control measure.
term editor: Matthew Diller
term 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
textual definition: A vector release site action specification for a Wolbachia control measure.
term editor: Matthew Diller
term 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
textual definition: The rate at which offspring of the Wolbachia-infected female mosquito subpopulation (of the overall mosquito population) are not infected with Wolbachia.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A vector control strategy that is realized by reducing the number of adults in a vector population.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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: interaction with host
textual 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.
term editor: Matthew Diller
term 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: interaction with host
textual 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.
term editor: Matthew Diller
term 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: interaction with host
textual 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.
term editor: Matthew Diller
term 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: interaction with host
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

Wolbachia release interval
type: Class
subclass of: seed release interval
textual definition: A seed release interval for a Wolbachia control measure.
term editor: Matthew Diller
term 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
textual definition: A data structure that specifies both the sample mean and the confidence interval generated by the measurement process.
term editor: Matthew Diller
term editor: William R. Hogan
Unique Apollo Label: MeanWithConfidenceInterval

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

number of Wolbachia-infected mosquitoes released per house
type: Class
subclass of: vector control action specification
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A predicted data item expressing the probability that a disease outcome occurs during the disease course of an organism.
term editor: Matthew Diller
term 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
textual definition: A name of a temporal region that is systematized according to a particular calendar system, such as the Gregorian calendar.
term editor: Matthew Diller
term 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: OBI_0001931
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A data item that specifies the smallest numerical value in a data set of scalar measurement data items.
term editor: Matthew Diller
term 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
textual definition: A data item that specifies the largest numerical value in a data set of scalar measurement data itmes.
term editor: Matthew Diller
term 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
textual definition: A predicted data item that estimates how reliable some method of statistical inference will be at estimating the population parameter of interest.
term editor: Matthew Diller
term 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
subclass of: BFO_0000038
textual definition: A one-dimensional temporal region occupied by a place closure control strategy.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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).
term editor: Matthew Diller
term 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: IAO_0000408
textual 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.
term editor: Matthew Diller
term 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
textual definition: A duration that measures the temporal interval between some vector bite n and some vector bite n+1.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A rate measurement datum that specifies the percentage of organisms within a population that have died over a given time interval.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: An average value that specifies the number of eggs produced during one reproductive cycle for each individual female within a population.
term editor: Matthew Diller
term 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: BFO_0000016
textual definition: A disposition of an organism to (i) undergo some bodily benefit that (ii) is triggered by a planned process.
term editor: Matthew Diller
term 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: BFO_0000015
textual 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.
term editor: Matthew Diller
term 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: BFO_0000015
textual 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.
term editor: Matthew Diller
term 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
textual 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).
term editor: Matthew Diller
term 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: IAO_0000408
textual 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.
term editor: Matthew Diller
term 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: IAO_0000408
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that denotes a drug product.
term editor: Matthew Diller
term 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
textual definition: A data structure that holds the mean, median, minimum value, and maximum value of one set of measurement data.
term editor: Matthew Diller
term 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: IAO_0000001
textual 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.
term editor: Matthew Diller
term 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: BFO_0000029
textual 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.
term editor: Matthew Diller
term 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
textual definition: A vector control action specification that is realized by releasing artificially-infected vector organisms at the specified time intervals.
term editor: Matthew Diller
term 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
textual definition: A vector control action specification that specifies the location of vector release sites according to some predetermined spatial interval.
term editor: Matthew Diller
term 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
textual definition: A vector control action specification that specifies the number of artificially-infected vectors to be released at each household.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier curated by IHTSDO that refers to some representational unit within its class hierarchy.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: An epidemic simulator action specification that specifies the minimum number of eggs that any simulated female mosquito will oviposit during a gonotrophic cycle.
term editor: Matthew Diller
term 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
textual 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).
term editor: Matthew Diller
term 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
textual definition: An epidemic simulator action specification that specifies the maximum number of larvae that can exist across all ovisites in a given house.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
subclass of: time measurement datum
textual definition: A time measurement datum of the length of the temporal interval occupied by a gonotropic period.
term editor: Matthew Diller
term 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: IAO_0000300
textual definition: A textual entity that specifies characteristics of some entity.
term editor: Matthew Diller
term 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
textual 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).
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining.
term editor: Matthew Diller
term editor: William R. Hogan
elucidation: A predicted data item that is the maximum value of larvae that some ovisite is capable of sustaining.

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

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

identifier of species of diseased organism
type: Class
subclass of: taxonomy identifier
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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 label: infectious disease control strategy to prevent infection acquisition by individuals traveling from one ecosystem to another ecosystem
textual definition: An infectious disease control strategy that has an objective specification of preventing infection acquisition by organisms traveling from one ecosystem to another ecosystem.
term 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 label: travel recommendation infectious disease control strategy
textual 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
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A duration that measures the temporal interval occupied by some colonization.
term editor: Matthew Diller
term 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
textual definition: A taxonomy identifier curated by the National Center for Biotechnology Information that specifies the taxonomic classification of some population of organisms.
term editor: Matthew Diller
term 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: IAO_0020000
textual 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.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier curated by the Regenstrief Institute to be used as a standard way of denoting each term in the LOINC database.
term editor: Matthew Diller
term 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
textual definition: A LOINC identifier that refers to some clinical laboratory test conducted in a particular context..
term editor: Matthew Diller
term 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: IAO_0020000
textual 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.
term editor: Matthew Diller
term 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
subclass of: IAO_0020000
textual definition: An identifier curated by ORCID, Inc. to denote some academic author.
term editor: Matthew Diller
term editor: William R. Hogan
elucidation: An identifier curated by ORCID, Inc. to denote some academic author.
IAO_0100001: http://purl.obolibrary.org/obo/IAO_0000708
Unique Apollo Label: orcId
deprecated: true

count of disease cases
type: Class
subclass of: count
textual definition: A count of individuals in a population who meet the criteria of some case definition during some time interval.
term editor: Matthew Diller
term 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
textual definition: A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A population census about the organisms specific to that population that were the host in some colonization acquisition.
term editor: Matthew Diller
term 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
textual definition: The efficacy measured for some instance(s) of drug treatment for preventing or ameliorating some disease outcome.
term editor: Matthew Diller
term 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: GEO_000000788
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A duration that measures a temporal region occupied by some contamination.
term editor: Matthew Diller
term 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
textual definition: A healthcare facility identifier that refers to some architectural structure that is the bearer of some healthcare function.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that refers to some disease transmission model model.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that denotes some architectural structure.
term editor: Matthew Diller
term editor: William R. Hogan
elucidation: An identifier that denotes some architectural structure.
Unique Apollo Label: FacilityId

taxonomy identifier
type: Class
subclass of: IAO_0020000
textual definition: An identifier that denotes a biological taxonomic group.
term editor: Matthew Diller
term editor: William R. Hogan
Unique Apollo Label: taxonId

disease case identifier
type: Class
subclass of: IAO_0020000
textual definition: An identifier that denotes an organism included in some infection case count.
term editor: Matthew Diller
term 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
textual definition: An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting
term 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
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

mean rate of hydrological precipitation
type: Class
subclass of: average value
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

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

potentially infectious sexual contacting
type: Class
subclass of: sexual activity
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

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

prioritization scheme for control measure
type: Class
subclass of: action specification
textual definition: An action specification that is part of an infectious disease control strategy that has at least one rule pertaining to some control measure.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that is an integer numeral that denotes some citation.
term editor: Matthew Diller
term 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: GEO_000000372
textual definition: A geographic region that contains a sampling process.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: congenital infection acquisition
alternative term: 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
editor preferred label: software source code version control repository
textual definition: A data set that comprises at least one set of source code files for software as well as provenance information about who contributed the set of files, and optionally multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc.
term 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: planned process
editor preferred label: process of compiling software
textual definition: A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions.
term 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 label: machine instructions compiled from software source code
textual definition: A software that is the specified output of some compilation of software process
term editor: William R. Hogan

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

scale-free network
type: Class
subclass of: graph of vertices
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A probability whose value is dependent upon the occurrence, known or presumed, of some process.
term editor: Matthew Diller
term 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
textual definition: A conditional probability whose value is dependent upon the duration of some colonization or infection.
term editor: Matthew Diller
term 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
textual definition: A data item that specifies the number of susceptible organisms necessary for an epidemic to occur within a population.
term editor: Matthew Diller
term editor: William R. Hogan

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

human air travel
type: Class
subclass of: human travel
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

human mobility data item
type: Class
subclass of: data item
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

software license
type: Class
subclass of: copyright license
textual 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.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that refers to a specific software license.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that, as part of a complete software license identifier, refers to one specific version of the software license.
term editor: Matthew Diller
term 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: IAO_0020000
textual definition: An identifier that refers to all versions of a specific software license.
term editor: Matthew Diller
term 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
textual definition: A unique resource locator that constitutes a reference to some software license.
term editor: Matthew Diller
term 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 label: model of population dynamics software application
textual 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.
term editor: Matthew Diller
term 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 label: disease surveillance objective specification
textual 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.
term editor: Matthew Diller
term 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 label: population mortality data set
textual 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.
term editor: Matthew Diller
term 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 label: pathogen evolution model software application
textual definition: A simulation software application that simulates the evolution over time of a particular pathogen of a particular biological taxon.
term editor: Matthew Diller
term 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
textual definition: A planned process that is the realization of a disease surveillance objective specification.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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).
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: An infectious disease control strategy that identifies and treats contacted organisms in a host population.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: A Susceptible-Infected-Resistant model that represents exactly two infections in ecosystem by exactly two pathogens.
term editor: Matthew Diller
term 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: OBI_0000312
  some values from: disease surveillance
textual definition: A data set that is about some disease surveillance.
term editor: Matthew Diller
term editor: William R. Hogan
elucidation: A data set that is about some disease surveillance.

disease transmission tree estimator
type: Class
subclass of: IAO_0000594
editor preferred label: disease transmission tree estimator software application
textual definition: A software application that implements an algorithm that has specified output some transmission tree.
term editor: Matthew Diller
term editor: William R. Hogan
elucidation: An algorithm that has specified output some transmission tree.

mechanical flight function
type: Class
subclass of: BFO_0000034
textual definition: A function inhering in some device that is realized by some movement process in the atmosphere in which the device is participant in.
term editor: Matthew Diller
term 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 label: software application that forecasts disease transmission
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: disease forecasting software
label: infectious disease forecasting software application

case series
type: Class
equivalent class: Class
  intersection of: OBI_0000066
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: RO_0000059
      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: OBI_0000293
        some values from: case definition
subclass of: OBI_0000066
textual 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.
term editor: Matthew Diller
term 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: OBI_0000312
  some values from: case series
textual definition: A data set that is the output of a case series investigation.
term editor: Matthew Diller
term 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
textual definition: A data set about an instance of an epidemic.
term editor: Matthew Diller
term 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 label: disease transmission model software application
term editor: Matthew Diller
term editor: William R. Hogan

data format converter
type: Class
subclass of: IAO_0000594
editor preferred label: data format converter software application
term editor: Matthew Diller
term editor: William R. Hogan

phylogenetic tree constructor
type: Class
subclass of: IAO_0000594
editor preferred label: phylogenetic tree constructor software application
textual definition: A software application that implements an algorithm that has specified output a phylogenetic tree
term editor: William R. Hogan

data visualizer
type: Class
subclass of: IAO_0000594
editor preferred label: data visualizer software application
textual definition: A software application that implements an algorithm that has some data visualizer software objective specification as part.
term editor: Matthew Diller
term editor: William R. Hogan

computational modeling toolkit
type: Class
subclass of: IAO_0000594
editor preferred label: computational modeling toolkit software application
term editor: Matthew Diller
term editor: William R. Hogan

data parsing
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: OBI_0000293
  some values from: data set
editor preferred label: data parsing process
textual 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.
term editor: William R. Hogan
alternative term: data reading process
alternative term: reading data

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

total fatal disease cases
type: Class
subclass of: data item
textual 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.
term editor: Matthew Diller
term 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: count
  intersection of: Restriction
    on property: is about
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: is bearer of
        some values from: disease
  intersection of: Restriction
    on property: OBI_0000312
    some values from: population infection survey
subclass of: count
textual definition: A count of the total number of diseased indivduals in a population during a particular time interval.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual definition: An abiotic ecosystem element that is participant in some biological contamination process.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term 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
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: influenza-like illness

epidemic start week
type: Class
subclass of: OBI_0001931
textual 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.
term editor: Amanda Hicks
term editor: Matthew Diller
term editor: William R. Hogan

epidemic peak week
type: Class
subclass of: OBI_0001931
textual definition: A scalar value specification whose measurement unit label is 'week', and that is part of the epidemic peak intensity.
term editor: Amanda Hicks
term editor: Matthew Diller
term editor: William R. Hogan

epidemic peak intensity
type: Class
subclass of: calculated datum
textual 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.
term editor: Amanda Hicks
term editor: Matthew Diller
term editor: William R. Hogan

aggregate of disease courses
type: Class
subclass of: BFO_0000015
textual 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.
term editor: Amanda Hicks
term editor: Matthew Diller
term editor: William R. Hogan

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

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

infectious disease forecast objective specification
type: Class
subclass of: objective specification
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

infectious disease nowcast objective specification
type: Class
subclass of: infectious disease forecast objective specification
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

infectious disease nowcaster
type: Class
subclass of: infectious disease forecaster
editor preferred label: infectious disease nowcasting software application
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

prospective infectious disease forecast
type: Class
subclass of: infectious disease forecast
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

prospective infectious disease nowcast
type: Class
subclass of: infectious disease nowcast
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

infectious disease forecast time specification
type: Class
subclass of: action specification
textual 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.
term editor: Matthew Diller
term editor: William R. Hogan

intensive care unit encounter
type: Class
subclass of: inpatient encounter
textual 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
textual definition: An objective specification that is realized when a diagram is drawn from one or more data sets.
term editor: Matthew Diller
term editor: William R. Hogan

treatment in the ICU control strategy
type: Class
subclass of: individual treatment control strategy
editor preferred label: treatment in the intensive care unit control strategy
textual definition: an individual treatment control strategy that is realized by one or more intensive care unit encounters for infected individuals in the population
term 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: BFO_0000111
    some values from: data item
subclass of: website
editor preferred label: website that has data as a part
term 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: BFO_0000002
        intersection of: Restriction
subclass of: data set
editor preferred label: climate data set
textual 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.
term editor: Matt Diller
term editor: William R. Hogan

A software application that has as part an objective specification that is achieved by only a metagenomics analysis.
type: Class
subclass of: IAO_0000594
editor preferred label: metagenomics analysis software application
term editor: Matthew Diller
term editor: William R. Hogan
label: metagenomics analysis software

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
editor preferred label: abiotic ecosystem data set
textual definition: A data set that is about some abiotic ecosystem or abiotic ecosystem element.
term editor: William R. Hogan
alternative term: abiotic ecosystem dataset
alternative term: 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: BFO_0000050
      has value: atmosphere of the Earth
subclass of: abiotic ecosystem data set
editor preferred label: atmospheric data set
textual definition: A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere.
term editor: William R. Hogan
elucidation: A data set that is about either the Earth's atmosphere or some part of the Earth's atmosphere.
label: data set about Earth's atmosphere or some part of it

treatment facility census
type: Class
subclass of: census
subclass of: Class
  intersection of: census
  intersection of: Restriction
    on property: BFO_0000051
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: facility
editor preferred label: census of treatment facility
textual definition: A census that counts the number of treatment facilities of some kind in a particular geographical region.
term editor: William R. Hogan
alternative term: census of treatment facilities
alternative term: treatment facilities census
alternative term: 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
equivalent class: Class
  intersection of: interspecies interaction between organisms
  intersection of: Class
    intersection of: Restriction
      on property: has occurrent part
      some values from: multi-organism behavior
    intersection of: Restriction
      on property: has_participant
      min qualified cardinality: 2
      on class: organism
subclass of: interspecies interaction between organisms
editor preferred label: symbiosis
textual definition: An interspecies interaction between two or more organisms in intimate association.
term editor: Matthew Diller
term 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: IAO_0000594
editor preferred label: data format validator software application
textual 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.
term editor: William R. Hogan

disease identifier
type: Class
equivalent class: Class
  intersection of: IAO_0020000
  intersection of: Restriction
    on property: IAO_0000219
    some values from: disease
subclass of: IAO_0020000
editor preferred label: disease identifier
textual definition: an identifier that denotes a disease.
term 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
editor preferred label: 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
textual definition: a dataset that is about infectious disease acquisitions at particular times and particular places.
term 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 label: dataset about hospital stays
example of usage: The datasets at this link are rdf:type this class: https://www.opendataphilly.org/dataset/covid-hospitalizations
textual definition: a dataset that is about two or more hospital stays involving two or more patients.
term editor: William R. Hogan
alternative term: hospital discharge dataset
alternative term: 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 label: human daily movement behavior
textual 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.
term 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
editor preferred label: human daily movement behavior data set
example of usage: https://www.google.com/covid19/mobility/
textual definition: a data set that is about the human daily movement behavior of the individual huamns in a given population.
term 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
editor preferred label: potentially infectious contact process data set in a population
textual definition: a data set that is about one or more potentially infectious contact processes in a population of host organisms.
term editor: William R. Hogan
alternative term: 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: data set
editor preferred label: infectious disease control strategy census
textual definition: a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem.
term 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
editor preferred label: school closure infectious disease control strategy census
textual definition: an infectious disease control strategy census that is about school closure infectious disease control strategies implemented in a particular geographical region.
term 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
editor preferred label: vaccination infectious disease control strategy census
term 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
editor preferred label: population vaccination census
example of usage: vaccine / immunization registry data, vaccination / immunization records extracted from an EHR
textual definition: a population treatment census that is about one or more vaccinations of organisms in a population.
term editor: William R. Hogan
alternative term: 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 label: dataset about excess mortality in a population
textual 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.
term 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: BFO_0000051
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: vaccine
editor preferred label: census of supplies of vaccine products
textual definition: A control strategy inventory census that counts available vaccine doses of one or more similar vaccines.
term editor: William R. Hogan
alternative term: 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: BFO_0000051
    some values from: Class
      intersection of: count
      intersection of: Restriction
        on property: is about
        some values from: facility
editor preferred label: census of facilities that conduct clinical laboratory tests
textual definition: A census of facilities that conduct clinical laboratory testing.
term editor: William R. Hogan
alternative term: 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 label: model for disease transmission parameter estimation
textual definition: An algoirthm that is used to estimate the "true" values of certain parameters of disease transmission and/or forecasting.
term 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
textual 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.
term 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 label: laboratory testing capacity action specification
textual 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.
term 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: RO_0000052
        has value: atmosphere of the Earth
subclass of: data set
editor preferred label: data set about Earth's atmospheric weather
textual definition: A data set about the Earth's atmospheric weather
term 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: RO_0000052
    some values from: NCBITaxon 9606
subclass of: monkeypox
editor preferred label: monkeypox disease inhering in a human being
textual definition: A monkeypox disease inhering in a human being.
term editor: William R. Hogan
date: 2022-09-18T18:51:00
comment: requested by MIDAS CC

epidemic simulator action specification
type: Class
subclass of: action specification
editor preferred label: epidemic simulator action specification
term editor: William R. Hogan

infectious disease control strategy action specification
type: Class
subclass of: action specification
editor preferred label: infectious disease control strategy action specification
term editor: William R. Hogan

individual treatment control strategy action specification
type: Class
subclass of: infectious disease control strategy action specification
editor preferred label: individual treatment control strategy action specification
term editor: William R. Hogan

dataset creating
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: OBI_0000299
    some values from: data set
subclass of: planned process
editor preferred label: creating a data set
textual definition: A planned process that has a data set as its specified output.
term editor: William R. Hogan
alternative term: data set creation
alternative term: dataset creation

creating a copyright license
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: OBI_0000299
    some values from: copyright license
subclass of: planned process
editor preferred label: creating a copyright license
textual definition: A planned process that has a copyright license as its specified output.
term editor: William R. Hogan
alternative term: 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: IAO_0000310
editor preferred label: copyright license for a creative work
textual 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.
term 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: IAO_0000594
editor preferred label: data service software application
textual definition: A software application that implements a data service.
term editor: William R. Hogan

TODO
type: Class
subclass of: BFO_0000001

facultative role
type: Class
subclass of: BFO_0000023
editor preferred label: facultative role
textual 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.

object_aggregate
type: Class
subclass of: BFO_0000040
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

BFO_0000038
type: Class
Unique Apollo Label: Interval

history
type: Class
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.

antiviral drug
type: Class
subclass of: BFO_0000023
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
textual 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
textual 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
textual 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
textual 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
textual 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: BFO_0000030
textual 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
term editor: William Hogan
imported from: http://purl.obolibrary.org/obo/dron.owl
creator: William Hogan

environmental material
type: Class
subclass of: BFO_0000040
textual 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: IAO_0000121
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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
textual 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: BFO_0000015
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
textual 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
textual 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: IAO_0000123
textual definition: A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research.
term editor: PERSON: Nicole Vasilevsky
alternative term: community genomic analysis
alternative term: ecogenomic analysis
alternative term: 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: IAO_0000310
textual 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
textual 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

GAZ_00000448
type: Class
imported from: GAZ
comment: definition is circular.

GEO_000000372
type: Class
textual definition: A site designated by some relative spatial orientation.
term editor: Matthew Diller
term 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

reproduction
type: Class
subclass of: biological process
textual definition: The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.
imported from: http://purl.org/obo/owl/gene_ontology
elucidation: The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.
Unique Apollo Label: Reproduction
has_alternative_id: GO:0019952
has_alternative_id: GO:0050876
has_obo_namespace: biological_process
in_subset: goslim generic
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok

response to stress
type: Class
subclass of: response to stimulus
textual definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
has_related_synonym: response to abiotic stress
has_related_synonym: response to biotic stress
id: GO:0006950
in_subset: gocheck do not manually annotate
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim plant
in_subset: gosubset prok
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.

defense response
type: Class
subclass of: response to stress
textual definition: Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0002217
has_alternative_id: GO:0042829
has_exact_synonym: defence response
has_exact_synonym: physiological defense response
has_obo_namespace: biological_process
has_related_synonym: antimicrobial peptide activity
has_related_synonym: defense/immunity protein activity
id: GO:0006952
in_subset: gosubset prok

inflammatory response
type: Class
subclass of: defense response
textual definition: The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
imported from: http://purl.obolibrary.org/obo/go.owl
has_broad_synonym: Inflammation
database_cross_reference: Wikipedia:Inflammation
has_obo_namespace: biological_process
id: GO:0006954
comment: This term was improved by GO_REF:0000022. It was moved.

eclose
type: Class
subclass of: organism emergence from protective structure
textual definition: The emergence of an adult insect from a pupa case.
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process
label: eclosion

female pregnancy
type: Class
subclass of: multi-organism reproductive process
textual definition: The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
imported from: http://purl.obolibrary.org/obo/go.owl
database_cross_reference: Wikipedia:Gestation
has_exact_synonym: gestation
has_obo_namespace: biological_process
has_related_synonym: carrying of young
id: GO:0007565
in_subset: goslim chembl

parturition
type: Class
subclass of: multi-organism reproductive process
textual definition: The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs.
imported from: http://purl.obolibrary.org/obo/go.owl
has_exact_synonym: giving birth
has_narrow_synonym: egg laying
has_obo_namespace: biological_process
id: GO:0007567

aging
type: Class
subclass of: developmental process
imported from: http://purl.org/obo/owl/gene_ontology
has_alternative_id: GO:0016280
has_obo_namespace: biological_process
in_subset: goslim generic

behavior
type: Class
subclass of: biological process
textual definition: The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli.
imported from: http://purl.obolibrary.org/obo/go.owl
Unique Apollo Label: Behavior
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
id: GO:0007610
in_subset: gocheck do not manually annotate
in_subset: goslim plant
in_subset: gosubset prok
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.

mating behavior
type: Class
subclass of: multi-organism reproductive behavior
textual definition: The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.
imported from: http://purl.obolibrary.org/obo/go.owl
database_cross_reference: Wikipedia:Mating_behaviour
has_exact_synonym: mating behaviour
has_obo_namespace: biological_process
id: GO:0007617

biological process
type: Class
subclass of: BFO_0000015
editor preferred label: biological_process
textual definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
imported from: http://purl.obolibrary.org/obo/ido.owl

multicellular organismal aging
type: Class
subclass of: aging
textual definition: An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700).
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
id: GO:0010259

regulation of cell death
type: Class
subclass of: regulation of cellular process
textual definition: Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
id: GO:0010941

oviposition
type: Class
subclass of: reproductive behavior
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process

modulation by virus of host morphology or physiology
type: Class
subclass of: modification by symbiont of host morphology or physiology
textual definition: The process in which a virus effects a change in the structure or processes of its host organism.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0044792
has_broad_synonym: virus-host interaction
database_cross_reference: Reactome:REACT_6323
database_cross_reference: VZ:886
has_exact_synonym: host-virus interaction
has_exact_synonym: modulation by virus of host anatomical structure or process
has_exact_synonym: modulation by virus of host anatomy or process
has_exact_synonym: viral interaction with host
has_exact_synonym: viral-host process
has_exact_synonym: virus-host process
has_obo_namespace: biological_process
id: GO:0019048
in_subset: goslim virus
in_subset: virus checked

induction by virus of host apoptotic process
type: Class
subclass of: positive regulation of apoptotic process by virus
textual definition: The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions.
imported from: http://purl.obolibrary.org/obo/go.owl
has_exact_synonym: activation by virus of host apoptosis
has_exact_synonym: activation by virus of host apoptotic programmed cell death
has_exact_synonym: activation of apoptosis in host by virus
has_exact_synonym: induction by virus of host apoptotic programmed cell death
has_exact_synonym: induction of apoptosis in host by virus
has_narrow_synonym: induction by virus of host apoptosis
has_obo_namespace: biological_process
id: GO:0019051

modulation by virus of host process
type: Class
subclass of: modulation by virus of host morphology or physiology
textual definition: The process in which a virus effects a change in the processes and activities of its host organism.
imported from: http://purl.obolibrary.org/obo/go.owl
database_cross_reference: Reactome:REACT_6222
has_exact_synonym: modification by virus of host cellular process
has_exact_synonym: regulation by virus of host cellular process
has_exact_synonym: regulation of cellular process in host by virus
has_exact_synonym: regulation of host cellular process by virus
has_exact_synonym: viral host cell process manipulation
has_obo_namespace: biological_process
has_related_synonym: modulation of cellular process in host by virus
id: GO:0019054
in_subset: virus checked

reproductive behavior
type: Class
subclass of: behavior
subclass of: multicellular organismal reproductive process
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process

reproductive process
type: Class
subclass of: biological process
textual 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.
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
id: GO:0022414
in_subset: gosubset prok

developmental process
type: Class
subclass of: biological process
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process
in_subset: goslim aspergillus
in_subset: goslim pir
in_subset: gosubset prok

multicellular organism reproduction
type: Class
subclass of: reproduction
textual definition: 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.
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
id: GO:0032504

multicellular organismal reproductive behavior
type: Class
subclass of: reproductive behavior
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process

social behavior
type: Class
subclass of: interspecies interaction between organisms
textual definition: Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
imported from: http://purl.obolibrary.org/obo/go.owl
database_cross_reference: Wikipedia:Social_behavior
has_exact_synonym: social behaviour
has_obo_namespace: biological_process
has_related_synonym: cooperative behavior
id: GO:0035176
comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior.

modification of morphology or physiology of other organism
type: Class
subclass of: regulation of biological quality
textual definition: The process in which an organism effects a change in the structure or processes of a second organism.
imported from: http://purl.obolibrary.org/obo/go.owl
created by: rfoulger
creation date: 2011-04-21T01:31:51Z
has_narrow_synonym: regulation of morphology of other organism
has_narrow_synonym: regulation of physiological process of other organism
has_narrow_synonym: regulation of physiology of other organism
has_obo_namespace: biological_process
has_related_synonym: regulation of morphology or physiology of other organism
id: GO:0035821

induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process
type: Class
subclass of: induction by virus of host apoptotic process
textual definition: Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process.
imported from: http://purl.obolibrary.org/obo/go.owl
created by: rfoulger
creation date: 2012-10-09T15:44:29Z
has_narrow_synonym: activation of host caspases by virus
has_narrow_synonym: induction by virus of host caspase activity
has_obo_namespace: biological_process
id: GO:0039651

regulation of programmed cell death
type: Class
subclass of: regulation of cell death
textual definition: Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0043070
has_narrow_synonym: regulation of non-apoptotic programmed cell death
has_obo_namespace: biological_process
id: GO:0043067

modification by symbiont of host morphology or physiology
type: Class
subclass of: modification of morphology or physiology of other organism involved in symbiotic interaction
textual definition: The process in which a symbiont organism effects a change in the structure or processes of its host organism.
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
id: GO:0044003
in_subset: gosubset prok

entry into host
type: Class
subclass of: biological process
textual 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.

interspecies interaction between organisms
type: Class
subclass of: multi-organism process
textual definition: Any process in which an organism has an effect on an organism of a different species.

modulation of programmed cell death in other organism
type: Class
subclass of: regulation of programmed cell death
textual definition: A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism.
imported from: http://purl.obolibrary.org/obo/go.owl
created by: janelomax
creation date: 2012-03-20T04:48:41Z
has_obo_namespace: biological_process
id: GO:0044531

multi-organism reproductive process
type: Class
subclass of: reproductive process
textual definition: A biological process that directly contributes to the process of producing new individuals, involving another organism.
imported from: http://purl.obolibrary.org/obo/go.owl
created by: janelomax
creation date: 2012-09-19T15:56:30Z
has_obo_namespace: biological_process
id: GO:0044703

multi-organism reproductive behavior
type: Class
subclass of: reproductive behavior
textual definition: The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species.
imported from: http://purl.obolibrary.org/obo/go.owl
created by: janelomax
creation date: 2012-09-19T16:02:12Z
has_obo_namespace: biological_process
id: GO:0044705

multicellular organismal reproductive process
type: Class
subclass of: reproductive process
textual 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.
imported from: http://purl.obolibrary.org/obo/go.owl
has_broad_synonym: organismal reproductive process
has_exact_synonym: reproductive process in a multicellular organism
has_obo_namespace: biological_process
id: GO:0048609

regulation of biological process
type: Class
subclass of: biological regulation
textual definition: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0050791
has_exact_synonym: regulation of physiological process
has_obo_namespace: biological_process
id: GO:0050789
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: gosubset prok

regulation of cellular process
type: Class
subclass of: regulation of biological process
textual definition: Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0051244
has_exact_synonym: regulation of cellular physiological process
has_obo_namespace: biological_process
id: GO:0050794
in_subset: gosubset prok

response to stimulus
type: Class
subclass of: biological process
textual definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0051869
has_exact_synonym: physiological response to stimulus
has_obo_namespace: biological_process
id: GO:0050896
in_subset: gocheck do not manually annotate
in_subset: goslim pir
in_subset: gosubset prok
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.

establishment of localization
type: Class
subclass of: biological process
editor preferred label: establishment of localization
textual definition: The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
imported from: http://purl.obolibrary.org/obo/ido.owl

interaction with host
type: Class
subclass of: interspecies interaction between organisms
textual 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.
imported from: http://purl.obolibrary.org/obo/go.owl
has_obo_namespace: biological_process
id: GO:0051701
in_subset: gosubset prok

multi-organism process
type: Class
subclass of: biological process
textual definition: A biological process which involves another organism of the same or different species.

multi-organism behavior
type: Class
subclass of: behavior
textual definition: Any process in which an organism has a behavioral effect on another organism of the same or different species.
imported from: http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl
has_alternative_id: GO:0023032
has_alternative_id: GO:0044709
database_cross_reference: GOC:ai
database_cross_reference: GOC:mah
has_exact_synonym: behavioral interaction between organisms
has_exact_synonym: behavioral interaction with other organism
has_exact_synonym: behavioural interaction between organisms
has_exact_synonym: behavioural interaction with other organism
has_narrow_synonym: behavioral signaling
has_narrow_synonym: behavioral signalling
has_obo_namespace: biological_process
id: GO:0051705
in_subset: goslim pir

modification of morphology or physiology of other organism involved in symbiotic interaction
type: Class
subclass of: modification of morphology or physiology of other organism
textual definition: The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction.
imported from: http://purl.obolibrary.org/obo/go.owl
has_narrow_synonym: regulation of morphology of other organism during symbiotic interaction
has_narrow_synonym: regulation of physiological process in other organism during symbiotic interaction
has_narrow_synonym: regulation of physiology of other organism during symbiotic interaction
has_obo_namespace: biological_process
has_related_synonym: modification of morphology or physiology of other organism during symbiotic interaction
has_related_synonym: modulation of morphology or physiology of other organism during symbiotic interaction
has_related_synonym: regulation of morphology or physiology of other organism during symbiotic interaction
id: GO:0051817
in_subset: gosubset prok

modulation by symbiont of host programmed cell death
type: Class
subclass of: modulation of programmed cell death in other organism involved in symbiotic interaction
textual definition: Any process in which an organism modulates the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0052152
has_exact_synonym: modulation of host PCD
has_narrow_synonym: modulation by symbiont of host non-apoptotic programmed cell death
has_obo_namespace: biological_process
id: GO:0052040
in_subset: gosubset prok

positive regulation by symbiont of host programmed cell death
type: Class
subclass of: modulation by symbiont of host programmed cell death
textual definition: Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0012504
has_alternative_id: GO:0052044
has_alternative_id: GO:0052045
has_alternative_id: GO:0052153
has_alternative_id: GO:0052397
has_alternative_id: GO:0052400
has_exact_synonym: activation by organism of host programmed cell death
has_exact_synonym: activation by organism of programmed cell death in other organism during symbiotic interaction
has_exact_synonym: enhancement of host programmed cell death
has_exact_synonym: enhancement of host programmed cell death by organism
has_exact_synonym: induction by organism of programmed cell death in other organism involved in symbiotic interaction
has_exact_synonym: induction by symbiont of host programmed cell death
has_exact_synonym: upregulation by symbiont of host programmed cell death
has_narrow_synonym: activation by organism of non-apoptotic programmed cell death in other organism
has_narrow_synonym: activation by symbiont of host programmed cell death
has_narrow_synonym: induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction
has_narrow_synonym: positive regulation by symbiont of host non-apoptotic programmed cell death
has_narrow_synonym: stimulation by symbiont of host programmed cell death
has_obo_namespace: biological_process
has_related_synonym: induction by organism of programmed cell death in other organism during symbiotic interaction
has_related_synonym: induction of non-apoptotic programmed cell death by other organism
id: GO:0052042
in_subset: gosubset prok

positive regulation by symbiont of host apoptotic process
type: Class
subclass of: positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction
textual definition: Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0033669
has_alternative_id: GO:0052030
has_exact_synonym: activation by organism of host apoptosis
has_exact_synonym: activation by organism of host apoptotic programmed cell death
has_exact_synonym: induction by organism of host apoptotic programmed cell death
has_exact_synonym: induction by symbiont of host apoptosis
has_exact_synonym: positive regulation by organism of host apoptotic programmed cell death
has_exact_synonym: up regulation by organism of host apoptotic programmed cell death
has_exact_synonym: up regulation by symbiont of host apoptosis
has_exact_synonym: up-regulation by organism of host apoptotic programmed cell death
has_exact_synonym: up-regulation by symbiont of host apoptosis
has_exact_synonym: upregulation by organism of host apoptotic programmed cell death
has_exact_synonym: upregulation by symbiont of host apoptosis
has_narrow_synonym: activation by symbiont of host apoptosis
has_narrow_synonym: positive regulation by symbiont of host apoptosis
has_narrow_synonym: stimulation by symbiont of host apoptosis
has_obo_namespace: biological_process
id: GO:0052151
in_subset: gosubset prok
comment: Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'.

modulation of programmed cell death in other organism involved in symbiotic interaction
type: Class
subclass of: modulation of programmed cell death in other organism
textual definition: Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0052459
has_narrow_synonym: modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction
has_obo_namespace: biological_process
has_related_synonym: modulation of programmed cell death in other organism during symbiotic interaction
id: GO:0052248
in_subset: gosubset prok

positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction
type: Class
subclass of: positive regulation by symbiont of host programmed cell death
textual definition: Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction.
imported from: http://purl.obolibrary.org/obo/go.owl
has_alternative_id: GO:0052388
has_exact_synonym: induction by organism of apoptosis in other organism involved in symbiotic interaction
has_narrow_synonym: activation by organism of apoptosis in other organism during symbiotic interaction
has_narrow_synonym: positive regulation by organism of apoptosis in other organism involved in symbiotic interaction
has_narrow_synonym: positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction
has_narrow_synonym: stimulation by organism of apoptosis in other organism during symbiotic interaction
has_obo_namespace: biological_process
has_related_synonym: activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction
has_related_synonym: induction by organism of apoptosis in other organism during symbiotic interaction
has_related_synonym: induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction
has_related_synonym: positive regulation by organism of apoptosis in other organism during symbiotic interaction
has_related_synonym: positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction
has_related_synonym: up regulation by organism of apoptosis in other organism during symbiotic interaction
has_related_synonym: up-regulation by organism of apoptosis in other organism during symbiotic interaction
has_related_synonym: upregulation by organism of apoptosis in other organism during symbiotic interaction
id: GO:0052501
in_subset: gosubset prok

positive regulation of apoptotic process by virus
type: Class
subclass of: positive regulation by symbiont of host apoptotic process
textual definition: Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
imported from: http://purl.obolibrary.org/obo/go.owl
has_narrow_synonym: positive regulation of apoptosis by virus
has_obo_namespace: biological_process
id: GO:0060139

modulation by virus of host cell cycle
type: Class
subclass of: modulation by virus of host process
textual definition: Any viral process that modulates the rate or extent of progression through the cell cycle.
imported from: http://purl.obolibrary.org/obo/go.owl
database_cross_reference: VZ:1636
has_exact_synonym: modulation of host cell cycle by virus
has_exact_synonym: regulation by virus of host cell cycle
has_exact_synonym: regulation of host cell cycle by virus
has_exact_synonym: viral process regulating host cell cycle
has_obo_namespace: biological_process
id: GO:0060153
in_subset: goslim virus

post-mating oviposition
type: Class
subclass of: oviposition
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process

biological regulation
type: Class
subclass of: biological process
textual definition: Any process that modulates a measurable attribute of any biological process, quality or function.
imported from: http://purl.obolibrary.org/obo/go.owl
has_broad_synonym: regulation
has_obo_namespace: biological_process
id: GO:0065007
in_subset: goslim pir
in_subset: gosubset prok

regulation of biological quality
type: Class
subclass of: biological regulation
textual definition: Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
imported from: http://purl.obolibrary.org/obo/go.owl
has_exact_synonym: regulation of biological attribute
has_exact_synonym: regulation of biological characteristic
has_obo_namespace: biological_process
id: GO:0065008
in_subset: gosubset prok

organism emergence from protective structure
type: Class
subclass of: biological process
imported from: http://purl.org/obo/owl/gene_ontology
has_obo_namespace: biological_process

measurement unit label
type: Class
subclass of: label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: IAO_0000125
textual 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
Unique Apollo Label: unitId

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: IAO_0000122
has curation status: IAO_0000125
textual 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: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: IAO_0000122
has curation status: IAO_0000123
textual definition: a directive information entity that describes an action the bearer will take
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch

label
type: Class
editor preferred label: label
has curation status: IAO_0000123
textual definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
Unique Apollo Label: label

software
type: Class
subclass of: plan specification
editor preferred label: software
has curation status: IAO_0000120
textual 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition source: GROUP: OBI

data item
type: Class
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
textual definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data

symbol
type: Class
editor preferred label: symbol
has curation status: IAO_0000125
textual definition: a smallish, word-like datum...
editor note: 20091104, MC: this needs work and will most probably change
term editor: PERSON: Jonathan Rees

information content entity
type: Class
subclass of: BFO_0000031
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
has curation status: IAO_0000125
textual definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor note: 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.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
has curation status: IAO_0000120
textual 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

directive information entity
type: Class
has curation status: IAO_0000122
has curation status: IAO_0000123
textual 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: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: IAO_0000120
textual definition: A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)

data set
type: Class
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: IAO_0000120
has curation status: IAO_0000125
textual 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
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
Unique Apollo Label: dataSets

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: BFO_0000051
  some values from: objective specification
subclass of: Restriction
  on property: BFO_0000051
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000120
has curation status: IAO_0000122
textual definition: a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
editor 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: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
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

measurement datum
type: Class
subclass of: data item
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: IAO_0000120
has curation status: IAO_0000125
textual 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?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI

version number
type: Class
subclass of: symbol
editor preferred label: version number
has curation status: IAO_0000123
has curation status: IAO_0000124
textual 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
term editor: GROUP: IAO

time measurement datum
type: Class
subclass of: scalar measurement datum
has curation status: IAO_0000123
textual definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg

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: IAO_0000123

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: BFO_0000051
  some values from: time stamped measurement datum
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: IAO_0000120
textual 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.
term editor: Alan Ruttenberg
alternative term: experimental time series

IAO_0020000
type: Class
Unique Apollo Label: name

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 label: Mus musculus
term editor: William R. Hogan
alternative term: House mouse

Virus
type: Class
subclass of: organism

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
term editor: Mirela L Vasconcelos
alternative term: monkey pox virus

Variola virus
type: Class
subclass of: Orthopoxvirus

H5N1 subtype
type: Class
subclass of: Influenza A virus
editor preferred label: 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
term editor: Mirela L Vasconcelos

Rotavirus
type: Class
subclass of: Sedoreovirinae
term editor: Mirela L Vasconcelos
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Hepatitis C virus group
alternative term: Hepatitis C viruses
alternative term: Hepatitis C-like viruses

Hepatitis C virus
type: Class
subclass of: Hepacivirus
term editor: Mirela L Vasconcelos
alternative term: hepatitis C virus HCV
alternative term: human hepatitis C virus
alternative term: human hepatitis C virus HCV
alternative term: human hepatitis virus C HCV
alternative term: post-transfusion hepatitis non A non B virus

Coronaviridae
type: Class
subclass of: Nidovirales
editor preferred label: Coronaviridae
imported from: http://purl.obolibrary.org/obo/obi.owl

Chlamydia/Chlamydophila group
type: Class
subclass of: Chlamydiaceae
term 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
term editor: Mirela L Vasconcelos
alternative term: Morbilliviruses

Measles virus
type: Class
subclass of: Morbillivirus

Pneumoviridae
type: Class
subclass of: Mononegavirales
term editor: Mirela L Vasconcelos
alternative term: Pneumovirinae

Pneumovirus
type: Class
subclass of: Pneumoviridae
term 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
term editor: Mirela L Vasconcelos

Lyssavirus
type: Class
subclass of: Rhabdoviridae
term editor: Mirela L Vasconcelos

Rabies lyssavirus
type: Class
subclass of: Lyssavirus
term editor: Mirela L Vasconcelos
alternative term: 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 label: H1N1 subtype of Influenza A virus

H2N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred label: H2N2 subtype of Influenza A virus

Influenza B virus
type: Class
subclass of: Influenzavirus B
term editor: Mirela L Vasconcelos
alternative term: Influenza virus type B

Bunyaviridae
type: Class
subclass of: ssRNA negative-strand virus
term 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
term editor: Mirela L Vasconcelos
alternative term: Phleboviruses

Rift Valley fever virus
type: Class
subclass of: Rift Valley fever phlebovirus
term 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 term: Lentivirinae

Primate lentivirus group
type: Class
subclass of: Lentivirus
alternative term: Primate immunodeficiency viruses

Human immunodeficiency virus 1
type: Class
subclass of: Primate lentivirus group
alternative term: HIV-1
alternative term: Human immunodeficiency virus type 1
alternative term: human immunodeficiency virus 1 HIV-1
alternative term: human immunodeficiency virus HIV-1
alternative term: human immunodeficiency virus type 1 HIV 1
alternative term: human immunodeficiency virus type 1 HIV-1
alternative term: human immunodeficiency virus type 1 HIV1
alternative term: human immunodeficiency virus type 1, HIV-1
alternative term: human immunodeficiency virus type I HIV-1
alternative term: human immunodeficiency virus type-1 HIV-1
alternative term: human immunodeficiency virus-1 HIV-1

Human immunodeficiency virus 2
type: Class
subclass of: Primate lentivirus group
alternative term: HIV type 2
alternative term: HIV-2
alternative term: Human immunodeficiency virus type 2
alternative term: Human immunodeficiency virus-2
alternative term: human immunodeficiency virus type 2 HIV-2
alternative term: human immunodeficiency virus type 2, HIV-2

Teleostomi
type: Class
subclass of: Gnathostomata

Euteleostomi
type: Class
subclass of: Teleostomi
alternative term: 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 label: H3N2 subtype of Influenza A virus

H7N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred label: H7N2 subtype of Influenza A virus

H7N7 subtype
type: Class
subclass of: Influenza A virus
editor preferred label: H7N7 subtype of Influenza A virus

H5N2 subtype
type: Class
subclass of: Influenza A virus
editor preferred label: H5N2 subtype of Influenza A virus

Caliciviridae
type: Class
subclass of: ssRNA positive-strand viruses, no DNA stage
term 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 term: Human poliovirus type 1
alternative term: Poliovirus type 1
alternative term: poliovirus type 1 PV1

Human poliovirus 3
type: Class
subclass of: Enterovirus C
alternative term: Human poliovirus type 3
alternative term: Poliovirus type 3

Hepatovirus
type: Class
subclass of: Picornaviridae
term editor: Mirela L Vasconcelos

Hepatovirus A
type: Class
subclass of: Hepatovirus
term editor: Mirela L Vasconcelos
alternative term: Hepatitis A virus

Aphthovirus
type: Class
subclass of: Picornaviridae
term editor: Mirela L Vasconcelos

Foot-and-mouth disease virus
type: Class
subclass of: Aphthovirus
term editor: Mirela L Vasconcelos
alternative term: Foot and mouth disease virus
alternative term: foot and mouth disease virus FMDV
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Alphaproteobacteraeota
alternative term: purple bacteria
alternative term: purple bacteria and relatives
alternative term: purple non-sulfur bacteria
alternative term: purple photosynthetic bacteria
alternative term: purple photosynthetic bacteria and relatives

Gammaproteobacteria
type: Class
subclass of: Proteobacteria
term editor: Mirela L Vasconcelos
alternative term: Proteobacteria gamma subdivision
alternative term: Purple bacteria, gamma subdivision
alternative term: gamma proteobacteria
alternative term: gamma subdivision
alternative term: gamma subgroup

Firmicutes
type: Class
subclass of: Terrabacteria group
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Hepatitis D virus
alternative term: hepatitis delta virus HDV

Dengue virus
type: Class
subclass of: Dengue virus group

Staphylococcus
type: Class
subclass of: Staphylococcaceae
editor preferred label: Staphylococcus
alternative term: Aurococcus

Vibrio cholerae O1
type: Class
subclass of: Vibrio cholerae
term editor: Mirela L Vasconcelos
alternative term: Vibrio cholerae serogroup O1

Staphylococcus aureus
type: Class
subclass of: Staphylococcus
editor preferred label: Staphylococcus aureus
alternative term: Micrococcus aureus
alternative term: Micrococcus pyogenes
alternative term: Staphlococcus pyogenes citreus
alternative term: Staphylococcus pyogenes aureus
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: respiratory syncytial virus RS
alternative term: respiratory syncytial virus RS virus
alternative term: respiratory syncytial virus RSV

Streptococcaceae
type: Class
subclass of: Lactobacillales
term editor: Mirela L Vasconcelos

Streptococcus
type: Class
subclass of: Streptococcaceae
term 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
term editor: Mirela L Vasconcelos
alternative term: Diplococcus pneumoniae
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Vibrionaceae group

Pasteurellales
type: Class
subclass of: Gammaproteobacteria
term editor: Mirela L Vasconcelos
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Coxsackievirus A
alternative term: Enterovirus EV-A
alternative term: Human coxsackievirus A
alternative term: Human enterovirus A

Enterovirus C
type: Class
subclass of: Enterovirus
alternative term: Enterovirus EV-C
alternative term: Human enterovirus C
alternative term: Poliovirus

Enterovirus D
type: Class
subclass of: Enterovirus

Bacillus anthracis
type: Class
subclass of: Bacillus cereus group
term editor: Mirela L Vasconcelos
alternative term: Bacillus cereus var. anthracis
alternative term: Bacteridium anthracis
alternative term: anthrax
alternative term: anthrax bacterium

Norovirus
type: Class
subclass of: Caliciviridae
term editor: Mirela L Vasconcelos
alternative term: 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

NCBITaxon_147711
type: Class
subclass of: Enterovirus
editor preferred label: 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
term editor: Mirela L Vasconcelos
alternative term: Bacillus difficilis
alternative term: Clostridium difficile
alternative term: 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
term 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
type: Class
subclass of: Actinobacteria
alternative term: Actinomycetes
alternative term: High GC gram-positive bacteria

Mycobacteriaceae
type: Class
subclass of: Corynebacteriales

Mycobacterium
type: Class
subclass of: Mycobacteriaceae
alternative term: 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 term: Bacillus tuberculosis
alternative term: Bacterium tuberculosis
alternative term: Mycobacterium tuberculosis typus humanus
alternative term: 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
term editor: Mirela L Vasconcelos

Terrabacteria group
type: Class
subclass of: Bacteria
term editor: Mirela L Vasconcelos

Ebolavirus
type: Class
subclass of: Filoviridae
alternative term: 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 term: Ebola virus Reston
alternative term: REBOV
alternative term: Reston Ebola virus

Sudan ebolavirus
type: Class
subclass of: Ebolavirus
alternative term: Ebolavirus Sudan
alternative term: SEBOV
alternative term: Sudan Ebola virus

Tai Forest ebolavirus
type: Class
subclass of: Ebolavirus
alternative term: CIEBOV
alternative term: Côte d'Ivoire Ebola virus
alternative term: Côte d'Ivoire ebolavirus
alternative term: Ivory Coast ebolavirus

Clostridia
type: Class
subclass of: Firmicutes
term editor: Mirela L Vasconcelos

Clostridiales
type: Class
subclass of: Clostridia
term editor: Mirela L Vasconcelos

Peptostreptococcaceae
type: Class
subclass of: Clostridiales
term editor: Mirela L Vasconcelos
alternative term: 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
term editor: Mirela L Vasconcelos

Clostridioides
type: Class
subclass of: Peptostreptococcaceae
term 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
term 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
term 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

Actinobacteria
type: Class
subclass of: Terrabacteria group
alternative term: 'Actinobacteria'
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Chlamydaeota

Chlamydiia
type: Class
subclass of: Chlamydiae
term editor: Mirela L Vasconcelos
alternative term: Chlamydiae

Neisseriales
type: Class
subclass of: Betaproteobacteria
term 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
term editor: Mirela L Vasconcelos

Helicobacter pylori
type: Class
subclass of: Helicobacter
term editor: Mirela L Vasconcelos
alternative term: Campylobacter pylori
alternative term: Campylobacter pylori subsp. pylori
alternative term: Campylobacter pyloridis
alternative term: Helicobacter nemestrinae

Campylobacterales
type: Class
subclass of: Epsilonproteobacteria
term editor: Mirela L Vasconcelos

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 label: 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

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
term editor: Mirela L Vasconcelos
alternative term: Proteobacteria beta subdivision
alternative term: Purple bacteria, beta subdivision
alternative term: beta proteobacteria
alternative term: beta subdivision
alternative term: beta subgroup

Porcine epidemic diarrhea virus
type: Class
subclass of: Alphacoronavirus
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Bacillus cholerae-suis
alternative term: Salmonella cholerae-suis
alternative term: Salmonella choleraesuis
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Proteobacteria epsilon subdivision
alternative term: Purple bacteria, epsilon subdivision
alternative term: epsilon proteobacteria
alternative term: epsilon subdivision
alternative term: epsilon subgroup
alternative term: not Epsilobacteria

Spondweni virus group
type: Class
subclass of: Flavivirus
editor preferred label: Spondweni virus group

Schistosomatoidea
type: Class
subclass of: Strigeidida
term editor: Mirela L Vasconcelos

Schistosomatidae
type: Class
subclass of: Schistosomatoidea
term editor: Mirela L Vasconcelos
alternative term: 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 term: 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 term: tetrapods

Amniota
type: Class
subclass of: Tetrapoda
alternative term: 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 label: 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 label: 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 term: 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
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: alveolates

Euglenozoa
type: Class
subclass of: Eukaryota
term editor: Mirela L Vasconcelos
alternative term: 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: Virus
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
label: dsDNA virus, no RNA stage

Retro-transcribing viruses
type: Class
subclass of: Virus
alternative term: Retroid viruses

ssRNA positive-strand viruses, no DNA stage
type: Class
subclass of: ssRNA virus
editor preferred label: 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: Virus
term editor: Mirela L Vasconcelos
alternative term: 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)
term editor: Matthew Diller
alternative term: 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: Virus
term 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 term: mammals

Plasmodium (Plasmodium)
type: Class
subclass of: Plasmodium
term editor: Matthew Diller
alternative term: plasmodium

Plasmodium (Laverania)
type: Class
subclass of: Plasmodium
term editor: Matthew Diller
alternative term: laverania

Culicoidea
type: Class
subclass of: Culicomorpha

Aconoidasida
type: Class
subclass of: Apicomplexa
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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: Virus

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
term editor: Mirela L Vasconcelos
alternative term: Acinetobacteraceae
alternative term: Branhamaceae

Acinetobacter
type: Class
subclass of: Moraxellaceae
term editor: Mirela L Vasconcelos

Acinetobacter baumannii
type: Class
subclass of: Acinetobacter calcoaceticus/baumannii complex
term editor: Mirela L Vasconcelos
alternative term: Acinetobacter genomosp. 2
alternative term: Acinetobacter genomospecies 2
alternative term: 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
term 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
term editor: Mirela L Vasconcelos

Neisseria
type: Class
subclass of: Neisseriaceae
term editor: Mirela L Vasconcelos
alternative term: "Gonococcus" Lindau 1898
alternative term: "Merismopedia" Zopf 1885
alternative term: Gonococcus

Neisseria gonorrhoeae
type: Class
subclass of: Neisseria
term editor: Mirela L Vasconcelos
alternative term: Diplococcus gonorrhoeae
alternative term: Gonococcus neisseri
alternative term: Merismopedia gonorrhoeae
alternative term: Micrococcus der gonorrhoe
alternative term: Micrococcus gonococcus
alternative term: Micrococcus gonorrhoeae

Neisseria meningitidis
type: Class
subclass of: Neisseria
term editor: Mirela L Vasconcelos
alternative term: Diplokokkus intracellularis meningitidis
alternative term: Micrococcus intracellularis
alternative term: Micrococcus meningitidis
alternative term: Micrococcus meningitidis cerebrospinalis
alternative term: 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
term 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
term editor: Mirela L Vasconcelos

Bordetella
type: Class
subclass of: Alcaligenaceae
term 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
term editor: Mirela L Vasconcelos
alternative term: Bacterium tussis-convulsivae
alternative term: Hemophilus pertussis
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Enterobacteraceae

Salmonella enterica subsp. enterica serovar Paratyphi A
type: Class
subclass of: Salmonella enterica subsp. enterica
term editor: Mirela L Vasconcelos
alternative term: Bacterium paratyphi
alternative term: Bacterium paratyphi typhus A
alternative term: Salmonella choleraesuis choleraesuis (serotype paratyphi A)
alternative term: Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A
alternative term: Salmonella paratyphi
alternative term: Salmonella paratyphi A
alternative term: 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
term editor: Mirela L Vasconcelos

Escherichia coli
type: Class
subclass of: Escherichia
term editor: Mirela L Vasconcelos
alternative term: Bacillus coli
alternative term: Bacterium coli
alternative term: Bacterium coli commune
alternative term: E. coli
alternative term: Enterococcus coli

Kinetoplastida
type: Class
subclass of: Euglenozoa
term editor: Mirela L Vasconcelos
alternative term: Kinetoplastea
alternative term: Protomonadida
alternative term: kinetoplasts

Trypanosomatidae
type: Class
subclass of: Kinetoplastida
term editor: Mirela L Vasconcelos

Bundibugyo ebolavirus
type: Class
subclass of: Ebolavirus
alternative term: Ebolavirus bundibugyo

Trypanosoma
type: Class
subclass of: Trypanosomatidae
term editor: Mirela L Vasconcelos

Trypanosoma cruzi
type: Class
subclass of: Schizotrypanum
term 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
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: 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
term editor: Matthew Diller
term editor: William R. Hogan
alternative term: haemosporidians
alternative term: haemosporina

Plasmodium
type: Class
subclass of: Plasmodiidae
term editor: Matthew Diller

Plasmodium falciparum
type: Class
subclass of: Plasmodium (Laverania)
term editor: Matthew Diller
term editor: Mirela L Vasconcelos
alternative term: malaria parasite P. falciparum
alternative term: plasmodium (laverania) falciparum

Plasmodium vivax
type: Class
subclass of: Plasmodium (Plasmodium)
term editor: Matthew Diller
alternative term: malaria parasite p. vivax

Plasmodium malariae
type: Class
subclass of: Plasmodium (Plasmodium)
term editor: Matthew Diller

Salmonella
type: Class
subclass of: Enterobacteriaceae
term editor: Mirela L Vasconcelos

Salmonella enterica subsp. enterica
type: Class
subclass of: Salmonella enterica
term editor: Mirela L Vasconcelos
alternative term: Salmonella cholerae-suis subsp. cholerae-suis
alternative term: Salmonella choleraesuis subsp. choleraesuis
alternative term: Salmonella enterica I
alternative term: Salmonella enterica subsp. I

Eumetazoa
type: Class
subclass of: Metazoa

Platyhelminthes
type: Class
subclass of: Bilateria
term editor: Mirela L Vasconcelos
alternative term: flatworms

Trematoda
type: Class
subclass of: Platyhelminthes
term editor: Mirela L Vasconcelos

Digenea
type: Class
subclass of: Trematoda
term editor: Mirela L Vasconcelos
alternative term: flukes

Strigeidida
type: Class
subclass of: Digenea
term editor: Mirela L Vasconcelos

Schistosoma
type: Class
subclass of: Schistosomatidae
term editor: Mirela L Vasconcelos

Schistosoma mansoni
type: Class
subclass of: Schistosoma
term editor: Mirela L Vasconcelos

Schistosoma haematobium
type: Class
subclass of: Schistosoma
term 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
term editor: Mirela L Vasconcelos

Zika virus
type: Class
subclass of: Spondweni virus group
editor preferred label: 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
term editor: Mirela L Vasconcelos
alternative term: Beneckea
alternative term: Listonella
alternative term: Microspira
alternative term: Pacinia

Arthropoda
type: Class
subclass of: Panarthropoda

Vibrio cholerae
type: Class
subclass of: Vibrio
term editor: Mirela L Vasconcelos
alternative term: Bacillo virgola del Koch
alternative term: Bacillus cholerae
alternative term: Bacillus cholerae-asiaticae
alternative term: Kommabacillus
alternative term: Liquidivibrio cholerae
alternative term: Microspira comma
alternative term: Pacinia cholerae-asiaticae
alternative term: Spirillum cholerae
alternative term: Spirillum cholerae-asiaticae
alternative term: Vibrio cholera
alternative term: Vibrio cholerae Pacini 1854
alternative term: Vibrio cholerae-asiaticae
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: 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
term 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 term: Coronavirus group 1
alternative term: 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
term editor: Mirela L Vasconcelos

Diptera
type: Class
subclass of: Endopterygota

Nematocera
type: Class
subclass of: Diptera

Culicidae
type: Class
subclass of: Culicoidea
alternative term: mosquitos

Aedes
type: Class
subclass of: Aedini

Aedes aegypti
type: Class
subclass of: Stegomyia
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Pseudomonaceae/Moraxellaceae group

Helicobacteraceae
type: Class
subclass of: Campylobacterales
term editor: Mirela L Vasconcelos
alternative term: 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
term editor: Mirela L Vasconcelos

Haemophilus influenzae
type: Class
subclass of: Haemophilus
term editor: Mirela L Vasconcelos
alternative term: Bacterium influenzae
alternative term: Coccobacillus pfeifferi
alternative term: Haemophilus meningitidis
alternative term: Influenza-bacillus
alternative term: 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 label: Nidovirales
imported from: http://purl.obolibrary.org/obo/obi.owl

Chordata
type: Class
subclass of: Deuterostomia
alternative term: chordates

Vertebrata
type: Class
subclass of: Craniata
alternative term: 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 term: 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
term editor: Mirela L Vasconcelos
alternative term: Burkholderia/Oxalobacter/Ralstonia group

Chlamydiaceae
type: Class
subclass of: Chlamydiales
term 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
term editor: Mirela L Vasconcelos
alternative term: Bedsonia
alternative term: Chlamydophila
alternative term: Miyagawanella
alternative term: Rakeia
alternative term: Rickettsiaformis

Chlamydia trachomatis
type: Class
subclass of: Chlamydia
term editor: Mirela L Vasconcelos
alternative term: Chlamydozoon trachomatis
alternative term: Rickettsia trachomae
alternative term: 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
alternative term: 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
term editor: Mirela L Vasconcelos
alternative term: Bacillus typhi
alternative term: Bacterium (subgen. Eberthella) typhi
alternative term: Salmonella choleraesuis serovar Typhi
alternative term: Salmonella choleraesuis typhi
alternative term: Salmonella enterica ser. typhi
alternative term: Salmonella enterica serotype Typhi
alternative term: Salmonella enterica serovar Typhi
alternative term: 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 label: Staphylococcaceae
alternative term: Staphylococcus group

Acinetobacter calcoaceticus/baumannii complex
type: Class
subclass of: Acinetobacter
term 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
term editor: Mirela L Vasconcelos
alternative term: Bacillus/Lactobacillus/Strptococcus group
alternative term: Firmibacteria

Enterobacterales
type: Class
subclass of: Gammaproteobacteria
term editor: Mirela L Vasconcelos
alternative term: Enterobacteriaceae and related endosymbionts
alternative term: Enterobacteriaceae group
alternative term: 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 term: Placentalia
alternative term: eutherian mammals
alternative term: placental mammals
alternative term: 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 term: Primata
alternative term: primate
alternative term: 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 term: Old World monkeys
alternative term: monkey
alternative term: monkeys

Cercopithecinae
type: Class
subclass of: Cercopithecidae

Macaca
type: Class
subclass of: Cercopithecinae
alternative term: macaque
alternative term: 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 term: Rhesus monkey
alternative term: rhesus macaque
alternative term: rhesus macaques
alternative term: rhesus monkeys

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: BFO_0000016
textual 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: RO_0000059
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: BFO_0000051
        some values from: objective specification
subclass of: BFO_0000015
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
textual 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.
term editor: Bjoern Peters
definition source: branch derived
imported from: obi.owl

processed material
type: Class
subclass of: BFO_0000040
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: IAO_0000122
textual definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg

intervention design
type: Class
subclass of: study design
editor preferred label: 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: IAO_0000125
textual 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.
term editor: Philppe Rocca-Serra
definition source: OBI branch derived
imported from: http://purl.obolibrary.org/obo/obi.owl

data encoding
type: Class
subclass of: IAO_0000572
editor preferred label: data encoding
example of usage: storage of measurement results from an assay into a text file, such as
has curation status: IAO_0000120
textual definition: a documenting process to encode an information entity into a digital document
term 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
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: IAO_0000122
textual 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI

averaging objective
type: Class
subclass of: data transformation objective
editor preferred label: 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: IAO_0000122
textual definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: http://purl.obolibrary.org/obo/obi.owl

scattered molecular aggregate
type: Class
subclass of: object_aggregate
editor preferred label: scattered molecular aggregate
example of usage: the sodium and chloride ions in a glass of salt water
has curation status: IAO_0000123
textual 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
term editor: PERSON: Alan Ruttenberg
alternative term: 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 label: data representational model
example of usage: gene regulatory graph model
example of usage: phylogenetic tree
example of usage: protein interaction network
has curation status: IAO_0000120
textual 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.
term editor: Melanie Courtot
alternative term: data structure
alternative term: data structure specification
definition source: GROUP: OBI
curator note: 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
imported from: http://purl.obolibrary.org/obo/obi.owl

center value
type: Class
subclass of: data item
editor preferred label: center value
has curation status: IAO_0000125
textual 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.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: 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: OBI_0000312
    some values from: averaging data transformation
subclass of: data item
editor preferred label: average value
has curation status: IAO_0000125
textual definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: arithmetic mean
alternative term: 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: IAO_0000038
editor preferred label: 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: IAO_0000123
textual 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.
term editor: Bjoern Peters
term editor: Chris Stoeckert
term 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 label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
has curation status: IAO_0000123
textual definition: A device is a processed material which is designed to perform some function or functions
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.
term editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI Vancouver workshop 2010
comment: would include reagents

computer cluster
type: Class
subclass of: computer
editor preferred label: computer cluster
has curation status: IAO_0000120
textual definition: A group of linked computers, working together closely so that in many respects they form a single computer.
term 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 label: 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: IAO_0000120
textual definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
term 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 label: environmental history design
has curation status: IAO_0000120
textual definition: A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
term 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 label: disease state design
has curation status: IAO_0000120
textual 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.
term 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 label: pathogenicity design
has curation status: IAO_0000120
textual 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.
term 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: OBI_0000312
        some values from: Class
subclass of: service
editor preferred label: data service
example of usage: Data analysis service such statistical abalysis or storage service such data backup.
has curation status: IAO_0000125
textual definition: A service that has some information content entity as input and output.
term editor: PERSON: Carlo Torniai
term 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 label: 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: IAO_0000120
textual definition: A scalar measurement datum that represents the number of events occuring over a time interval
term editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: http://purl.obolibrary.org/obo/obi.owl

investigation description
type: Class
subclass of: IAO_0000300
editor preferred label: investigation description
has curation status: IAO_0000120
textual definition: A textual entity that describes an investigation.
term 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

investigation identifier
type: Class
subclass of: IAO_0000577
editor preferred label: investigation identifier
has curation status: IAO_0000120
textual definition: A CRID symbol used to identify an investigation.
term 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: IAO_0020000
editor preferred label: grant identifier
has curation status: IAO_0000120
textual definition: A CRID symbol used to identify a grant.
term 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

systematic review study design
type: Class
subclass of: study design
editor preferred label: 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: IAO_0000120
textual 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.
term editor: PERSON: Bill Hogan

digital object identifier
type: Class
subclass of: IAO_0020000
editor preferred label: 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: IAO_0000120
textual 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/
term editor: OBI developers
alternative term: 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
editor preferred label: organism
has curation status: IAO_0000121
textual 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.
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 label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: IAO_0000125
textual definition: A data transformation is a process which produces output data from input data
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: http://purl.obolibrary.org/obo/obi.owl

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: IAO_0000122
textual definition: A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
term 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: OBI_0000299
    some values from: average value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: data transformation
editor preferred label: averaging data transformation
has curation status: IAO_0000123
textual definition: An averaging data transformation is a data transformation that has objective averaging.
term 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 label: 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: IAO_0000125
textual definition: observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
term 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 label: predicted data item
has curation status: IAO_0000120
textual 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.
term 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: IAO_0000572
editor preferred label: digital curation
example of usage: PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
has curation status: IAO_0000120
textual 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.
term editor: Philippe Rocca-Serra
definition source: wikipedia
imported from: http://purl.obolibrary.org/obo/obi.owl

computer
type: Class
subclass of: device
editor preferred label: computer
example of usage: Apple PowerBook, Dell OptiPlex
has curation status: IAO_0000122
textual definition: A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
term editor: Melanie Courtot
term editor: Trish Whetzel
definition source: http://en.wikipedia.org/wiki/Computer

study design
type: Class
subclass of: plan specification
editor preferred label: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: IAO_0000122
textual 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.
term editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

time series design
type: Class
subclass of: study design
editor preferred label: 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: IAO_0000125
textual definition: Groups of assays that are related as part of a time series.
term 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
textual definition: A planned process that realizes the concretization of a software.
term editor: ITPPR
alternative term: operation
definition source: ITPPR
imported from: http://purl.obolibrary.org/obo/OBIws.owl

web service execution
type: Class
subclass of: software execution
textual definition: A software execution that is provided by the web service, and involves invoking software execution over network.
term editor: ITPPR
alternative term: web service operation
definition source: ITPPR
imported from: http://purl.obolibrary.org/obo/OBIws.owl

clinical finding
type: Class
subclass of: data item
textual 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.
term 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
textual 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.
term 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: BFO_0000019
textual 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.
term 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
textual definition: A clinically abnormal phenotype.
term 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: BFO_0000016
textual definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
term editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:21:20Z
Unique Apollo Label: disease

homeostasis
type: Class
subclass of: BFO_0000016
textual 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.
term editor: Albert Goldfain
term editor: Barry Smith
term editor: Richard H. Scheuermann
term 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: BFO_0000040
textual definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
term 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: http://purl.obolibrary.org/obo/ogms.owl

disease course
type: Class
subclass of: BFO_0000015
editor preferred label: disease course
textual definition: The totality of all processes through which a given disease instance is realized.
term 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: http://purl.obolibrary.org/obo/ido.owl
imported from: http://purl.obolibrary.org/obo/ogms.owl

extended organism
type: Class
subclass of: object_aggregate
textual 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.
term editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-01-25T04:51:11Z
imported from: http://purl.obolibrary.org/obo/ogms.owl

treatment
type: Class
subclass of: planned process
textual definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
term 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
textual definition: A processual entity which has as parts all the processes in which a given organism is participant.
term 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: BFO_0000015
textual 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
term 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: health care process
textual 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
term 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
textual definition: TODO
term 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
textual definition: TODO
term 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
textual definition: TODO
term 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
textual definition: TODO
term 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: BFO_0000015
textual definition: A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course.
term 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: IAO_0020000
textual definition: A CRID that constitutes a reference to an Internet resource.
term editor: Mathias Brochhausen
alternative term: 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: Restriction
  on property: RO_0000052
  some values from: NCBITaxon 9606
textual definition: A social role inhering in a human being.
term editor: Mathias Brochhausen
term editor: William R. Hogan
imported from: http://purl.obolibrary.org/obo/omrse.owl

gender role
type: Class
subclass of: BFO_0000023
textual definition: A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture.
term editor: Mathias Brochhausen
definition source: http://en.wikipedia.org/wiki/Gender_role
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: sex

male gender role
type: Class
subclass of: gender role
textual definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question.
term editor: Mathias Brochhausen
alternative term: male gender
imported from: http://purl.obolibrary.org/obo/omrse.owl

female gender role
type: Class
subclass of: gender role
textual definition: A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question.
term editor: Mathias Brochhausen
alternative term: female gender
imported from: http://purl.obolibrary.org/obo/omrse.owl

human health care role
type: Class
subclass of: role in human social processes
textual 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.
term editor: William R. Hogan
alternative term: health care role
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Mathias Brochhausen

patient role
type: Class
subclass of: human health care role
textual definition: A human health care role that inheres in an organism [human?] as the recipient of a health care service.
textual definition: A role borne by an organism being as the recipient of a health care service.
term editor: Amanda Hicks
term editor: Mathias Brochhausen
alternative term: patient
definition source: http://en.wikipedia.org/wiki/Patient
imported from: http://purl.obolibrary.org/obo/omrse.owl

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

collection of organisms
type: Class
equivalent class: PCO:collection of organisms
equivalent class: Class
  intersection of: object_aggregate
  intersection of: Restriction
    on property: RO_0002351
    some values from: organism
  intersection of: Restriction
    on property: RO_0002351
    all values from: organism
subclass of: object_aggregate
textual definition: An object aggregate of organisms.
elucidation: This term refers to a real population, such as the population of Allegheny County or of the U.S. As a set, it could null (size zero), for example the population of people in Allegheny County older than 130 years of age. It could also be a single organism. The population is not restricted to members of one species.
comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class.

collection of humans
type: Class
equivalent class: Class
  intersection of: collection of organisms
  intersection of: Restriction
    on property: RO_0002351
    some values from: NCBITaxon 9606
  intersection of: Restriction
    on property: RO_0002351
    all values from: NCBITaxon 9606
subclass of: collection of organisms of the same species
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: An object aggregate all of whose components are human beings.

role in human social processes
type: Class
subclass of: BFO_0000023
textual definition: A role inhering in an entity realized by social interactions in human society.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Previous definition: A role played by an entity in human social processes.

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

organism social role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: RO_0000052
  some values from: organism
textual definition: A role in human social processes that inheres in an organism.
term editor: William R. Hogan Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants.
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
textual definition: An organization social role that is realized by a health care process.
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: Previous definition: An organization social role played by an organization in health care processes.

aggregate of organizations
type: Class
equivalent class: Class
  intersection of: object_aggregate
  intersection of: Restriction
    on property: RO_0002351
    some values from: organization
  intersection of: Restriction
    on property: RO_0002351
    all values from: organization
subclass of: object_aggregate
textual definition: An aggregate of organizations that have some feature in common, but is not itself an organization.
term editor: William R. Hogan
comment: It is often convenient to group organizations together that otherwise might not even interact with one another.

aggregate of sovereign states
type: Class
subclass of: aggregate of geopolitical organizations
textual definition: An aggregate of sovereign states that share some feature in common, but is not an organization nor necessarily the outcome of some treaty among them.
term editor: William R. Hogan

aggregate of geopolitical organizations
type: Class
subclass of: aggregate of organizations
textual definition: An aggregate of geopolitical organizations with some feature in common.
term editor: William R. Hogan
comment: Examples: all sovereign states whose territory is part of North America, all British Crown Dependencies, all midwestern US States, all US dependencies, etc.

aggregate of dependencies
type: Class
subclass of: aggregate of geopolitical organizations

aggregate of major administrative subdivisions
type: Class
subclass of: aggregate of geopolitical organizations

hospital function
type: Class
subclass of: BFO_0000034
textual definition: A function inhering in a facility that manifests by the facility participating in providing inpatient and outpatient healthcare to a patient population.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

school function
type: Class
subclass of: BFO_0000034
textual definition: A function inhering in a facility that manifests by the facility participating in providing formal education to a student population.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

hospital role
type: Class
subclass of: health care provider organization role
textual definition: A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

school role
type: Class
subclass of: BFO_0000023
term editor: An organization social role that inheres in an organization and is realized by providing formal education to students.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

hospital organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: is bearer of
    some values from: hospital role
subclass of: organization
textual definition: An organization that is the bearer of a hospital role.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

school organization
type: Class
equivalent class: Class
  intersection of: organization
  intersection of: Restriction
    on property: is bearer of
    some values from: school role
subclass of: organization
textual definition: An organization that is the bearer of a school role.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

student role
type: Class
subclass of: human social role
textual definition: A human social role that is realized by the process of formal education that the bearer undergoes.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

nursery school role
type: Class
subclass of: school role
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: preschool
comment: Key motivating use case was Synthia synthetic population data.

primary school role
type: Class
subclass of: school role
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: primarySchool
comment: Key motivating use case was Synthia synthetic population data.

architectural structure
type: Class
subclass of: BFO_0000040
textual definition: A material entity that is a human made strcuture with firm connection between its foundation and the ground.
term editor: Mathias Brochhausen
definition source: http://de.wikipedia.org/wiki/Bauwerk
imported from: http://purl.obolibrary.org/obo/omrse.owl
comment: "Building" is a subclass of this.
comment: This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".

facility
type: Class
subclass of: architectural structure
textual definition: An architectural structure that bears some function.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl

hospital facility
type: Class
subclass of: health care facility
textual definition: A facility that is run by a hospital organization and is the bearer of a hospital function.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: HealthcareFacility

school facility
type: Class
subclass of: facility
textual definition: A facility that is run by a school organization and is the bearer of a school function.
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: SchoolFacility

secondary school role
type: Class
subclass of: school role
term editor: Mathias Brochhausen
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: secondarySchool
comment: Key motivating use case was Synthia synthetic population data.

housing unit
type: Class
subclass of: BFO_0000040
textual definition: A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function.
term editor: Amanda Hicks
definition source: https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: houses
comment: Housing units are individuated by their residence functions.

household
type: Class
subclass of: BFO_0000040
textual definition: A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of its residence function.
term editor: Amanda Hicks
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: Household

workplace facility
type: Class
subclass of: facility
term editor: Amanda Hicks
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: workplace

workplace function
type: Class
subclass of: BFO_0000034
textual definition: a function inhering in a material entity that is realized by that material entity being the site where the work of some organization is carried out
term editor: Amanda Hicks
imported from: http://purl.obolibrary.org/obo/omrse.owl

racial identity datum
type: Class
subclass of: identity datum
textual definition: A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
imported from: http://purl.obolibrary.org/obo/omrse.owl
Unique Apollo Label: race

health care facility
type: Class
subclass of: facility
term editor: A facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
imported from: http://purl.obolibrary.org/obo/omrse.owl

identity datum
type: Class
subclass of: information content entity
imported from: http://purl.obolibrary.org/obo/omrse.owl
creator: Amanda Hicks
creator: An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.

distance
type: Class
subclass of: physical quality
textual 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: BFO_0000019
editor preferred label: biological sex
textual 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
textual 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: http://purl.obolibrary.org/obo/pato.owl
has_obo_namespace: quality
id: PATO:0000051
in_subset: attribute slim

structure
type: Class
subclass of: morphology
textual 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
textual 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 label: female
textual 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 label: male
textual 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
textual 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: http://purl.obolibrary.org/obo/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: BFO_0000019
textual definition: A quality which inheres in a continuant.
imported from: http://purl.obolibrary.org/obo/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.

1-D extent
type: Class
subclass of: PATO_0000117
textual 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

in contact with
type: Class
subclass of: structure
textual 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: PATO_0000122
textual 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.
textual definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative term: group of organisms
alternative term: 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: BFO_0000177
  some values from: biotic ecosystem
textual 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
textual 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: IAO_0000122
textual 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
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term 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: IAO_0000122
textual definition: statistical sample size is a count evaluating the number of individual experimental units
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term 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: IAO_0000122
textual 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
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: specificity

true positive rate
type: Class
subclass of: measurement datum
has curation status: IAO_0000122
textual 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
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: recall
alternative term: 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
textual 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.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: risk ratio
definition source: IAO_0000122
imported from: http://purl.obolibrary.org/obo/stato.owl

categorical variable
type: Class
subclass of: variable
has curation status: IAO_0000122
textual 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
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: discrete variable
alternative term: nominal variable
alternative term: 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: IAO_0000122
textual 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.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term 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: IAO_0000123
textual definition: Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.
term editor: Camille Maumet
term editor: Karl Helmer
term editor: Philippe Rocca-Serra
term 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: IAO_0000123
textual 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.
term editor: Alejandra Gonzalez-Beltran
term editor: Matthew Diller
term editor: Orlaith Burke
term 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

anatomical structure
type: Class
subclass of: material anatomical entity
textual definition: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.
imported from: http://purl.obolibrary.org/obo/uberon.owl
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:67135
database_cross_reference: GAID:781
database_cross_reference: HAO:0000003
database_cross_reference: MA:0003000
database_cross_reference: MESH:A13
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_obo_namespace: uberon
id: UBERON:0000061
in_subset: upper level

material anatomical entity
type: Class
subclass of: BFO_0000040
textual definition: Anatomical entity that has mass.
imported from: http://purl.obolibrary.org/obo/uberon.owl
database_cross_reference: AAO:0010264
database_cross_reference: AEO:0000006
database_cross_reference: BILA:0000006
database_cross_reference: CARO:0000006
database_cross_reference: EHDAA2:0003006
database_cross_reference: FBbt:00007016
database_cross_reference: FMA:67165
database_cross_reference: HAO:0000006
database_cross_reference: TAO:0001836
database_cross_reference: TGMA:0001826
database_cross_reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in_subset: upper level

anatomical system
type: Class
subclass of: anatomical group
textual 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
textual 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
textual 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

immune system
type: Class
subclass of: anatomical system
textual 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
textual definition: An anatomical structure that has more than one cell as a part.
imported from: http://purl.obolibrary.org/obo/uberon.owl
database_cross_reference: CARO:0010000
database_cross_reference: FBbt:00100313
has_exact_synonym: multicellular structure
has_obo_namespace: uberon
id: UBERON:0010000
in_subset: upper level

life cycle temporal boundary
type: Class
subclass of: BFO_0000015
textual 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
textual definition: A life cycle temporal boundary that marks the end of the life cycle of the organism.
imported from: http://purl.obolibrary.org/obo/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

UO_0000003
type: Class
subclass of: measurement unit label
imported from: UO
Unique Apollo Label: unitOfTime

dimensionless unit
type: Class
subclass of: measurement unit label
textual 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
textual 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
textual 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
textual 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
textual 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: OBI_0000312
    some values from: vaccine preparation
  intersection of: Restriction
    on property: is 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
textual 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.
term editor: YH, BP, BS, MC, LC, XZ, RS
term 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
textual definition: A vaccine contraindication is a contraindication that increases the risks of a vaccination.
term editor: YH
alternative term: contraindication for vaccination
imported from: http://purl.obolibrary.org/obo/vo.owl
Unique Apollo Label: VaccineContraindications

vaccine function
type: Class
subclass of: BFO_0000034
textual 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.
term editor: YH, MC, XZ, and AR
imported from: http://purl.obolibrary.org/obo/vo.owl

vaccine preparation
type: Class
subclass of: planned process
textual definition: vaccine preparation is a manufacturing process to produce a vaccine.
term editor: YH, BP
alternative term: vaccine generation
alternative term: vaccine production
imported from: http://purl.obolibrary.org/obo/vo.owl

obsolete specificity of case detection
type: Class
subclass of: true negative rate
textual 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.
term 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
subclass of: true negative rate
textual 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
term 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
subclass of: true positive rate
textual 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
term 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

news article
type: Class
subclass of: IAO_0000310
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
textual definition: Genomic data is data about the genomes of an organism.
term editor: James Malone

Obsolete Class
type: Class

organism population universal
type: NamedIndividual

atmosphere of the Earth
type: NamedIndividual
type: atmosphere

week
type: NamedIndividual
type: UO_0000003
comment: "A time unit which is equal to 7 days." [Wikipedia:Wikipedia]

GEO_000000005
Unique Apollo Label: administrativeLocations

IAO_0000301
has curation status: IAO_0000125
Unique Apollo Label: Reference

IAO_0000311
has curation status: IAO_0000120
Unique Apollo Label: publication

IAO_0000321
has curation status: IAO_0000120
Unique Apollo Label: authors

IAO_0000324
has curation status: IAO_0000120
Unique Apollo Label: acknowledgements

IAO_0000403
has curation status: IAO_0000124
has curation status: IAO_0000123
Unique Apollo Label: CartesianCircleLocationDefinition

IAO_0000591
Unique Apollo Label: softwareType
has curation status: IAO_0000123

OBI_0001620
Unique Apollo Label: Latitude

OBI_0001621
Unique Apollo Label: Longitude

UO_0000001
Unique Apollo Label: unitOfDistance
imported from: UO

bad_pno_import_1

bad_pno_import_2

bad_pno_import_3

bad_pno_import_4

Class
intersection of: BFO_0000038
intersection of: Restriction
  on property: has temporal occupant
  qualified cardinality: 1
  on class: history