VIO: Vaccine Investigation Ontology
type: Ontology
date: 05-22-2018
subject: A biomedical ontology supporting standardized vaccine investigation.
format: OWL-DL
description: VIO is an VO-extended ontology with the aim to standardize the metadata types in various vaccine investigation studies.
version info: Vision Release: 1.0.01
creator: Yongqun "Oliver" He (YH)

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

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

editor preferred label
type: AnnotationProperty
label: editor preferred term
label: editor preferred term~editor preferred label
editor preferred label: editor preferred term~editor preferred label
term editor: PERSON:Daniel Schober
editor preferred label: editor preferred term
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred label: editor preferred label
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has curation status: IAO_0000122

example of usage
type: AnnotationProperty
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: example
has curation status: IAO_0000122

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

definition
type: AnnotationProperty
label: textual definition
editor preferred label: definition
editor preferred label: textual definition
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
has curation status: IAO_0000122

editor note
type: AnnotationProperty
is metadata tag: 1
database_cross_reference: IAO:0000116
id: editor_note
shorthand: editor_note
has_obo_namespace: uberon
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: editor note
has curation status: IAO_0000122

term editor
type: AnnotationProperty
label: definition editor
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor: PERSON:Daniel Schober
editor preferred label: definition editor
editor preferred label: term editor
has curation status: IAO_0000122

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: alternative term
has curation status: IAO_0000125

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: definition source
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has curation status: IAO_0000122

curator notes
type: AnnotationProperty
label: curator note
is metadata tag: 1
database_cross_reference: IAO:0000232
id: curator_notes
shorthand: curator_notes
has_obo_namespace: uberon
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg
editor preferred label: curator note
has curation status: IAO_0000122

imported from
type: AnnotationProperty
definition: For external terms/classes, the ontology from which the term was imported
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred label: imported from
has curation status: IAO_0000125

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

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

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

has_specified_input
type: AnnotationProperty
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
editor preferred label: has_specified_input
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
imported from: obi.owl
imported from: Vaccine Ontology
type: ObjectProperty
sub property of: has participant

has_specified_output
type: AnnotationProperty
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
editor preferred label: has_specified_output
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: PERSON: Alan Ruttenberg
has curation status: IAO_0000122
imported from: obi.owl
imported from: Vaccine Ontology
type: ObjectProperty
sub property of: has participant

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

logical macro assertion
type: AnnotationProperty
definition: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

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

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

contributor
type: AnnotationProperty
id: dc-contributor
shorthand: dc-contributor
is metadata tag: true
has_obo_namespace: uberon

creator
type: AnnotationProperty

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

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

database_cross_reference
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

shorthand
type: AnnotationProperty

label
type: AnnotationProperty
editor preferred label: label

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

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

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

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

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

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

specifically depends on at all times
type: ObjectProperty
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
BFO OWL specification label: s-depends-on_at
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 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]
example of usage: A pain s-depends_on the organism that is experiencing the pain
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
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])
example of usage: a gait s-depends_on the walking object. (All at some specific time.)
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])
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: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
BFO CLIF specification label: specificallyDependsOn
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]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
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]
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.
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])
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
example of usage: a shape s-depends_on the shaped object
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])
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 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
sub property of: specifically depends on at some time
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

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

has occurrent part
type: ObjectProperty
type: TransitiveProperty
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.
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])
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.
definition: b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO OWL specification label: o-has-part
has associated axiom(fol): (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
editor note: [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
BFO CLIF specification label: hasOccurrentPart
example of usage: [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
domain: occurrent
range: occurrent
inverse of: part of occurrent
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

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

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

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

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

part of occurrent
type: ObjectProperty
type: TransitiveProperty
editor note: BFO2 Reference: occurrent
BFO CLIF specification label: occurrentPartOf
BFO OWL specification label: o-part-of
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]
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])
has associated axiom(fol): (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
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 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]
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.
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.
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])
example of usage: the first set of the tennis match occurrent_part_of the tennis match.
range: occurrent
domain: occurrent
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

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

projects onto spatial region at some time
type: ObjectProperty
BFO OWL specification label: st-projects-onto-s_st
range: spatial region
domain: spatiotemporal region
inverse of: spatial projection of spatiotemporal at some time
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

spatial projection of spatiotemporal at some time
type: ObjectProperty
BFO OWL specification label: s-projection-of-st_st
domain: spatial region
range: spatiotemporal region
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

projects onto temporal region
type: ObjectProperty
BFO OWL specification label: st-projects-onto-t
range: temporal region
domain: spatiotemporal region
sub property of: exists at
inverse of: temporal projection of spatiotemporal
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

temporal projection of spatiotemporal
type: ObjectProperty
BFO OWL specification label: t-projection-of-st
domain: temporal region
range: spatiotemporal region
sub property of: during which exists
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

occupies temporal region
type: ObjectProperty
BFO OWL specification label: spans
BFO CLIF specification label: occupiesTemporalRegion
elucidation: p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
domain: occurrent
range: temporal region
sub property of: exists at
inverse of: has temporal occupant
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

has temporal occupant
type: ObjectProperty
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])
BFO OWL specification label: span-of
BFO CLIF specification label: spanOf
range: occurrent
domain: temporal region
sub property of: during which exists
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

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

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

has specific dependent at all times
type: ObjectProperty
BFO OWL specification label: has-s-dep_at
sub property of: has specific dependent at some time
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

specifically depends on at some time
type: ObjectProperty
BFO OWL specification label: s-depends-on_st
editor note: BFO2 Reference: specifically dependent continuant\; process; process boundary
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 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]
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)
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 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 z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
example of usage: A pain s-depends_on the organism that is experiencing the pain
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.
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])
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
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
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])
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 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: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
BFO CLIF specification label: specificallyDependsOn
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 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 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 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
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology
range: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
domain: Class
  union of: process
  union of: specifically dependent continuant

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

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

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

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

is_specified_output_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
editor preferred label: is_specified_output_of
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
has curation status: IAO_0000122
sub property of: participates in
imported from: obi.owl
imported from: Vaccine Ontology

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
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.
editor preferred label: achieves_planned_objective
curator notes: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
has curation status: IAO_0000120
imported from: obi.owl
imported from: Vaccine Ontology

inheres in
type: ObjectProperty
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor preferred label: inheres in
alternative term: inheres_in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
temporal interpretation: RO_0001901
sub property of: inheres in part of
imported from: ro.owl
imported from: Vaccine Ontology

participates in
type: ObjectProperty
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
editor preferred label: participates in
alternative term: participates_in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
imported from: obi.owl
imported from: Vaccine Ontology

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

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

role of
type: ObjectProperty
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
alternative term: is role of
alternative term: role_of
example of usage: this investigator role is a role of this person
sub property of: inheres in
imported from: ro.owl
imported from: Vaccine Ontology

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

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

inheres in part of
type: ObjectProperty
definition: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
term editor: Chris Mungall
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
temporal interpretation: RO_0001901
sub property of: depends on
imported from: ro.owl
imported from: Vaccine Ontology
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205

depends on
type: ObjectProperty
term editor: Chris Mungall
imported from: ro.owl
imported from: Vaccine Ontology

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

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

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

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: Class
      union of: specifically dependent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: specifically depends on at some time
  all values from: Nothing
BFO CLIF specification label: IndependentContinuant
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: an organism
BFO OWL specification label: ic
example of usage: a chair
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
imported from: BFO
imported from: obi.owl
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

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

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

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

disposition
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: role
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: role
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
BFO CLIF specification label: Disposition
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89
example of usage: an atom of element X has the disposition to decay to an atom of element Y
BFO OWL specification label: disposition
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocitosis and exocitosis
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
imported from: oae.owl
imported from: obi.owl
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

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

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

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

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

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

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

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

immaterial entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: immaterial entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    complement of: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    complement of: material entity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
imported from: obi.owl
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

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

objective specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
alternative term: goal specification
editor preferred label: objective specification
has curation status: IAO_0000122
has curation status: IAO_0000125
imported from: obi.owl
imported from: Vaccine Ontology

data item
type: Class
subclass of: information content entity
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
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
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
alternative term: data
editor preferred label: data item
has curation status: IAO_0000125
imported from: iao.owl
imported from: obi.owl
imported from: Vaccine Ontology

information content entity
type: Class
subclass of: generically dependent continuant
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
definition: A generically dependent continuant that is about some thing.
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
term editor: PERSON: Chris Stoeckert
editor preferred label: information content entity
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
has curation status: IAO_0000122
has curation status: IAO_0000125
imported from: iao.owl
imported from: obi.owl
imported from: Vaccine Ontology

scalar measurement datum
type: Class
subclass of: measurement datum
example of usage: 10 feet. 3 ml.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
has curation status: IAO_0000120
imported from: iao.owl
imported from: Vaccine Ontology

directive information entity
type: Class
subclass of: information content entity
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
has curation status: IAO_0000122
has curation status: IAO_0000123
imported from: iao.owl
imported from: obi.owl
imported from: Vaccine Ontology

measurement datum
type: Class
subclass of: data item
editor note: 2/2/2009 is_specified_output of some assay?
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
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,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred label: measurement datum
term editor: person:Chris Stoeckert
has curation status: IAO_0000120
has curation status: IAO_0000125
imported from: iao.owl
imported from: obi.owl
imported from: Vaccine Ontology

planned process
type: Class
subclass of: process
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.)
curator notes: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
term editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition source: branch derived
editor preferred label: planned process
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
curator notes: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
has curation status: IAO_0000122
imported from: obi.owl
imported from: Vaccine Ontology

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

material to be added role
type: Class
subclass of: role
curator notes: 9 March 09 from discussion with PA branch
definition source: OBI
term editor: Role Branch
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
editor preferred label: material to be added role
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
has curation status: IAO_0000120
imported from: obi.owl
imported from: Vaccine Ontology

target of material addition role
type: Class
subclass of: role
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
term editor: GROUP: Role Branch
definition source: OBI
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
editor preferred label: target of material addition role
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
has curation status: IAO_0000120
imported from: obi.owl
imported from: Vaccine Ontology

host role
type: Class
subclass of: role
definition source: 30 Mar09 submitted by vaccine community
editor note: 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
term editor: GROUP: Role Branch
example of usage: In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
definition source: OBI
editor preferred label: host role
definition: host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
definition source: http://en.wikipedia.org/wiki/Host_(biology)
has curation status: IAO_0000120
imported from: obi.owl
imported from: Vaccine Ontology

organism
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: genome
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
definition source: WEB: http://en.wikipedia.org/wiki/Organism
example of usage: animal
example of usage: fungus
editor preferred label: organism
example of usage: plant
example of usage: virus
has curation status: IAO_0000121
has curation status: IAO_0000122
imported from: obi.owl
imported from: OGG: Ontology of Genes and Genomes
imported from: Vaccine Ontology

administering substance in vivo
type: Class
subclass of: planned process
editor note: 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
definition: A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
example of usage: Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
term editor: Person:Bjoern Peters
term editor: Bjoern Peters
editor note: Different routes and means of administration should go as children underneath this
definition source: IEDB
editor note: Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
editor preferred label: administering substance in vivo
example of usage: injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
editor note: needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
has curation status: IAO_0000125
imported from: obi.owl
imported from: Vaccine Ontology

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

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

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

frequency
type: Class
subclass of: physical quality
definition: A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
editor preferred label: frequency
imported from: Vaccine Ontology
imported from: PATO

physical quality
type: Class
subclass of: quality of a single physical entity
definition: A quality of a single physical entity that exists through action of continuants at the physical level of organisation.
editor preferred label: physical quality
imported from: Vaccine Ontology
imported from: PATO

quality of a single physical entity
type: Class
subclass of: physical object quality
definition: A physical object quality which inheres in a single-bearer.
editor preferred label: quality of a single physical entity
imported from: Vaccine Ontology
imported from: PATO

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
editor preferred label: physical object quality
imported from: Vaccine Ontology
imported from: PATO

vaccine
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: vaccine preparation
  intersection of: Restriction
    on property: has function
    some values from: Class
      intersection of: vaccine function
      intersection of: Restriction
        on property: realized in
        some values from: vaccine immunization
subclass of: processed material
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
see also: MeSH: D014612
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.
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.
imported from: Vaccine Ontology

vaccination
type: Class
equivalent class: Class
  intersection of: administering substance in vivo
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: material to be added role
      intersection of: Restriction
        on property: role of
        some values from: vaccine
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: target of material addition role
      intersection of: Restriction
        on property: role of
        some values from: organism
subclass of: administering substance in vivo
subclass of: Restriction
  on property: has participant
  some values from: vaccine
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: has role
      some values from: vaccine host role
definition: a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response.
alternative term: vaccine administration
term editor: YH, BP
imported from: Vaccine Ontology

vaccination frequency
type: Class
subclass of: frequency
term editor: YH
definition: Vaccination frequency is a qualitative term that represents how many times vaccination has occurred.
imported from: Vaccine Ontology

colony forming unit
type: Class
subclass of: titer
alternative term: CFU
editor note: Colony-forming unit (CFU) is a titer measurement of viable bacterial or fungal numbers. Unlike in direct microscopic counts where all cells, dead and living, are counted, CFU measures viable cells. By convenience the results are given as CFU/mL (colony-forming units per milliliter) for water, and CFU/g (colony-forming units per gram) for soil or other porous material.
term editor: YH
definition source: WEB: http://en.wikipedia.org/wiki/Colony-forming_unit
imported from: Vaccine Ontology

vaccine function
type: Class
equivalent class: Class
  union of: preventive vaccine function
  union of: therapeutic vaccine function
subclass of: function
term editor: YH, MC, XZ, and AR
editor note: PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term.
definition: 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.
imported from: Vaccine Ontology

preventive vaccine function
type: Class
subclass of: vaccine function
subclass of: Restriction
  on property: realized in
  some values from: induction of adaptive immune response to antigen
subclass of: Restriction
  on property: realized in
  some values from: disorder prevention
subclass of: Restriction
  on property: realized in
  some values from: vaccination
definition: preventive vaccine function is a vaccine function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which protects against a specific disorder.
alternative term: prophylactic vaccine function
term editor: YH
imported from: Vaccine Ontology

immunization
type: Class
subclass of: process
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
definition: immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens.
editor note: YH, XZ, BP
imported from: Vaccine Ontology

active immunization
type: Class
subclass of: immunization
term editor: YH, XZ
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
comment: Active immunization entails the introduction of a foreign molecule into the body, which causes the body itself to generate immunity against the target. This immunity comes from the T cells and the B cells with their antibodies. Active immunization can occur naturally when a person comes in contact with, for example, a microbe. If the person has not yet come into contact with the microbe and has no pre-made antibodies for defense (like in passive immunization), the person becomes immunized. The immune system will eventually create antibodies and other defenses against the microbe. The next time, the immune response against this microbe can be very efficient; this is the case in many of the childhood infections that a person only contracts once, but then is immune. Artificial active immunization is where the microbe, or parts of it, are injected into the person before they are able to take it in naturally. If whole microbes are used, they are pre-treated, Attenuated vaccine. (Wikipedia)
definition: Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target.
imported from: Vaccine Ontology

vaccine immunization
type: Class
subclass of: active immunization
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: immunization objective
subclass of: Restriction
  on property: has_specified_input
  some values from: vaccine
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: vaccine host role
    intersection of: Restriction
      on property: inheres in
      some values from: organism
definition: artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.
alternative term: artificial active immunization
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
term editor: YH, XZ
imported from: Vaccine Ontology

induction of adaptive immune response to antigen
type: Class
subclass of: active immunization
term editor: YH, XZ
definition: induction of adaptive immune response to antigen is an active immunization process that results in induction of adaptive immune response to some antigens, for example, in a vaccine.
imported from: Vaccine Ontology

disorder prevention
type: Class
subclass of: process
definition: disorder prevention is a processual entity that prevents a disorder that is the physical basis of a disease.
term editor: YH, XZ
imported from: Vaccine Ontology

disorder treatment
type: Class
subclass of: process
definition: disorder treatment is a processual entity that leads to treat a disorder that is the physical basis of a disease.
term editor: YH, XZ
imported from: Vaccine Ontology

modification of adaptive immune response to antigen
type: Class
subclass of: active immunization
definition: modification of adaptive immune response to antigen is an active immunization process that results in modification of an adaptive immune response to some antigens, for example, in a therapeutic vaccine.
term editor: YH, XZ
imported from: Vaccine Ontology

titer
type: Class
subclass of: measurement datum
term editor: YH
definition: A titer (or titre) is a measure of concentration. Titer testing employs serial dilution to obtain approximate quantitative information from an analytical procedure that inherently only evaluates as positive or negative. The titer corresponds to the highest dilution factor that still yields a positive reading; for example, positive readings in the first 8 serial twofold dilutions translate into a titer of 1:256.
definition source: WEB:http://en.wikipedia.org/wiki/Titer
imported from: Vaccine Ontology

therapeutic vaccine function
type: Class
subclass of: vaccine function
subclass of: Restriction
  on property: realized in
  some values from: vaccination
subclass of: Class
  union of: Restriction
    on property: realized in
    some values from: induction of adaptive immune response to antigen
  union of: Restriction
    on property: realized in
    some values from: modification of adaptive immune response to antigen
subclass of: Restriction
  on property: realized in
  some values from: disorder treatment
term editor: YH
definition: The therapeutic vaccine function is a function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which ameliorates a specific disorder.
imported from: Vaccine Ontology

immunization objective
type: Class
subclass of: objective specification
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
term editor: YH, XZ
definition: immunization objective is the specification of an objective to achieve immunization.
imported from: Vaccine Ontology

vaccine preparation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: vaccine target specification
subclass of: Restriction
  on property: has_specified_output
  some values from: vaccine
alternative term: vaccine production
alternative term: vaccine generation
definition: vaccine preparation is a manufacturing process to produce a vaccine.
term editor: YH, BP
imported from: Vaccine Ontology

vaccination dose
type: Class
subclass of: dose
term editor: YH
editor note: vaccination dose is a dose of vaccine that is used in a vaccination. Vaccination dose may be and may be not the same as the vaccine dose.
imported from: Vaccine Ontology

dose
type: Class
subclass of: scalar measurement datum
term editor: YH, MC
definition: dose is a measurement data that measures the quantity of something that may be eaten by or administered to an organism, or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
definition source: WEB: http://en.wikipedia.org/wiki/Dose_%28biochemistry%29
imported from: Vaccine Ontology

challenge dose
type: Class
subclass of: dose
definition: challenge dose is a dose of a virulent pathogen used for a vaccine challenge process.
term editor: YH
imported from: Vaccine Ontology

reduction of colony forming unit
type: Class
subclass of: titer
term editor: YH, ZX
definition: reduction of colony-forming unit (CFU) is a titer measurement of viable bacterial or fungal numbers. It equals to a reduction of a CFU count from another CFU count. This term is often used as a measurement of a vaccine protection study.
imported from: Vaccine Ontology

vaccine strain datum
type: Class
subclass of: measurement datum
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition: a measurement datum that represents a vaccine strain. Different strains can be represented using distinct digital numbers.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
imported from: Vaccine Ontology

vaccine viability datum
type: Class
subclass of: measurement datum
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
definition: a measurement datum that represents vaccine viability. 0 = live; 1 = irradiated; 2 = killed.
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
imported from: Vaccine Ontology

vaccine adjuvant usage datum
type: Class
subclass of: measurement datum
term editor: YH
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition: a measurement datum that indicates the usage of a vaccine adjuvant. Different digital numbers can be used to represent different adjuvants.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
imported from: Vaccine Ontology

vaccine protective antigen datum
type: Class
subclass of: measurement datum
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
definition: a measurement datum that represents a specific protective antigen used in a vaccine. The antigen can be represented by a described digit.
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
imported from: Vaccine Ontology

mutated gene in vaccine strain datum
type: Class
subclass of: measurement datum
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
definition: a measurement datum that represents a specific mutated gene from a vaccine strain. The mutated can be represented by a described digit.
imported from: Vaccine Ontology

vaccination mouse strain datum
type: Class
subclass of: measurement datum
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
term editor: YH
definition: a measurement datum that represents a specific mouse strain used for vaccination. Different strains can be represented using discretized digitals. For example, 0 = BALB/c; 1 = CD1; 2 = mixed/outbred; 3 = C57BL/6; 4 = OF1; 5 = 129/Sv; 6 = Swiss albino.
imported from: Vaccine Ontology

biological sex datum
type: Class
subclass of: measurement datum
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
definition: A measurement datum that represents the biological sex of an animal. The result can be represented using a discretized digit, for example, 0 = female; 1 = male; 2 = unknown.
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
term editor: YH
imported from: Vaccine Ontology

vaccination route datum
type: Class
subclass of: measurement datum
definition: a measurement datum that represents a specific route (e.g., i.p.) used for vaccination. Different routes can be represented using discretized digitals. 0 = IP; 1 = PO; 2 = SC; 3 = IM; 4 = IN; 6 = IG; 7 = IV; 8 = ID.
term editor: YH
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
imported from: Vaccine Ontology

vaccination dose (unit: CFU)
type: Class
subclass of: vaccination dose
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
term editor: YH
definition: a vaccination dose that is used with the unit of colony forming units (CFU).
imported from: Vaccine Ontology

animal age at vaccination in days
type: Class
subclass of: measurement datum
term editor: YH
definition: A measurement datum that represents the animal age (unit: day) at the time of vaccination.
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
imported from: Vaccine Ontology

pathogen strain for challenge datum
type: Class
subclass of: measurement datum
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
definition: a measurement datum that represents a specific pathogen strain used for animal challenge study. Different pathogen strains can be represented using discretized digitals.
term editor: YH
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
imported from: Vaccine Ontology

pathogen challenge datum
type: Class
subclass of: measurement datum
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
definition: a measurement datum that represents a specific pathogen used for animal challenge study. Different pathogens can be represented using discretized digitals.
imported from: Vaccine Ontology

challenge dose (unit: CFU)
type: Class
subclass of: challenge dose
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
term editor: YH
definition: a challenge dose that is represented with the unit of colony forming units (CFU).
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
imported from: Vaccine Ontology

vaccination-challenge interval in days
type: Class
subclass of: measurement datum
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
definition: a measurement datum that represents a length of days as the interval between a vaccination and a challenge in a specific vaccine protection study.
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
imported from: Vaccine Ontology

CFU per spleen
type: Class
subclass of: colony forming unit
definition: A colony forming unit (CFU) from the sample of mouse spleen.
term editor: YH
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
imported from: Vaccine Ontology

CFU reduction per spleen
type: Class
subclass of: reduction of colony forming unit
definition: a reduction of CFU that was measured with the unit of colony forming units (CFU) from the sample of mouse spleen.
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
term editor: YH
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
imported from: Vaccine Ontology

vaccine protection efficacy datum
type: Class
subclass of: measurement datum
definition source: Todd TE, Tibi O, Lin Y, Sayers S, Bronner DN, Xiang Z, He Y. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics. 2013, 14(Suppl 6):S3. PMID: 23735014. PMCID: PMC3633026.
term editor: YH
definition: a measurement datum that represents a type of vaccine protection efficacy as an outcome of a vaccine protection study. The result can be represented as a digit, for example, 0 = no protection, and 1 = protection (determined by a p-value cutoff).
definition source: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. URL: http://www.hegroup.org/docs/ANOVA_Vaccine_usecase_camera.pdf
imported from: Vaccine Ontology

vaccine host role
type: Class
subclass of: host role
subclass of: Restriction
  on property: inheres in
  some values from: organism
subclass of: Restriction
  on property: realized in
  some values from: immunization
definition: a role of host that contains vaccine. It is a role that inheres in an organism that is the target of a vaccine administration (vaccination process).
term editor: YH, ZX
imported from: Vaccine Ontology

vaccine target specification
type: Class
subclass of: objective specification
definition: The objective that intends to produce vaccine via the vaccine preparation process.
creator: YH
imported from: Vaccine Ontology

OGG: Ontology of Genes and Genomes
date: 12-01-2016
subject: A biological ontology in the area of genes and genomes.
creator: Bin Zhao
description: OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
format: OWL-DL
version info: Vision Release: 1.0.59
creator: Yongqun "Oliver" He (YH)
creator: Yue Liu
license: http://creativecommons.org/licenses/by/3.0/

Vaccine Ontology
creator: Edison Ong
creator: Lindsay Cowell
creator: Alexander D. Diehl
creator: Alan Ruttenburg
date: April 1, 2018
contributor: Erica Marcos
creator: Jason Hu
creator: Bjoern Peters
contributor: Chris mungall
creator: Rebecca Racz
creator: Richard H. Scheuermann
creator: Samantha G. Sayers (SGS)
creator: Thomas Todd
creator: Melanie Courtot
creator: Omar Tibi
creator: Barry Smith
subject: An ontology in the domain of vaccine and vaccination
contributor: Ningxian Fan
creator: Ningxian Fan
format: OWL-DL
creator: Ronak Sutariya
contributor: Shunzhou Deng
description: The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is initiated and primarily developed by Dr. Yongqun "Oliver" He at the University of Michigan Medical School. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
version info: Vision Release; 1.0.799
default language: en
contributor: Ryan R. Brinkman
creator: Yongqun "Oliver" He (YH)
creator: Yu Lin (YL)
creator: Zuoshuang "Allen" Xiang
license: http://creativecommons.org/licenses/by/3.0/