ogsf-merged.owl
type: Ontology
version info: 2.0
creator: 'Asiyah' Yu Lin (YL)
contributor: 'Oliver' Yongqun He (YH)
license: New BSD license
definition: Ontology of Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a biological process.
date: 11-22-2014
imports: bfo.owl

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

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

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

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

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

definition
type: AnnotationProperty
label: textual definition
ReO alternative term: Definition
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition 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.
editor preferred term: definition
has curation status: ready for release

editor note
type: AnnotationProperty
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: ready for release

definition editor
type: AnnotationProperty
label: term editor
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
ReO alternative term: definition_editor
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
definition editor: PERSON:Daniel Schober
editor preferred term: definition editor
editor preferred term: term editor
has curation status: ready for release

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

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

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

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

elucidation
type: AnnotationProperty

has associated axiom(nl)
type: AnnotationProperty

has associated axiom(fol)
type: AnnotationProperty

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

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

reo_requires_feedback_to
type: AnnotationProperty
definition: FLAG to record classes where we have issues or suggestions to feedback to an external ontology regarding a class imported into the home/current ontology (ie ReO). Most often used to address cases where imported term definitions are felt to be unclear, incomplete, erroneous, or inconsistent.
sub property of: REO_0000182

ReO alternative term
type: AnnotationProperty
sub property of: alternative term

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

part_of
type: ObjectProperty
type: TransitiveProperty
label: is part of
label: part of
shorthand: part_of
imported from: BFO
imported from: ro.owl
imported from: vo.owl

has part
type: ObjectProperty
type: TransitiveProperty
shorthand: has_part
imported from: BFO
imported from: ro.owl
imported from: vo.owl

inheres in
type: ObjectProperty
label: inheres in at all times
BFO CLIF specification label: inheresInAt
BFO OWL specification label: inheres-in_at
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: BFO2 Reference: independent continuant that is not a spatial region
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)'.
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.)
editor note: BFO2 Reference: specifically dependent continuant
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: vo.owl
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region

bearer of at some time
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]
editor note: BFO2 Reference: independent continuant that is not a spatial region
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 some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & '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])
BFO CLIF specification label: bearerOfAt
BFO OWL specification label: bearer-of_st
range: specifically dependent continuant
sub property of: has specific dependent at some time
imported from: vo.owl
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region

is realized by
type: ObjectProperty
label: realized in
has associated axiom(fol): (forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002]
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])
has associated axiom(nl): if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002])
BFO OWL specification label: realized-in
BFO CLIF specification label: realizedIn
range: process
domain: realizable entity
imported from: vo.owl

realizes
type: ObjectProperty
has associated axiom(fol): (forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [059-003]
BFO CLIF specification label: realizes
BFO OWL specification label: realizes
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])
domain: process
range: realizable entity
inverse of: is realized by
imported from: vo.owl

participates_in
type: ObjectProperty
label: participates in
label: participates in at some time
editor note: [copied from inverse property 'has participant at some time'] BFO2 Reference: process
editor note: [copied from inverse property 'has participant 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 participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t)
editor note: [copied from inverse property 'has participant at some time'] BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant
BFO OWL specification label: participates-in_st
elucidation: [copied from inverse property 'has participant at some time'] has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003])
editor note: [copied from inverse property 'has participant at some time'] BFO 2 Reference: Spatial regions do not participate in processes.
BFO CLIF specification label: participatesInAt
alternative term: participates_in
range: process
imported from: obi.owl
imported from: vo.owl
domain: Class
  intersection of: continuant
  intersection of: Class
    complement of: spatial region

has participant
type: ObjectProperty
label: has participant at some time
has associated axiom(fol): (forall (x y t) (if (hasParticipantAt x y t) (Continuant y))) // axiom label in BFO2 CLIF: [088-001]
BFO OWL specification label: has-participant_st
BFO CLIF specification label: hasParticipantAt
editor note: BFO2 Reference: process
has associated axiom(fol): (forall (x y t) (if (hasParticipantAt x y t) (Occurrent x))) // axiom label in BFO2 CLIF: [087-001]
has associated axiom(fol): (forall (x y t) (if (hasParticipantAt x y t) (existsAt y t))) // axiom label in BFO2 CLIF: [089-001]
has associated axiom(fol): (forall (x y t) (if (and (hasParticipantAt x y t) (GenericallyDependentContinuant y)) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (genericallyDependsOn y z t) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [091-003]
has associated axiom(fol): (forall (x y t) (if (and (hasParticipantAt x y t) (SpecificallyDependentContinuant y)) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t) (specificallyDependsOnAt y z t))))) // axiom label in BFO2 CLIF: [090-003]
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 participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t)
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.
editor preferred term: has participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant
alternative term: has_participant
elucidation: has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003])
has associated axiom(nl): if b has_participant c at t & c is a generically dependent continuant, then there is some independent continuant that is not a spatial region d, and which is such that c g-depends on d at t & b s-depends_on d at t. (axiom label in BFO2 Reference: [091-003])
has associated axiom(nl): if b has_participant c at t & c is a specifically dependent continuant, then there is some independent continuant that is not a spatial region d, c s-depends_on d at t & b s-depends_on d at t. (axiom label in BFO2 Reference: [090-003])
has associated axiom(nl): if b has_participant c at t then b is an occurrent. (axiom label in BFO2 Reference: [087-001])
has associated axiom(nl): if b has_participant c at t then c exists at t. (axiom label in BFO2 Reference: [089-001])
has associated axiom(nl): if b has_participant c at t then c is a continuant. (axiom label in BFO2 Reference: [088-001])
range: continuant
domain: occurrent
domain: process
inverse of: participates_in
imported from: obi.owl
imported from: ro.owl
imported from: vo.owl
property chain axiom: realizes
property chain axiom: inheres in
range: Class
  intersection of: continuant
  intersection of: Class
    complement of: spatial region

concretized by at some time
type: ObjectProperty
label: is concretization of
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 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 poem as a pattern of memory traces in your head
example of usage: [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
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
imported from: vo.owl

concretizes
type: ObjectProperty
label: concretizes at some time
BFO CLIF specification label: concretizesAt
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]
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]
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)
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])
BFO OWL specification label: concretizes_st
example of usage: You may concretize a piece of software by installing it in your computer
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
inverse of: concretized by at some time
imported from: vo.owl

preceded by
type: ObjectProperty
type: TransitiveProperty
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
editor preferred term: preceded by
alternative term: preceded_by
range: occurrent
domain: occurrent
inverse of: precedes
sub property of: starts_before
imported from: ro.owl
property chain axiom: ends_during
property chain axiom: happens_during

is preceded by
type: ObjectProperty
type: TransitiveProperty
alternative term: preceded by
alternative term: preceded_by
sub property of: ends_after
imported from: ro.owl
property chain axiom: starts_during
property chain axiom: happens_during

precedes
type: ObjectProperty
type: TransitiveProperty
editor preferred term: precedes
range: occurrent
domain: occurrent
sub property of: temporally related to
imported from: ro.owl

specifically depends on at all times
type: ObjectProperty
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
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])
BFO CLIF specification label: specificallyDependsOn
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: 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: BFO2 Reference: specifically dependent continuant\; process; process boundary
BFO OWL specification label: s-depends-on_at
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: 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 (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: 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 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 headache s-depends_on some head
example of usage: one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
sub property of: specifically depends on at some time
imported from: vo.owl

occupies spatial region at some time
type: ObjectProperty
BFO CLIF specification label: occupiesSpatialRegionAt
BFO OWL specification label: located-at-r_st
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]
has associated axiom(fol): (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
has associated axiom(fol): (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
editor note: BFO2 Reference: independent continuant
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])
domain: independent continuant
range: spatial region
inverse of: has spatial occupant at some time
imported from: vo.owl

has function at some time
type: ObjectProperty
BFO CLIF specification label: hasFunctionAt
has associated axiom(fol): (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001]
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 function at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has function@en'(x,y,t)
definition: a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001])
BFO OWL specification label: has-f_st
range: function
sub property of: bearer of at some time
imported from: vo.owl

has quality at some time
type: ObjectProperty
BFO OWL specification label: has-q_st
range: quality
sub property of: bearer of at some time
imported from: vo.owl

has role 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 'has role at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has role@en'(x,y,t)
has associated axiom(fol): (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001]
definition: a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001])
BFO CLIF specification label: hasRoleAt
BFO OWL specification label: has-r_st
range: role
sub property of: bearer of at some time
imported from: vo.owl

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

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

has occurrent part
type: ObjectProperty
type: TransitiveProperty
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 first set of the tennis match occurrent_part_of the tennis match.
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.
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 OWL specification label: o-has-part
BFO CLIF specification label: hasOccurrentPart
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'] 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])
domain: occurrent
range: occurrent
imported from: vo.owl

has proper occurrent part
type: ObjectProperty
type: TransitiveProperty
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])
BFO CLIF specification label: hasProperOccurrentPart
BFO OWL specification label: o-has-ppart
definition: b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
range: occurrent
domain: occurrent
sub property of: has occurrent part
imported from: vo.owl

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

has spatial occupant at some time
type: ObjectProperty
BFO OWL specification label: r-location-of_st
editor note: [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
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'] 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: vo.owl

has specific dependent at some time
type: ObjectProperty
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 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'] 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: [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
BFO OWL specification label: has-s-dep_st
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
example of usage: [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
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'] 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'] 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'] a gait s-depends_on the walking object. (All at some specific time.)
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
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'] 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: [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
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'] 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'] 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: [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
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'] 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'] A pain s-depends_on the organism that is experiencing the pain
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 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'] BFO2 Reference: specifically dependent continuant\; process; process boundary
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
imported from: vo.owl
range: Class
  union of: process
  union of: specifically dependent continuant
domain: Class
  union of: process
  union of: specifically dependent continuant
  union of: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region

has spatiotemporal occupant
type: ObjectProperty
BFO OWL specification label: occupied-by
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.
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
imported from: vo.owl

occupies spatiotemporal region
type: ObjectProperty
BFO OWL specification label: occupies
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 CLIF specification label: occupiesSpatiotemporalRegion
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
inverse of: has spatiotemporal occupant
imported from: vo.owl

part of occurrent
type: ObjectProperty
type: TransitiveProperty
definition: [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
editor note: BFO2 Reference: occurrent
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 t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
BFO CLIF specification label: occurrentPartOf
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]
BFO OWL specification label: o-part-of
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
has associated axiom(fol): (forall (x y 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]
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
inverse of: has occurrent part
imported from: vo.owl

temporal part of
type: ObjectProperty
type: TransitiveProperty
BFO OWL specification label: t-part-of
has associated axiom(fol): (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
has associated axiom(fol): (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
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])
BFO CLIF specification label: temporalPartOf
has associated axiom(fol): (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
definition: b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
definition: b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
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
inverse of: has temporal part
sub property of: part of occurrent
imported from: vo.owl

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: vo.owl

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: vo.owl

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: vo.owl

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: vo.owl

occupies temporal region
type: ObjectProperty
BFO CLIF specification label: occupiesTemporalRegion
BFO OWL specification label: spans
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: vo.owl

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 CLIF specification label: spanOf
BFO OWL specification label: span-of
range: occurrent
domain: temporal region
sub property of: during which exists
imported from: vo.owl

during which exists
type: ObjectProperty
BFO OWL specification label: during-which-exists
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])
editor note: [copied from inverse property 'exists at'] BFO2 Reference: entity
editor note: [copied from inverse property 'exists at'] BFO2 Reference: temporal region
range: entity
domain: temporal region
imported from: vo.owl

specifically depends on at some time
type: ObjectProperty
BFO OWL specification label: s-depends-on_st
has associated axiom(fol): (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
has associated axiom(fol): (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
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: BFO2 Reference: specifically dependent continuant\; process; process boundary
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
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 one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
BFO CLIF specification label: specificallyDependsOn
has associated axiom(fol): (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
has associated axiom(fol): (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
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 (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: 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 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): 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 headache s-depends_on some head
example of usage: one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
example of usage: one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
example of usage: one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
example of usage: one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
example of usage: reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
example of usage: reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
example of usage: reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
example of usage: the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
example of usage: the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
example of usage: the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
example of usage: the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
example of usage: the two-sided reciprocal s-dependence of the roles of husband and wife [20
inverse of: has specific dependent at some time
imported from: vo.owl
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) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
has associated axiom(fol): (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
BFO CLIF specification label: continuantPartOfAt
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]
editor note: BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
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: 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: 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]
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)
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): (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
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])
BFO OWL specification label: c-part-of_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 '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)
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 arm continuant_part_of Mary in the time of her life prior to her operation
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.
domain: continuant
range: continuant
inverse of: has continuant part at some time
imported from: vo.owl

part of continuant at all times
type: ObjectProperty
type: TransitiveProperty
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (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]
editor note: BFO2 Reference: continuant
BFO CLIF specification label: continuantPartOfAt
BFO OWL specification label: c-part-of_at
editor note: [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
has associated axiom(fol): (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
has associated axiom(fol): (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
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])
definition: [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
editor note: BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
editor note: Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
has associated axiom(fol): (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
has associated axiom(fol): (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
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]
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 arm continuant_part_of Mary in the time of her life prior to her operation
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.
sub property of: part of continuant at some time
imported from: vo.owl

has continuant part at some time
type: ObjectProperty
BFO OWL specification label: c-has-part_st
editor note: [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
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.
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])
BFO CLIF specification label: hasContinuantPartAt
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
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: 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'] 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 some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
has associated axiom(fol): (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
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)
definition: b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
domain: continuant
range: continuant
imported from: vo.owl

part of continuant at all times that whole exists
type: ObjectProperty
type: TransitiveProperty
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: [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])
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
BFO OWL specification label: c-part-of-object_at
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
domain: continuant
range: continuant
inverse of: has continuant part at all times
sub property of: part of continuant at some time
imported from: vo.owl

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: 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'] BFO2 Reference: continuant
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
editor note: [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
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'
BFO OWL specification label: c-has-part-object_at
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)'.
example of usage: [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
definition: forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
range: continuant
domain: continuant
inverse of: part of continuant at all times
sub property of: has continuant part at some time
imported from: vo.owl

has_phase
type: ObjectProperty

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

is_manufactured_by
type: ObjectProperty
definition editor: Alan Ruttenberg
definition editor: Liju Fan
definition: c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
alternative term: has_make
alternative term: has_manufacturer
example of usage: http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
editor preferred term: is_manufactured_by
imported from: obi.owl
imported from: vo.owl

is_specified_output_of
type: ObjectProperty
definition editor: PERSON:Bjoern Peters
editor preferred term: is_specified_output_of
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
sub property of: participates_in
inverse of: has_specified_output
imported from: obi.owl
imported from: vo.owl

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
definition 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 term: achieves_planned_objective
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: obi.owl
imported from: vo.owl

is_allele_of_gene
type: ObjectProperty
definition: allele of is a relation to link an allele with its original form
range: gene
domain: allele

is positive supporting statistical evidence of
type: ObjectProperty
sub property of: is about

is negative statistical evidence of
type: ObjectProperty
sub property of: is about

before_or_simultaneous_with
type: ObjectProperty
comment: Primitive instance level timing relation between events
alternative term: <=
sub property of: temporally related to
imported from: ro.owl

simultaneous_with
type: ObjectProperty
type: TransitiveProperty
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
sub property of: before_or_simultaneous_with
imported from: ro.owl

before
type: ObjectProperty
type: TransitiveProperty
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
sub property of: before_or_simultaneous_with
imported from: ro.owl

during_which_ends
type: ObjectProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
inverse of: ends_during
sub property of: temporally related to
imported from: ro.owl

encompasses
type: ObjectProperty
type: TransitiveProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
alternative term: di
sub property of: has part
sub property of: during_which_starts
inverse of: happens_during
imported from: ro.owl

ends_after
type: ObjectProperty
type: TransitiveProperty
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
sub property of: temporally related to
imported from: ro.owl
property chain axiom: ends_during
property chain axiom: is preceded by

immediately_preceded_by
type: ObjectProperty
alternative term: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
sub property of: is preceded by
inverse of: immediately_precedes
imported from: ro.owl

during_which_starts
type: ObjectProperty
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
inverse of: starts_during
sub property of: temporally related to
imported from: ro.owl

starts_before
type: ObjectProperty
type: TransitiveProperty
sub property of: temporally related to
imported from: ro.owl
property chain axiom: starts_during
property chain axiom: preceded by

immediately_precedes
type: ObjectProperty
alternative term: ends_at_start_of
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
alternative term: meets
sub property of: preceded by
imported from: ro.owl

starts_during
type: ObjectProperty
alternative term: io
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
range: occurrent
domain: occurrent
sub property of: temporally related to
imported from: ro.owl

happens_during
type: ObjectProperty
type: TransitiveProperty
alternative term: d
alternative term: during
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
sub property of: part_of
sub property of: ends_during
imported from: ro.owl

ends_during
type: ObjectProperty
alternative term: o
alternative term: overlaps
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
sub property of: temporally related to
imported from: ro.owl

actively participates in
type: ObjectProperty
alternative term: agent in
definition: x actively participates in y if and only if x participates in y and x realizes some active role
sub property of: participates_in
has curation status: pending final vetting
inverse of: has active participant
imported from: ro.owl

has active participant
type: ObjectProperty
alternative term: has agent
definition: x has participant y if and only if x realizes some active role that inheres in y
sub property of: has participant
has curation status: pending final vetting
imported from: ro.owl

temporally related to
type: ObjectProperty
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
definition source: Allen
range: occurrent
domain: occurrent
has curation status: pending final vetting
imported from: ro.owl

starts
type: ObjectProperty
definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
sub property of: part_of
has curation status: pending final vetting
sub property of: temporally related to
imported from: ro.owl

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

ends
type: ObjectProperty
definition: inverse of ends with
sub property of: part_of
has curation status: pending final vetting
sub property of: temporally related to
inverse of: ends with
imported from: ro.owl

ends with
type: ObjectProperty
type: TransitiveProperty
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
alternative term: finished by
sub property of: has part
has curation status: pending final vetting
sub property of: temporally related to
imported from: ro.owl

vaccine immunization for host
type: ObjectProperty
definition editor: YL
definition editor: Yongqun He
range: organism
domain: vaccine
imported from: vo.owl

vaccine immunization against microbe
type: ObjectProperty
definition editor: Yongqun He
imported from: vo.owl

bearer_of
type: ObjectProperty
imported from: http://purl.org/obo/owl/ro_proposed
definition: A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in
editor preferred term: bearer_of
imported from: vo.owl

inheres_in
type: ObjectProperty
type: FunctionalProperty
imported from: http://purl.org/obo/owl/ro_proposed
definition: A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation.
editor preferred term: inheres_in
range: independent continuant
domain: specifically dependent continuant
sub property of: inheres_in_part_of
imported from: vo.owl

inheres_in_part_of
type: ObjectProperty
imported from: http://purl.org/obo/owl/ro_proposed
editor preferred term: inheres_in_part_of
imported from: vo.owl

role_of
type: ObjectProperty
imported from: http://purl.org/obo/owl/ro_proposed
definition: A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role
editor preferred term: role_of
sub property of: inheres_in
imported from: vo.owl

has_part
type: ObjectProperty

member_of
type: ObjectProperty
type: TransitiveProperty

variant_of
type: ObjectProperty

hasIntervalRelation
type: ObjectProperty
comment: This is OGI specific relation. We extended the allen caculus relation from temporal domain to material interval domain. Reference: Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)

isAdjacentAfter
type: ObjectProperty
definition: isAdjacentAfter(X,Y) : genetic interval X is adjacent the end part of genetic interval Y If genetic interval X is adjacent to the end part of genetic interval Y, then the start of X is after the start of Y and the end of X is after the end of Y, and the end of X is the same as the start of Y.
description: isAdjacentAfter(X,Y) ↔ (hasStartPoint(x1,X) & hasStartPoint(y1,Y) & isLocatedAfter(x1,y1)) & (hasEndPoint(x2,X) & hasEndPoint(y2,Y) & isLocatedAfter(x2,y2)) & ((pointInterval(x2,X) == pointInterval(y1,X))
sub property of: hasIntervalRelation

isAdjacentBefore
type: ObjectProperty
definition: isAdjacentBefore(X,Y) : genetic interval X is adjacent to the start of genetic interval Y If genetic interval X is adjacent to the start of genetic interval Y, then the start of X is before the start of Y and the end of X is before the end of Y, and the end of X is identical with the start of Y.
description: isAdjacentBefore(X,Y) ↔ (hasStartPoint(x1,X) & hasStartPoint(y1,Y) & isLocatedBefore(x1,y1)) & (hasEndPoint(x2,X) & hasEndPoint(y2,Y) & isLocatedBefore(x2,y2)) & ((pointInterval(x2,X) == pointInterval(y1,X))
sub property of: hasIntervalRelation

isContainedIn
type: ObjectProperty
definition: isContainedIn(X,Y) genetic interval X is contained inside genetic interval Y If genetic interval X is contained in genetic interval Y, then start of X is after the start of Y and the end of X is before the end of Y and the start of X is unique with thestart of Y, the end of X is unique with the end of Y.
comment: unsolved problem, Is isContainedIn a transitive relation?
description: isContainedIn(X,Y) ↔ (hasStartPoint(x1,X) & hasStartPoint(y1,Y) & isLocatedAfter(x1,y1)) & (hasEndPoint(x2,X) & hasEndPoint(y2,Y) & isLocatedBefore(x2,y2)) & ((pointInterval(x1,X) & pointInterval(y1,X)) & ((pointInterval(x2,X) & pointInterval(y2,X))
domain: biological material interval
range: biological material interval
sub property of: hasIntervalRelation

isEndsWith
type: ObjectProperty
definition: isEndsWith(X,Y) : genetic interval X ends with genetic interval Y If genetic interval X ends with genetic interval Y, then the end of X and the end of Y are identical and the start of X is after the start of Y.
description: isEndsWith(X,Y) ↔ ((hasEndPoint(x1,X) & hasEndPoint(x1,Y)) & (hasStartPoint(x2,X) & hasStartPoint(y,Y) & isLocatedAfter(x2,y))
sub property of: hasIntervalRelation

isLocatedAfter
type: ObjectProperty
definition: isLocatedAfter(X,Y) : genetic interval X is located after genetic interval Y If genetic interval X is located after genetic interval Y, then the start of X is after the end of Y; or the end of Y is before the start of X. If isLocatedBefore(X,Y), then isLocatedAfter(Y,X)
description: isLocatedAfter(X,Y) ↔ (hasStartPoint(x1,X) & hasEndPoint(y1,Y) & isLocatedAfter(x1,y1)) OR (hasEndPoint(x2,X) &. hasStartPoint(y2,Y) & isLocatedBefore(y2,x2)) isLocatedAfter(X,Y) == isLocatedBefore(Y,X)
sub property of: hasIntervalRelation
inverse of: isLocatedBefore

isLocatedBefore
type: ObjectProperty
definition: isLocatedBefore is both a Class-Class and an Instance-Instance relation. isLocatedBefore(X,Y): genetic interval X is located before genetic interval Y If genetic interval X is located before genetic interval Y, then the end of X is before the start of Y.
description: isLocatedBefore(X,Y) ↔ hasEndPoint(x,X) & hasStartPoint(y,Y) & isLocatedBefore(x,y)
sub property of: hasIntervalRelation

isWrittenBy
type: ObjectProperty
comment: is short relation for author 'participate in' some ('writing book process' and ( 'has specific output of' some book))
range: author
domain: book

is substituent group from
type: ObjectProperty

hasSize
type: DatatypeProperty
domain: human study subject group
range: int
sub property of: topDataProperty

hasOddsRatio
type: DatatypeProperty
range: float

hasPvalue
type: DatatypeProperty
range: float

entity
type: Class
subclass of: Restriction
  on property: exists at
  some values from: temporal region
BFO OWL specification label: entity
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
BFO CLIF specification label: Entity
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: obi.owl
imported from: vo.owl

continuant
type: Class
subclass of: entity
BFO CLIF specification label: Continuant
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) (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]
BFO OWL specification label: continuant
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
example of usage: a heart
example of usage: a person
example of usage: a symphony orchestra
editor preferred term: continuant
alternative term: endurant
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])
example of usage: the color of a tomato
example of usage: the disposition of blood to coagulate
example of usage: the lawn and atmosphere in front of our building
example of usage: the mass of a cloud
imported from: BFO
imported from: obi.owl
imported from: vo.owl

occurrent
type: Class
subclass of: entity
BFO CLIF specification label: Occurrent
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: 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 OWL specification label: occurrent
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
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
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
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: obi.owl
imported from: vo.owl

independent 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: specifically dependent continuant
      union of: generically dependent continuant
subclass of: Restriction
  on property: occupies spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: specifically depends on at some time
  all values from: Nothing
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
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): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
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 chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a symphony orchestra
example of usage: an orchestra.
example of usage: an organism
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])
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a person
example of usage: a spatial region
example of usage: an atom
editor preferred term: independent continuant
alternative term: substantial entity
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
example of usage: the lawn and atmosphere in front of our building
imported from: BFO
imported from: obi.owl
imported from: vo.owl

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

temporal region
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has occurrent part
  all values from: temporal region
subclass of: Restriction
  on property: has temporal occupant
  has self: true
subclass of: Restriction
  on property: part of occurrent
  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]
BFO OWL specification label: t-region
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
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])
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
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
imported from: vo.owl

spatiotemporal region
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has occurrent part
  all values from: spatiotemporal region
subclass of: Restriction
  on property: projects onto temporal region
  some values from: temporal region
subclass of: Restriction
  on property: projects onto spatial region at some time
  some values from: spatial region
subclass of: Restriction
  on property: has spatiotemporal occupant
  has self: true
subclass of: Restriction
  on property: part of occurrent
  all values from: spatiotemporal region
subclass of: Restriction
  on property: occupies spatiotemporal region
  has self: true
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
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])
BFO CLIF specification label: SpatiotemporalRegion
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]
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): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
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: vo.owl

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has occurrent part
  all values from: Class
    union of: process
    union of: process boundary
subclass of: Restriction
  on property: part of occurrent
  all values from: process
subclass of: Restriction
  on property: specifically depends on at some time
  some values from: material entity
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 sleeping
BFO OWL specification label: process
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]
example of usage: a process of meiosis
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])
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: vo.owl

disposition
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: role
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: role
BFO OWL 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]
BFO CLIF specification label: Disposition
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 [89
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])
example of usage: an atom of element X has the disposition to decay to an atom of element Y
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
imported from: vo.owl

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: quality
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  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]
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
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]
BFO CLIF specification label: RealizableEntity
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])
editor note: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
editor preferred term: realizable entity
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
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 the reproductive organs
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: obi.owl
imported from: vo.owl

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: realizable entity
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: realizable entity
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]
BFO CLIF specification label: Quality
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
BFO OWL specification label: quality
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: vo.owl

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: independent continuant
    intersection of: Class
      complement of: spatial region
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: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: generically dependent continuant
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]
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.
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.
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])
alternative term: mode
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
alternative term: property
editor preferred term: specifically dependent continuant
example of usage: the color of a tomato
example of usage: the disposition of fish to decay
example of usage: the disposition of this fish to decay
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
example of usage: the function of this heart: to pump blood
example of usage: the liquidity of blood
example of usage: the mass of a cloud
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 mozzarella
example of usage: the smell of this portion of mozzarella
alternative term: trope
imported from: obi.owl
imported from: vo.owl

role
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: part of continuant at some time
  all values from: Class
    complement of: disposition
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: Class
    complement of: disposition
BFO OWL specification label: role
BFO CLIF specification label: Role
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
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])
editor preferred term: role
example of usage: the priest role
example of usage: the role of a biological grandfather as legal guardian in the context of a system of laws
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 chemical compound in an experiment
example of usage: the role of a patient relative as defined by a hospital administrative form
example of usage: the role of a person as a surgeon
example of usage: the role of a stone in marking a property boundary
example of usage: the role of a student in a university
example of usage: the role of a woman as a legal mother in the context of system of laws
example of usage: the role of ingested matter in digestion
example of usage: the role of subject in a clinical trial
example of usage: the student role
imported from: obi.owl
imported from: vo.owl

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

generically dependent continuant
type: Class
subclass of: 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 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: part of continuant at some time
  all values from: Class
    complement of: Class
      union of: independent continuant
      union of: specifically dependent continuant
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.
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: a certain PDF file that exists in different and in several hard drives
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])
editor preferred term: generically dependent continuant
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: vo.owl

function
type: Class
subclass of: disposition
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])
BFO OWL specification label: function
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [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 CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
imported from: vo.owl

process boundary
type: Class
subclass of: occurrent
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
subclass of: Restriction
  on property: exists at
  all values from: zero-dimensional temporal region
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(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
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])
BFO OWL specification label: p-boundary
example of usage: the boundary between the 2nd and 3rd year of your life.
imported from: vo.owl

material entity
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  all values from: material entity
subclass of: Restriction
  on property: has continuant part at some time
  all values from: Class
    union of: material entity
    union of: immaterial entity
subclass of: Restriction
  on property: occupies spatial region at some time
  all values from: three-dimensional spatial region
subclass of: Restriction
  on property: part of continuant at some time
  all values from: material entity
subclass of: Restriction
  on property: has continuant part at all times that part exists
  all values from: Class
    union of: material entity
    union of: immaterial entity
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
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])
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])
editor note: Examples: collection of random bacteria, a chair, dorsal surface of the body
editor note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
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])
editor preferred term: material entity
example of usage: the undetached arm of a human being
imported from: BFO
imported from: obi.owl
imported from: vo.owl

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

zero-dimensional temporal region
type: Class
subclass of: temporal region
subclass of: Restriction
  on property: has proper occurrent part
  all values from: Nothing
BFO OWL specification label: 0d-t-region
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
BFO CLIF specification label: ZeroDimensionalTemporalRegion
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: vo.owl

formaldehyde
type: Class
subclass of: molecular entity
database_cross_reference: Beilstein:1209228
has_related_synonym: CH2O
has_alternative_id: CHEBI:14274
id: CHEBI:16842
has_alternative_id: CHEBI:24077
has_alternative_id: CHEBI:337763
has_alternative_id: CHEBI:5142
database_cross_reference: ChEMBL:7381846
database_cross_reference: ChemIDplus:50-00-0
database_cross_reference: CiteXplore:18837732
has_exact_synonym: FORMALDEHYDE
has_related_synonym: FORMALIN
has_related_synonym: Formaldehyd
has_exact_synonym: Formaldehyde
has_related_synonym: Formalin
database_cross_reference: Gmelin:445
has_related_synonym: InChI=1S/CH2O/c1-2/h1H2
has_related_synonym: InChIKey=WSFSSNUMVMOOMR-UHFFFAOYSA-N
database_cross_reference: KEGG COMPOUND:50-00-0
database_cross_reference: KEGG COMPOUND:C00067
has_related_synonym: Methanal
has_related_synonym: Methylene oxide
database_cross_reference: NIST Chemistry WebBook:50-00-0
has_related_synonym: Oxomethane
has_related_synonym: Oxomethylene
database_cross_reference: PDBeChem:FLH
definition: The simplest aldehyde.
database_cross_reference: UM-BBD:c0122
database_cross_reference: Wikipedia:Formaldehyde
has_related_synonym: [H]C([H])=O
has_exact_synonym: formaldehyde
imported from: chebi.owl
imported from: vo.owl

molecular entity
type: Class
subclass of: chemical entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
id: CHEBI:23367
has_related_synonym: entidad molecular
has_related_synonym: entidades moleculares
has_related_synonym: entite moleculaire
has_related_synonym: molecular entities
has_exact_synonym: molecular entity
has_related_synonym: molekulare Entitaet
imported from: chebi.owl
imported from: vo.owl

chemical entity
type: Class
subclass of: material entity
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
id: CHEBI:24431
imported from: chebi.owl
imported from: vo.owl

amino-acid residue
type: Class
subclass of: genetic interval base residue
id: CHEBI:33708
definition: When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
has_related_synonym: amino acid residue
has_exact_synonym: amino-acid residue
has_related_synonym: amino-acid residues
has_obo_namespace: chebi_ontology
imported from: chebi.owl

nucleotide residue
type: Class
subclass of: genetic interval base residue
id: CHEBI:50319
has_obo_namespace: chebi_ontology
has_related_synonym: nucleotide residues
imported from: chebi.owl

thimerosal
type: Class
subclass of: molecular entity
definition: An organomercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent.
database_cross_reference: Beilstein:8169555
has_related_synonym: C9H9HgNaO2S
has_related_synonym: C9H9HgO2S.Na
id: CHEBI:9546
database_cross_reference: ChemIDplus:54-64-8
database_cross_reference: CiteXplore:18837732
database_cross_reference: CiteXplore:21616561
database_cross_reference: Gmelin:1677155
has_related_synonym: InChI=1S/C7H6O2S.C2H5.Hg.Na/c8-7(9)5-3-1-2-4-6(5)10;1-2;;/h1-4,10H,(H,8,9);1H2,2H3;;/q;;2*+1/p-2
has_related_synonym: InChIKey=RTKIYNMVFMVABJ-UHFFFAOYSA-L
database_cross_reference: KEGG COMPOUND:C08044
has_related_synonym: Merthiolate
has_exact_synonym: Thimerosal
has_related_synonym: Thiomersal
has_related_synonym: [(o-carboxyphenyl)thio]ethylmercury sodium salt
has_related_synonym: [Na+].CC[Hg]Sc1ccccc1C([O-])=O
has_related_synonym: ethyl(2-mercaptobenzoato-S)mercury sodium salt
has_related_synonym: ethylmercurithiosalicylate sodium
has_related_synonym: mercurothiolate
has_related_synonym: o-(ethylmercurithio)benzoic acid sodium salt
has_exact_synonym: sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-)
has_exact_synonym: sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-)
has_related_synonym: sodium ethylmercurithiosalicylate
has_related_synonym: thiomersalate
imported from: chebi.owl
imported from: vo.owl

clinical trial
type: Class
subclass of: investigation
subclass of: Restriction
  on property: BFO_0000167
  some values from: human study subject group
example of usage: A clinical trial to evaluate the efficacy of a new drug.
definition: An interventional study that contains a set of procedures in medical research and drug development that are conducted to allow safety (or more specifically, information about adverse drug reactions and adverse effects of other treatments) and efficacy data to be collected for health interventions (e.g., drugs, diagnostics, devices, therapy protocols) that is performed over phases.
definition editor: PERSON: Nicole Vasilevsky
definition source: http://en.wikipedia.org/wiki/Clinical_trial
has curation status: metadata complete
imported from: ero.owl

genome wide association study
type: Class
subclass of: case control genetic association study
definition: A genome wide association study is an examination of genetic variation across a given genome, designed to identify genetic associations with observable traits.
definition editor: PERSON: Karen Corday
editor preferred term: genome wide association study
definition source: http://en.wikipedia.org/wiki/Genome-wide_association_study
alternative term: GWAS
has curation status: metadata incomplete
imported from: ero.owl

case-only study
type: Class
subclass of: investigation
definition source: A Dictionary of Epidemiology, Fifth Edition, Edited by Miquel Porta. p. 33. ISBN:978-0-19-531449-6 http://prsinfo.clinicaltrials.gov/definitions.html
definition: Observational study whereby there is a single group of individuals with specific characteristics. This is a method that analyzes data from a case series and is used in case-crossover studies, in case-specular designs, and in molecular and genetic epidemiology to assess relationships between environmental exposures and genotypes.
definition editor: PERSON: Melissa Haendel
editor preferred term: case-only study
has curation status: metadata incomplete
imported from: ero.owl

cellular_component
type: Class
subclass of: material entity
id: GO:0005575
has_alternative_id: GO:0008372
database_cross_reference: NIF_Subcellular:sao1337158144
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
definition: The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
has_exact_synonym: cellular component
has_narrow_synonym: cellular component unknown
has_obo_namespace: cellular_component
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast
in_subset: gosubset prok

nucleus
type: Class
subclass of: organelle
definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
id: GO:0005634
database_cross_reference: NIF_Subcellular:sao1702920020
database_cross_reference: Wikipedia:Cell_nucleus
has_exact_synonym: cell nucleus
has_obo_namespace: cellular_component
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast

chromosome
type: Class
subclass of: organelle
subclass of: Restriction
  on property: isStructurePartOf
  some values from: nuclear genome
subclass of: Restriction
  on property: hasStructurePart
  all values from: Class
    union of: Dexyribonuleic acid molecule
    union of: histone
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
id: GO:0005694
database_cross_reference: Wikipedia:Chromosome
has_obo_namespace: cellular_component
has_related_synonym: chromatid
has_narrow_synonym: interphase chromosome
has_narrow_synonym: prophase chromosome
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim yeast
in_subset: gosubset prok

mitochondrion
type: Class
subclass of: organelle
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
id: GO:0005739
database_cross_reference: NIF_Subcellular:sao1860313010
database_cross_reference: Wikipedia:Mitochondrion
has_obo_namespace: cellular_component
has_exact_synonym: mitochondria
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim yeast

DNA replication
type: Class
subclass of: biological_process
id: GO:0006260
has_alternative_id: GO:0055133
database_cross_reference: Reactome:REACT_100559
database_cross_reference: Reactome:REACT_101280
database_cross_reference: Reactome:REACT_101497
database_cross_reference: Reactome:REACT_102679
database_cross_reference: Reactome:REACT_103614
database_cross_reference: Reactome:REACT_104547
database_cross_reference: Reactome:REACT_105292
database_cross_reference: Reactome:REACT_105467
database_cross_reference: Reactome:REACT_105835
database_cross_reference: Reactome:REACT_106018
database_cross_reference: Reactome:REACT_106104
database_cross_reference: Reactome:REACT_106382
database_cross_reference: Reactome:REACT_106434
database_cross_reference: Reactome:REACT_106732
database_cross_reference: Reactome:REACT_107075
database_cross_reference: Reactome:REACT_107423
database_cross_reference: Reactome:REACT_108461
database_cross_reference: Reactome:REACT_108634
database_cross_reference: Reactome:REACT_108739
database_cross_reference: Reactome:REACT_108768
database_cross_reference: Reactome:REACT_108929
database_cross_reference: Reactome:REACT_109137
database_cross_reference: Reactome:REACT_112472
database_cross_reference: Reactome:REACT_113703
database_cross_reference: Reactome:REACT_29423
database_cross_reference: Reactome:REACT_29444
database_cross_reference: Reactome:REACT_29691
database_cross_reference: Reactome:REACT_29764
database_cross_reference: Reactome:REACT_30149
database_cross_reference: Reactome:REACT_31024
database_cross_reference: Reactome:REACT_31919
database_cross_reference: Reactome:REACT_32546
database_cross_reference: Reactome:REACT_32932
database_cross_reference: Reactome:REACT_33572
database_cross_reference: Reactome:REACT_33874
database_cross_reference: Reactome:REACT_50018
database_cross_reference: Reactome:REACT_53588
database_cross_reference: Reactome:REACT_6729
database_cross_reference: Reactome:REACT_6738
database_cross_reference: Reactome:REACT_6750
database_cross_reference: Reactome:REACT_6769
database_cross_reference: Reactome:REACT_6798
database_cross_reference: Reactome:REACT_6869
database_cross_reference: Reactome:REACT_6936
database_cross_reference: Reactome:REACT_6939
database_cross_reference: Reactome:REACT_77532
database_cross_reference: Reactome:REACT_79188
database_cross_reference: Reactome:REACT_79450
database_cross_reference: Reactome:REACT_80432
database_cross_reference: Reactome:REACT_80571
database_cross_reference: Reactome:REACT_80896
database_cross_reference: Reactome:REACT_80988
database_cross_reference: Reactome:REACT_81803
database_cross_reference: Reactome:REACT_83095
database_cross_reference: Reactome:REACT_84829
database_cross_reference: Reactome:REACT_85561
database_cross_reference: Reactome:REACT_86410
database_cross_reference: Reactome:REACT_86739
database_cross_reference: Reactome:REACT_87233
database_cross_reference: Reactome:REACT_87449
database_cross_reference: Reactome:REACT_87590
database_cross_reference: Reactome:REACT_88085
database_cross_reference: Reactome:REACT_88384
database_cross_reference: Reactome:REACT_88529
database_cross_reference: Reactome:REACT_89355
database_cross_reference: Reactome:REACT_89439
database_cross_reference: Reactome:REACT_89725
database_cross_reference: Reactome:REACT_90512
database_cross_reference: Reactome:REACT_90809
database_cross_reference: Reactome:REACT_90838
database_cross_reference: Reactome:REACT_91184
database_cross_reference: Reactome:REACT_91302
database_cross_reference: Reactome:REACT_92527
database_cross_reference: Reactome:REACT_92644
database_cross_reference: Reactome:REACT_92706

transcription, DNA-dependent
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: part_of
  some values from: gene expression
has_exact_synonym: DNA-dependent transcription
has_alternative_id: GO:0006350
id: GO:0006351
has_alternative_id: GO:0061018
has_alternative_id: GO:0061022
definition: The cellular synthesis of RNA on a template of DNA.
database_cross_reference: Wikipedia:Transcription_(genetics)
has_obo_namespace: biological_process
has_broad_synonym: cellular transcription
has_exact_synonym: cellular transcription, DNA-dependent
has_broad_synonym: transcription
has_related_synonym: transcription regulator activity
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim metagenomics
in_subset: goslim pombe
in_subset: gosubset prok

translation
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: part_of
  some values from: gene expression
id: GO:0006412
has_alternative_id: GO:0006416
has_alternative_id: GO:0006453
has_alternative_id: GO:0043037
database_cross_reference: Reactome:REACT_100338
database_cross_reference: Reactome:REACT_100851
database_cross_reference: Reactome:REACT_101045
database_cross_reference: Reactome:REACT_101324
database_cross_reference: Reactome:REACT_1014
database_cross_reference: Reactome:REACT_103420
database_cross_reference: Reactome:REACT_105544
database_cross_reference: Reactome:REACT_29980
database_cross_reference: Reactome:REACT_33559
database_cross_reference: Reactome:REACT_77710
database_cross_reference: Reactome:REACT_79784
database_cross_reference: Reactome:REACT_81734
database_cross_reference: Reactome:REACT_81833
database_cross_reference: Reactome:REACT_82171
database_cross_reference: Reactome:REACT_83429
database_cross_reference: Reactome:REACT_83530
database_cross_reference: Reactome:REACT_86996
database_cross_reference: Reactome:REACT_95535
database_cross_reference: Reactome:REACT_96394
definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome.
database_cross_reference: Wikipedia:Translation_(genetics)
has_obo_namespace: biological_process
has_exact_synonym: protein anabolism
has_exact_synonym: protein biosynthesis
has_exact_synonym: protein biosynthetic process
has_exact_synonym: protein formation
has_exact_synonym: protein synthesis
has_exact_synonym: protein translation
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: gosubset prok

biological_process
type: Class
subclass of: process
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
id: GO:0008150
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_narrow_synonym: biological process unknown
has_obo_namespace: biological_process
has_exact_synonym: physiological process
imported from: go.owl
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
in_subset: gosubset prok

gene expression
type: Class
subclass of: biological_process
id: GO:0010467
database_cross_reference: Reactome:REACT_100537
database_cross_reference: Reactome:REACT_101147
database_cross_reference: Reactome:REACT_101952
database_cross_reference: Reactome:REACT_105649
database_cross_reference: Reactome:REACT_108313
database_cross_reference: Reactome:REACT_29068
database_cross_reference: Reactome:REACT_34240
database_cross_reference: Reactome:REACT_71
database_cross_reference: Reactome:REACT_78136
database_cross_reference: Reactome:REACT_78959
database_cross_reference: Reactome:REACT_79662
database_cross_reference: Reactome:REACT_85241
database_cross_reference: Reactome:REACT_85359
database_cross_reference: Reactome:REACT_86357
database_cross_reference: Reactome:REACT_89816
database_cross_reference: Reactome:REACT_91657
database_cross_reference: Reactome:REACT_91965
database_cross_reference: Reactome:REACT_93586
database_cross_reference: Reactome:REACT_93968
database_cross_reference: Reactome:REACT_94814
database_cross_reference: Reactome:REACT_98256
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
database_cross_reference: Wikipedia:Gene_expression
has_obo_namespace: biological_process
imported from: go.owl
in_subset: gosubset prok

organelle
type: Class
subclass of: cellular_component
id: GO:0043226
database_cross_reference: NIF_Subcellular:sao1539965131
definition: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
database_cross_reference: Wikipedia:Organelle
has_obo_namespace: cellular_component
imported from: go.owl
in_subset: goslim generic
in_subset: goslim pir
in_subset: gosubset prok

objective specification
type: Class
subclass of: directive information entity
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor preferred term: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: pending final vetting
imported from: obi.owl
imported from: vo.owl

data item
type: Class
subclass of: information content entity
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.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition 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 term: data item
has curation status: pending final vetting
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
definition editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor preferred term: information content entity
has curation status: pending final vetting
imported from: iao.owl
imported from: obi.owl
imported from: vo.owl

directive information entity
type: Class
subclass of: information content entity
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
has curation status: metadata incomplete
imported from: iao.owl
imported from: obi.owl
imported from: vo.owl

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

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

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

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

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

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

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

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

Viruses
type: Class
subclass of: organism
editor preferred term: Viruses
imported from: ncbitaxon.owl
imported from: vo.owl

Chordopoxvirinae
type: Class
subclass of: dsDNA viruses, no RNA stage
editor preferred term: Chordopoxvirinae
imported from: ncbitaxon.owl
imported from: vo.owl

Variola virus
type: Class
subclass of: Chordopoxvirinae
editor preferred term: Variola virus
imported from: ncbitaxon.owl
imported from: vo.owl

Orthomyxoviridae
type: Class
subclass of: ssRNA negative-strand viruses
editor preferred term: Orthomyxoviridae
imported from: ncbitaxon.owl
imported from: vo.owl

unidentified influenza virus
type: Class
subclass of: unclassified Orthomyxoviridae
editor preferred term: unidentified influenza virus
imported from: ncbitaxon.owl
imported from: vo.owl

Influenza A virus
type: Class
subclass of: Influenzavirus A
editor preferred term: Influenza A virus
imported from: ncbitaxon.owl
imported from: vo.owl

H1N1 subtype
type: Class
subclass of: Influenza A virus
editor preferred term: H1N1 subtype
imported from: ncbitaxon.owl
imported from: vo.owl

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

Influenzavirus A
type: Class
subclass of: Orthomyxoviridae
editor preferred term: Influenzavirus A
imported from: ncbitaxon.owl
imported from: vo.owl

Influenzavirus B
type: Class
subclass of: Orthomyxoviridae
editor preferred term: Influenzavirus B
imported from: ncbitaxon.owl
imported from: vo.owl

Influenzavirus C
type: Class
subclass of: Orthomyxoviridae
editor preferred term: Influenzavirus C
imported from: ncbitaxon.owl
imported from: vo.owl

Eukaryota
type: Class
subclass of: organism
editor preferred term: Eukaryota
imported from: ncbitaxon.owl
imported from: vo.owl

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

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

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

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred term: Opisthokonta
imported from: ncbitaxon.owl
imported from: vo.owl

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

dsDNA viruses, no RNA stage
type: Class
subclass of: Viruses
editor preferred term: dsDNA viruses, no RNA stage
imported from: ncbitaxon.owl
imported from: vo.owl

ssRNA negative-strand viruses
type: Class
subclass of: ssRNA viruses
editor preferred term: ssRNA negative-strand viruses
imported from: ncbitaxon.owl
imported from: vo.owl

unclassified Orthomyxoviridae
type: Class
subclass of: Orthomyxoviridae
editor preferred term: unclassified Orthomyxoviridae
imported from: ncbitaxon.owl
imported from: vo.owl

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

ssRNA viruses
type: Class
subclass of: Viruses
editor preferred term: ssRNA viruses
imported from: ncbitaxon.owl
imported from: vo.owl

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

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

Homo sapiens
type: Class
subclass of: Simiiformes
editor preferred term: Homo sapiens
imported from: ncbitaxon.owl
imported from: vo.owl

adverse event
type: Class
subclass of: pathological bodily process
editor note: YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
comment: The OAE official website is: http://www.oae-ontology.org/.
alternative term: AE
editor note: YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
editor note: Mélanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
definition source: WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
editor note: YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
definition: a pathological bodily process that occurs after a medical intervention.
editor note: YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
definition source: WEB: http://en.wikipedia.org/wiki/Adverse_event
alternative term: adverse reaction
definition editor: YH
imported from: oae.owl

vaccine adverse event
type: Class
equivalent class: Class
  intersection of: adverse event
  intersection of: Restriction
    on property: is preceded by
    some values from: vaccination
subclass of: adverse event
definition editor: YH
definition: an adverse event that is induced by vaccination.
imported from: oae.owl

wheezing AE
type: Class
subclass of: adverse event
definition: a respiratory system AE which has an outcome of wheezing
see also: MedDRA ID: 10047924
definition editor: SS, YH
imported from: oae.owl

systematic adverse event
type: Class
subclass of: adverse event
definition editor: YH
definition: an adverse event that occurs systematically in a patient's body.
imported from: oae.owl

fever AE
type: Class
subclass of: adverse event
comment: Fever is a frequent medical sign that describes an increase in internal body temperature to levels above normal. Fever is characterized as a temporary elevation in the body's thermoregulatory set-point, usually by about 1-2 °F).
definition editor: YH, SS
alternative term: pyrexia AE
definition source: WEB: http://en.wikipedia.org/wiki/Pyrexia
definition: an abnormal body temperature AE which has an outcome of fever
see also: MedDRA: 10037660
see also: MedDRA: 10005911
alternative term: febrile response
alternative term: body temperature increased AE
imported from: oae.owl

Guillain-Barre syndrome AE
type: Class
subclass of: adverse event
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/23299621
see also: MedDRA: 10018767
definition editor: YH, SS
alternative term: GBS AE
see also: MedDRA ID: 10018767
definition: a nervous system AE that has the symptom of GBS. Guillain-Barre syndrome (GBS) is a disorder in which the body's immune system attacks part of the peripheral nervous system. The first symptoms of this disorder include varying degrees of weakness or tingling sensations in the legs. In many instances, the weakness and abnormal sensations spread to the arms and upper body. These symptoms can increase in intensity until the muscles cannot be used at all and the patient is almost totally paralyzed. In these cases, the disorder is life-threatening and is considered a medical emergency. Usually Guillain-Barre occurs a few days or weeks after the patient has had symptoms of a respiratory or gastrointestinal viral infection. Occasionally, surgery or vaccinations will trigger the syndrome. Reference: http://www.ninds.nih.gov/disorders/gbs/gbs.htm.
imported from: oae.owl

multiple sclerosis AE
type: Class
subclass of: adverse event
definition: multiple sclerosis AE is an immune system disorder AE, or an autoimmune condition in which the immune system attacks the central nervous system, leading to demyelination.
alternative term: encephalomyelitis disseminata
see also: MedDRA ID: 10028245
alternative term: MS
alternative term: disseminated sclerosis
definition editor: YH
imported from: oae.owl

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 note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
definition editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
definition source: branch derived
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
editor preferred term: planned process
has curation status: ready for release
imported from: obi.owl
imported from: vo.owl

regulation-assigned role
type: Class
subclass of: regulatory role
example of usage: Approval letter
definition editor: Person: Jennifer Fostel
definition: Regulation-assigned role is a regulatory role defined by legislation or governmental orders
editor preferred term: regulation-assigned role
has curation status: metadata incomplete
imported from: obi.owl
imported from: vo.owl

regulatory role
type: Class
subclass of: role
definition editor: GROUP: Role branch
definition source: OBI, CDISC
example of usage: Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
definition: a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
curator note: govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
editor preferred term: regulatory role
has curation status: metadata complete
imported from: obi.owl
imported from: vo.owl

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.
definition editor: PERSON: Alan Ruttenberg
editor preferred term: processed material
has curation status: ready for release
imported from: obi.owl
imported from: vo.owl

investigation
type: Class
subclass of: planned process
curator note: Could add specific objective specification
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
definition editor: Bjoern Peters
definition source: OBI branch derived
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred term: investigation
has curation status: ready for release
imported from: obi.owl

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

study group role
type: Class
subclass of: role
example of usage: The group of randomized participants that are assigned to a treatment arm of the trial
alternative term: study group population
editor preferred term: study group role
definition editor: Jennifer Fostel
definition: a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
has curation status: metadata incomplete
imported from: obi.owl

p-value
type: Class
subclass of: data item
editor note: May be outside the scope of OBI long term, is needed so is retained
definition source: WEB: http://en.wikipedia.org/wiki/P-value
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
definition editor: PERSON:Chris Stoeckert
editor preferred term: p-value
has curation status: organizational term
imported from: obi.owl

population
type: Class
subclass of: BFO_0000027
subclass of: material entity
definition editor: PERSON: Philippe Rocca-Serra
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
definition source: adapted from Oxford English Dictionnary
editor preferred term: population
curator note: rem1: collection somehow always involve a selection process
has curation status: pending final vetting
imported from: obi.owl

organization
type: Class
subclass of: material entity
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition: An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
editor preferred term: organization
has curation status: ready for release
imported from: obi.owl
imported from: vo.owl

material to be added role
type: Class
subclass of: role
curator note: 9 March 09 from discussion with PA branch
definition source: OBI
definition editor: Role Branch
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
editor preferred term: 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: metadata complete
imported from: obi.owl
imported from: vo.owl

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.
definition 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 term: 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: metadata complete
imported from: obi.owl
imported from: vo.owl

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
definition 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 term: 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: metadata complete
imported from: obi.owl
imported from: vo.owl

primary structure of DNA macromolecule
type: Class
subclass of: primary structure of biological interval
definition editor: BP et al
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
editor preferred term: primary structure of DNA macromolecule
has curation status: metadata incomplete
imported from: obi.owl

primary structure of RNA molecule
type: Class
subclass of: primary structure of biological interval
definition editor: Person:Bjoern Peters
definition: The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
editor preferred term: primary structure of RNA molecule
has curation status: metadata incomplete
imported from: obi.owl

secondary structure of sequence macromolecule
type: Class
subclass of: biological interval structure
editor note: 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
definition editor: Person: Philippe Rocca-Serra
definition source: Wikipedia
editor preferred term: secondary structure of sequence macromolecule
has curation status: example to be eventually removed
imported from: obi.owl

secondary structure of RNA molecule
type: Class
subclass of: secondary structure of sequence macromolecule
editor note: 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
example of usage: PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
definition editor: Person: Philippe Rocca-Serra
editor preferred term: secondary structure of RNA molecule
has curation status: metadata incomplete
imported from: obi.owl

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: part_of
  some values from: genotype information
definition editor: Group: OBI group
definition source: Group: OBI group
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
editor preferred term: genetic population background information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
editor note: proposed and discussed on San Diego OBI workshop, March 2011
has curation status: metadata complete
imported from: obi.owl

wild type organism genotype information
type: Class
subclass of: genotype information
example of usage: C57BL/6J wild type
definition source: Group: OBI group
definition editor: Group: OBI group
definition: a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
editor preferred term: wild type organism genotype information
has curation status: metadata complete
imported from: obi.owl

genotype information
type: Class
subclass of: genetic characteristics information
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: genetic population background information
  intersection of: Restriction
    on property: has part
    some values from: genetic alteration information
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
definition editor: Group: OBI group
definition source: Group: OBI group
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
editor preferred term: genotype information
has curation status: metadata complete
imported from: obi.owl

allele information
type: Class
subclass of: genetic alteration information
definition source: MO_58 Allele
definition editor: Person: Chris Stoeckert, Jie Zheng
definition: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
editor preferred term: allele information
editor note: discussed on San Diego OBI workshop, March 2011
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: metadata complete
imported from: obi.owl

genetic alteration information
type: Class
subclass of: genetic characteristics information
definition source: Group: OBI group
definition editor: Group: OBI group
definition: a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
editor preferred term: genetic alteration information
editor note: proposed and discussed on San Diego OBI workshop, March 2011
has curation status: metadata complete
imported from: obi.owl

wild type allele information
type: Class
subclass of: allele information
definition source: MO_605 genotype
definition editor: Person: Chris Stoeckert, Jie Zheng
definition: an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
editor note: discussed on San Diego OBI workshop, March 2011
editor preferred term: wild type allele information
has curation status: metadata complete
imported from: obi.owl

genetic characteristics information
type: Class
subclass of: data item
definition source: MO_66 IndividualGeneticCharacteristics
definition editor: Person: Chris Stoeckert, Jie Zheng
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
editor preferred term: genetic characteristics information
has curation status: metadata complete
imported from: obi.owl

organism
type: Class
subclass of: material entity
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')
definition editor: GROUP: OBI Biomaterial Branch
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
definition source: WEB: http://en.wikipedia.org/wiki/Organism
example of usage: animal
example of usage: fungus
editor preferred term: organism
example of usage: plant
example of usage: virus
has curation status: organizational term
imported from: obi.owl
imported from: vo.owl

data transformation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
definition editor: Philippe Rocca-Serra
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
definition: A data transformation is a process which produces output data from input data
definition source: Branch editors
definition editor: Elisabetta Manduchi
definition editor: Helen Parkinson
definition editor: James Malone
definition editor: Melanie Courtot
definition editor: Richard Scheuermann
definition editor: Ryan Brinkman
definition editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
editor preferred term: data transformation
has curation status: pending final vetting
imported from: obi.owl

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
example of usage: Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
definition editor: Person:Bjoern Peters
definition editor: Bjoern Peters
editor note: Different routes and means of administration should go as children underneath this
definition source: IEDB
editor preferred term: 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: pending final vetting
imported from: obi.owl
imported from: vo.owl

three dimention structure of biological interval
type: Class
subclass of: biological interval structure

biological material interval
type: Class
subclass of: material entity
subclass of: Restriction
  on property: hasStartPoint
  cardinality: 1
subclass of: Restriction
  on property: hasIntervalRelation
  some values from: biological material interval
subclass of: Restriction
  on property: hasStartPoint
  all values from: start point of interval
subclass of: Restriction
  on property: hasEndPoint
  cardinality: 1
subclass of: Restriction
  on property: hasEndPoint
  all values from: end point of interval
subclass of: Restriction
  on property: hasPrimarySequence
  all values from: biological sequence
subclass of: Restriction
  on property: hasIntervalRelation
  all values from: biological material interval
definition: the spatial continuous physical entity which contains ordered biological sets (DNA segments, Genetic Markers, Nucleic Acid Base Residues, RNA segments, Protein segments) between two boundaries: start boundary and end boundary on a chromosome, RNA or protein.

genetic interval
type: Class
subclass of: biological material interval
subclass of: Class
  union of: DNA interval
  union of: RNA interval
disjoint with: genetic interval base residue
disjoint with: protein interval
elucidation: It is genomic, so that protein is not the child of this class. it is continuous, so that neither genome(colletive of chormosomes), nor genotype diploid(collective alleles comes from different chromosomes), nor gene family(collective of genes of same homolog located to different chromosomes) are genomic interval. Whereas gene cluster which are juxtapositioned genes can be subclass of genomic interval. By length, the longest Genomic Interval is the interval with same start point and end point with chromosome, and smallest is when one start point and end point are equal( one residue of DNA or RNA). Interval holds property interval relation.
definition source: Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)
alternative term: genetic material interval
alternative term: genomic material interval
definition: the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points(Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.

DNA interval
type: Class
subclass of: genetic interval
disjoint with: RNA interval

gene
type: Class
subclass of: genetic interval
subclass of: Restriction
  on property: isTranscribedTo
  some values from: transcript
subclass of: Restriction
  on property: isComponentPartOf
  some values from: nuclear genome
subclass of: Restriction
  on property: isCodeFor
  some values from: Class
    union of: protein
    union of: RNA molecule
subclass of: Restriction
  on property: hasGeneLocus
  some values from: gene locus
comment: in RNA virus, there will be RNA interval codes for protein.
definition source: Miko, I. & LeJeune, L., eds. Essentials of Genetics. Cambridge, MA: NPG Education, 2009
definition: a genertically dependent continuant that correspond to one or more DNA sequences that carry the coding information required to produce a specific protein, and that protein in turn carries out a particular function within te cell.

RNA interval
type: Class
subclass of: genetic interval

DNA segment
type: Class
subclass of: DNA interval
subclass of: Restriction
  on property: hasPrimaryDNASequence
  some values from: DNA sequence
subclass of: Restriction
  on property: isStructurePartOf
  all values from: Dexyribonuleic acid molecule
subclass of: Restriction
  on property: hasPrimaryDNASequence
  all values from: DNA sequence
subclass of: Restriction
  on property: hasCytogeneticMapLocation
  some values from: location on cytogenetic map
subclass of: Restriction
  on property: isStructurePartOf
  some values from: Dexyribonuleic acid molecule
definition: naturally material segment of DNA molecule located in a chromosome

textual sequence of genetic interval
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: BFO_0000165
  some values from: primary structure of biological interval
elucidation: The textual sequence refects the order of the nucleotide residue within a gene or a choromsome or any genetic interval. The chromosome includes not only the nucelotide residues interwined into DNA helix but also proteins such as Histone, so we make a distinction that the textual sequence of genetic interval only reflects the primary structure of a genetic interval.
example of usage: a sepcific gene sequence stored in a EntrezGene database
definition: the textual sequencial sets of 'A,T,C,G' or 'A,U,C,G' represent the primary structure of a genetic interval.

allele
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: BFO_0000159
  some values from: genetic polymorohism
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Homo sapiens
definition source: http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp
comment: One of two or more DNA sequences occurring at a particular gene locus. Typically one allele (normal DNA sequence) is common, and other alleles (mutations) are rare.
definition: Mutually exclusive alternative forms of the same genetic interval occupying the same locus on homologous chromosomes, differing in DNA sequence and governing the same biochemical and developmental process.

genetic interval base residue
type: Class
subclass of: biological material interval
disjoint with: protein interval

protein interval
type: Class
subclass of: biological material interval
definition: The biological material interval that is a protein, which is made of amino acid chain.

biological interval structure
type: Class
subclass of: quality

genetic variation
type: Class
subclass of: quality
subclass of: Restriction
  on property: BFO_0000080
  some values from: genetic interval
definition source: http://en.wikipedia.org/wiki/Genetic_variation
definition: Genetic variationis a variation in alleles of genes, occurs both within and among populations.
elucidation: The genetic variation is the differences of the genetic intervals, such as DNA gene or RNA gene, that occupies the same location along the chromosome within or among a population. The genetic variation is counted at the population level, at the individual level, only the maxim two different forms of the sequencial sets of nucleotide exists, which is called allele. We assert it as quality because it must be beared by an independent entity, such as a genetic interval.
comment: needs to align with SO: seuqeunce variant (SO_0001060)

primary structure of biological interval
type: Class
subclass of: biological interval structure

biological sequence
type: Class
subclass of: material entity
subclass of: Restriction
  on property: hasStructure
  some values from: linear
subclass of: Restriction
  on property: hasStructure
  all values from: linear
definition: the liner sequence of simple repeating units composes DNA molecule, RNA molecule or Protein.

two dimention structure of biological interval
type: Class
subclass of: biological interval structure

circular
type: Class
subclass of: primary structure of biological interval

linear
type: Class
subclass of: primary structure of biological interval

genetic marker role
type: Class
subclass of: role

genetic interval aggregate
type: Class
equivalent class: Restriction
  on property: BFO_0000172
  on class: genetic interval
  min qualified cardinality: 2
subclass of: BFO_0000027

genomic site
type: Class
subclass of: BFO_0000029

location on map
type: Class
subclass of: BFO_0000029

locus
type: Class
subclass of: genomic site
definition: a unique chromosomal location defining the position of an individual gene or DNA sequence.
definition source: Human Molecular Genetics3

gene locus
type: Class
subclass of: locus
subclass of: Restriction
  on property: isOccupiedBy
  some values from: Class
    union of: gene
    union of: allele

linked loci
type: Class
subclass of: locus
subclass of: Restriction
  on property: isOccupiedBy
  some values from: linkage interval

amino acid sequence
type: Class
subclass of: biological sequence

polymorphic site
type: Class
subclass of: genomic site
subclass of: Restriction
  on property: isOccupiedBy
  some values from: allele of polymorphism
definition: a genomic site that is occupied by alleles of polymorphism
curator note: this seems similar with SO's sequence feature.

sequence tagged site
type: Class
subclass of: genomic site
subclass of: Restriction
  on property: isOccupiedBy
  some values from: STS marker
alternative term: STS
definition: any unique piece of DNA for which a specific PCR assay has been designed, so that any DNA sample can be easily tested for its presence or absense.

location on cytogenetic map
type: Class
subclass of: location on map

ensembl cytogenetic band
type: Class
subclass of: location on cytogenetic map

entrez gene cytogenetic band
type: Class
subclass of: location on cytogenetic map

HGNC cytogenetic band
type: Class
subclass of: location on cytogenetic map

location on genetic physical map
type: Class
subclass of: location on map

alternative allele of SNP
type: Class
subclass of: allele of SNP
subclass of: Restriction
  on property:
    inverse of: is about
  some values from: minor allele frequency
disjoint with: allele of HLA gene
definition: allele of SNP that designated by smaller allele frequency in a population than a more common allele's frequency.

location on linkage map
type: Class
subclass of: location on map

allele of gene
type: Class
subclass of: allele
subclass of: Restriction
  on property: is_allele_of_gene
  some values from: gene
subclass of: Restriction
  on property: hasOccupiesLocus
  some values from: gene locus
definition: allele that is a set of alternative forms of the same gene occupying the same gene locus.

allele of phenotype
type: Class
subclass of: allele

allele of polymorphism
type: Class
subclass of: allele
subclass of: Restriction
  on property: hasOccupiesLocus
  some values from: polymorphic site
subclass of: Restriction
  on property: has quality at some time
  some values from: genetic polymorohism
definition: allele that is set of alternative form of the polymorphic region that occupy the same locus on chromosomes.

allele shared by sibs
type: Class
subclass of: allele

CDS
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: hasPart
  some values from: exon
subclass of: Restriction
  on property: hasPart
  all values from: exon

chromosome part
type: Class
subclass of: DNA segment

exon
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: isContainedIn
  some values from: gene

gene regulatory element
type: Class
subclass of: DNA segment

haplotype
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property:
    inverse of: isContainedIn
  on class: allele of polymorphism
  min qualified cardinality: 2

intergenic region
type: Class
subclass of: DNA segment
comment: The DNA segment between genes.

intron
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: isContainedIn
  some values from: gene

linkage disequilibrium block
type: Class
subclass of: DNA segment
alternative term: LD block
curator note: need a definition. Also consider the place for 'linkage disequilibrium'

linkage interval
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: hasLinkedLoci
  some values from: linked loci
curator note: definition and term 'linkage'

mutant
type: Class
subclass of: DNA segment

part of exon
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: isStructurePartOf
  all values from: exon

part of intron
type: Class
subclass of: DNA segment
subclass of: Restriction
  on property: isStructurePartOf
  all values from: intron

genetic marker
type: Class
subclass of: DNA interval
subclass of: Restriction
  on property: hasMarkerRole
  all values from: genetic marker role
subclass of: Restriction
  on property: hasMarkerProbe
  some values from: genetic marker probe
subclass of: Restriction
  on property: hasOccupiesSite
  some values from: Class
    union of: location on genetic physical map
    union of: location on linkage map
subclass of: Restriction
  on property: hasPolymorphismQuality
  some values from: genetic polymorohism
subclass of: Restriction
  on property: hasMarkerRole
  some values from: genetic marker role
definition: A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.
comment: genetic marker sounds as a role
definition source: http://en.wikipedia.org/wiki/Genetic_marker

DNA marker
type: Class
subclass of: genetic marker

protein marker
type: Class
subclass of: genetic marker

polymorphic DNA marker
type: Class
subclass of: DNA marker
subclass of: Restriction
  on property: hasMarkerRole
  all values from: genetic marker role
disjoint with: STS non polymorphic marker

STS marker
type: Class
subclass of: DNA marker
subclass of: Restriction
  on property: hasMarkerRole
  all values from: genetic marker role
subclass of: Restriction
  on property: hasMarkerRole
  some values from: genetic marker role

microsatellite marker
type: Class
subclass of: polymorphic DNA marker
disjoint with: SNP marker

non STS microsatellite marker
type: Class
subclass of: microsatellite marker
disjoint with: STS microsatellite marker

STS microsatellite marker
type: Class
subclass of: STS marker
subclass of: microsatellite marker
subclass of: Restriction
  on property: hasMarkerRole
  some values from: genetic marker role
subclass of: Restriction
  on property: hasMarkerRole
  all values from: genetic marker role

SNP marker
type: Class
subclass of: polymorphic DNA marker

allel of repeat sequnce polymorphism
type: Class
subclass of: allele of polymorphism

allele of copy number polymorphism
type: Class
subclass of: allele of polymorphism

allele of SNP
type: Class
subclass of: allele of polymorphism
subclass of: Restriction
  on property: has quality at some time
  some values from: SNP
definition: The two alternative forms of SNP that occupying the same SNP site on the chromosome.

allele of microsatellite
type: Class
subclass of: allel of repeat sequnce polymorphism

probe
type: Class
subclass of: DNA interval
definition: a fragment of DNA of variable length (usually 100-1000 bases long), which is used to detect in DNA or RNA samples the presence of nucleotide sequences (the DNA target) that are complementary to the sequence in the probe.

genetic marker probe
type: Class
subclass of: probe

RNA segment
type: Class
subclass of: RNA interval

adenine residue
type: Class
subclass of: nucleotide residue
disjoint with: cytosine residue
disjoint with: guanine residue
disjoint with: thymine residue

cytosine residue
type: Class
subclass of: nucleotide residue
disjoint with: guanine residue
disjoint with: thymine residue

guanine residue
type: Class
subclass of: nucleotide residue
disjoint with: thymine residue

thymine residue
type: Class
subclass of: nucleotide residue

nucleotide sequence
type: Class
subclass of: biological sequence

RNA sequence
type: Class
subclass of: nucleotide sequence

DNA sequence
type: Class
subclass of: nucleotide sequence

genetics map
type: Class
subclass of: material entity
comment: "A map represents order and distance among markers along a chromosome."(GDB description of its object Map) we can think genetic map as a marker sequence modeling same with DNA seuqence.

radiation hybrid map
type: Class
subclass of: genetics map
definition: A map based on the co-occurrence of markers in a panel of radiation hybrid cell lines, resulting in an ordering of markers along a chromosome backbone.
alternative term: RH map
definition source: http://binfo.ym.edu.tw/binfo/lectures/jou1/tsld008.htm

linkage map
type: Class
subclass of: genetics map
definition: A map based upon frequency of recombination between genomic segments, resulting in the ordering of markers along a chromosome backbone, usually measured in centiMorgans (cM).

genetic physical map
type: Class
subclass of: genetics map
definition: An ordered set of genomic DNA clones demarcated with restriction endonuclease recognition or sequence tagged sites. The distance between sites is mesured in base pair.

cytogenetic map
type: Class
subclass of: genetics map
comment: a map of a chromosome based on its banding pattern.

sequence feature map
type: Class
subclass of: genetic physical map
comment: High resolution physical maps indicating nucleotide-level features of the genome such as exons, introns, regulatory regions, etc.

contig
type: Class
subclass of: genetic interval aggregate

gene family
type: Class
subclass of: genetic interval aggregate

genotype
type: Class
subclass of: genetic interval aggregate
subclass of: Restriction
  on property: BFO_0000172
  on class: allele
  min qualified cardinality: 2
definition: collective of allele which comes from different homologus chromosomes respecitvely.
alternative term: genotype diploid

mitochondiral genome
type: Class
subclass of: genome
subclass of: Restriction
  on property: hasComponentPart
  some values from: Mitochondrial DNA
subclass of: Restriction
  on property: BFO_0000082
  some values from: mitochondrion
definition: genome that is located in mitochondria.

nuclear genome
type: Class
subclass of: genome
subclass of: Restriction
  on property: hasComponentPart
  some values from: genomic DNA
subclass of: Restriction
  on property: BFO_0000082
  some values from: nucleus
comment: set of 24 different chromosomal DNA molecules located in nucleus

SNP interval
type: Class
equivalent class: Restriction
  on property: BFO_0000159
  some values from: SNP
subclass of: genetic interval
definition: a genetic interval that bears the SNP quality and has only one nucleotide residue
alternative term: single nucleotide polymorphism interval

chromosome abnormality
type: Class
subclass of: genetic variation
definition source: http://en.wikipedia.org/wiki/Chromosome_abnormality
definition: A chromosome anomaly, abnormality or aberration reflects an atypical number of chromosomes or a structural abnormality in one or more chromosomes.

genomic aberration
type: Class
subclass of: genetic variation

mutation
type: Class
subclass of: genetic variation
subclass of: Restriction
  on property: hasBearer
  some values from: mutant
definition source: http://en.wikipedia.org/wiki/Mutation
definition: In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element.
comment: Mutation may align to SO: sequence alternation And it may be a process that leads to the existence of genetic polymorphism

genetic polymorohism
type: Class
subclass of: genetic variation
subclass of: Restriction
  on property: BFO_0000080
  some values from: DNA segment
comment: Looser usages among molecular genetics include (1) any sequence variant present at a frequency >1% in a population (2) any non-pathogenic sequence variant, regardless of frequency.
definition: strictly, the existense of two or more variants(alleles, phenotypes, sequence variants, chromosomal structural variants) at significant frequencies (i.e. more than 1%) in the population.
definition source: Human Molecular Genetics3

SNP
type: Class
subclass of: genetic polymorohism

copy number polymorphism
type: Class
subclass of: genetic polymorohism
subclass of: Restriction
  on property: hasBearer
  some values from: allele of copy number polymorphism

deletion polymorphism
type: Class
subclass of: genetic polymorohism

insertion polymorphism
type: Class
subclass of: genetic polymorohism

repeat sequence polymorphism
type: Class
subclass of: genetic polymorohism
subclass of: Restriction
  on property: hasBearer
  some values from: allel of repeat sequnce polymorphism

restriction fragment length polymorphism
type: Class
subclass of: genetic polymorohism
comment: RFLPs

single-strand conformatinal polymorphism
type: Class
subclass of: genetic polymorohism
comment: SSCP

microsatellite polymorphism
type: Class
subclass of: repeat sequence polymorphism

minisatellite polymorphism
type: Class
subclass of: repeat sequence polymorphism
comment: VNTR

satellite polymorphism
type: Class
subclass of: repeat sequence polymorphism

point mutation
type: Class
subclass of: mutation

segmental Mutation
type: Class
subclass of: mutation

interactive gene group
type: Class
equivalent class: Restriction
  on property: BFO_0000172
  on class: gene
  min qualified cardinality: 2
subclass of: genetic interval aggregate

allele of HLA gene
type: Class
label: ancestrol allele of SNP
subclass of: allele of SNP
comment: is equal to anscestor allele in dbSNP.

minor allele frequency
type: Class
subclass of: data item
definition: is the ratio of chromosomes in the population carrying the less common variant to those with the more common variant.

biomolecule boundary
type: Class
subclass of: BFO_0000140
definition: biomolecule boundary is the surface of a biomolecule ,which is a lower dimensional part of a molecule. biomolecule bounday can separate a biological molecule from the rest of the existing entities in the world.(for example, DNA molecule is separate from rest part in the cell nucleus by DNA molecule boundary)
comment: different with DNA segment, which is part of DNA molecule, and is surrounding by other DNA segment.

boundary point of interval
type: Class
subclass of: BFO_0000142
comment: The starts and ends of biological interval, which associate to a location on a genetic or physical map.

end point of interval
type: Class
subclass of: boundary point of interval

start point of interval
type: Class
subclass of: boundary point of interval

genetic predisposition to disease of type X
type: Class
subclass of: genetic susceptibility
definition: A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition editor: Albert Goldfain
comment: The incorrect usage of 'constitutional abnormalty' was discussed through OGMS-discussion group. A suggestion is to replace 'abnormality' with 'variant'. See: https://groups.google.com/forum/?fromgroups=#!topic/ogms-discuss/7SYug0AWAcE (commented by YL, Feb.13 2013)
curator note: creation date: 2009-06-23T11:23:07Z
imported from: ogms.owl

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

genetic susceptibility
type: Class
subclass of: disposition
subclass of: Restriction
  on property: BFO_0000113
  some values from: genetic susceptibility factor
creator: YL,YH
definition: a disposition that is physically based on some genetic material, such as one or more gene mutations or variant, such that if the genome of an organism has the genetic material as its part, the organism may have an increased likelihood or chance to develop: 1) a particular disease; 2) a peculiar biological/bodily process.
alternative term: genetic predisposition

genetic susceptibility to pathological bodily process
type: Class
equivalent class: Class
  intersection of: genetic susceptibility
  intersection of: Restriction
    on property: is realized by
    some values from: pathological bodily process
subclass of: genetic susceptibility
definition: a genetic susceptibility that lead to the increased possibilities to initiate a patholoical bodily process in the organism, whose genome has related genetic susceptibility factor (he physical basis of this genetic susceptibility) as its part.

genetic susceptibility to biological process
type: Class
equivalent class: Class
  intersection of: genetic susceptibility
  intersection of: Restriction
    on property: is realized by
    some values from: biological_process
subclass of: genetic susceptibility
definition: a genetic susceptibility that lead to the increased possibilities to initiate a biological process in an organism, whose genome has related genetic susceptibility factor (he physical basis of this genetic susceptibility) as its part.

genetic susceptibility to adverse event
type: Class
equivalent class: Class
  intersection of: genetic susceptibility to pathological bodily process
  intersection of: Restriction
    on property: is realized by
    some values from: adverse event
subclass of: genetic susceptibility to pathological bodily process
definition: a genetic susceptibility that lead to the increased possibilities to initiate adverse event in an organism, whose genome has related genetic susceptibility factor (he physical basis of this genetic susceptibility) as its part.

genetic susceptibility factor
type: Class
equivalent class: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility
subclass of: material entity
subclass of: Restriction
  on property:
    inverse of: is about
  some values from: textual conclusion of genetic susceptibility
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility
editor note: Many types of genetic material can be called a genetic susceptibility factor, such as a gene, a haplotype, a microsatellite, a genotype and so on. The notion of the genetic susceptibility factor based on the output of a scientific investigation that aims to elucidate the association between a phenotype and genotype. The statistical methods, study population and geographical characteristic of the population often has an impact on the assessment of the 'genetic susceptibility'. The more replicate result among different study groups the stronger evidence can be used to determine the 'genetic susceptibility factor'. (YL. Feb. 13, 2013)
creator: YL, YH
definition: a genetic material that is the material base of genetic susceptibility

susceptibility gene
type: Class
subclass of: gene
definition: genetic susceptibility factor that is a gene

susceptibility haplotype
type: Class
equivalent class: Class
  intersection of: haplotype
  intersection of: genetic susceptibility factor
subclass of: genetic susceptibility factor
subclass of: Restriction
  on property:
    inverse of: isContainedIn
  on class: susceptibility allele of SNP
  min qualified cardinality: 2
definition: genetic susceptibility factor that is a haplotype

susceptibility allele of SNP
type: Class
equivalent class: Class
  intersection of: allele of SNP
  intersection of: susceptibility allele
subclass of: genetic susceptibility factor
comment: The susceptibility allele of SNP is usually the minor allele of SNP
definition: genetic susceptibility factor that is a Simple Nucleotide Polymorphism (SNP).

susceptibility genotype
type: Class
equivalent class: Class
  intersection of: genotype
  intersection of: genetic susceptibility factor
subclass of: genetic susceptibility factor
creator: YL, YH
definition: genetic susceptibility factor that is a genotype

susceptibility allele
type: Class
equivalent class: Class
  intersection of: allele
  intersection of: genetic susceptibility factor
subclass of: genetic susceptibility factor
comment: Usually the susceptibility allele is the minor allele. We may set up rules here.
definition: genetic susceptibility factor that is an allele

genetic susceptibility to vaccine adverse event
type: Class
subclass of: genetic susceptibility to adverse event
definition: a genetic susceptibility to adverse event that is proceded by a vaccination process.

susceptibility gene
type: Class
subclass of: genetic susceptibility factor

textual conclusion of genetic susceptibility
type: Class
subclass of: conclusion textual entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: genetic association investigation
subclass of: Restriction
  on property: is about
  some values from: genetic susceptibility factor
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: biological_process
    union of: pathological bodily process
subclass of: Restriction
  on property: concretized by at some time
  some values from: genetic susceptibility
alternative term: textual conclusion of genetic association

susceptibility interactive gene group
type: Class
equivalent class: Class
  intersection of: interactive gene group
  intersection of: genetic susceptibility factor
subclass of: genetic susceptibility factor

genetic susceptibility to drug adverse event
type: Class
subclass of: genetic susceptibility to adverse event
definition: a genetic susceptibility to adverse event that is proceded by a drug administration

genetic association investigation
type: Class
subclass of: investigation
subclass of: Restriction
  on property: BFO_0000167
  some values from: human study subject group
definition source: http://en.wikipedia.org/wiki/Genetic_association
comment: Genetic association can be between phenotypes, such as visible characteristics such as flower colour or height, between a phenotype and a genetic polymorphism, such as a single nucleotide polymorphism (SNP), or between two genetic polymorphisms. Association between genetic polymorphisms occurs when there is non-random association of their alleles as a result of their proximity on the same chromosome; this is known as genetic linkage. Linkage disequilibrium (LD) is a term used in the study of population genetics for the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is not the same as linkage, which is the phenomenon whereby two or more loci on a chromosome have reduced recombination between them because of their physical proximity to each other. LD describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies. Genetic association studies are performed to determine whether a genetic variant is associated with a disease or trait: if association is present, a particular allele, genotype or haplotype of a polymorphism or polymorphisms will be seen more often than expected by chance in an individual carrying the trait. Thus, a person carrying one or two copies of a high-risk variant is at increased risk of developing the associated disease or having the associated trait.
definition: investigation that aims to test whether single-locus alleles or genotype frequencies (or more generally, multilocus haplotype frequencies) differ between two groups of individuals (usually diseased subjects and healthy controls). Genetic association studies are based on the principle that genotypes can be compared "directly", i.e. with the sequences of the actual genomes.

case control genetic association study
type: Class
subclass of: genetic association investigation
comment: The case group and control group are differed by their phenotyp outcome measurement, for example, the case group is a group of people that has disease A, but control group has no disease A. Usually other characteristics of the control and case group are carefully matched (e.g. by age, sex, enviroment) to avoid other variables's co-effets on the variable that is under investigation.
definition: Genetic association investigation that use to observe the non-random differences of a genetic factor's frequency between case group and control group.

initial GWAS study
type: Class
subclass of: genome wide association study
definition: The first Genome Wide Association Study that conducted in a population to observe the genetic association with a phenotype or trait.

replicate GWAS study
type: Class
subclass of: genome wide association study
comment: Tthe repeated observation of associations between covariates by different investigative teams, in different populations, using different designs and methods is typically taken as evidence that the association is not an artifact. ref: Replication in Genome-Wide Association Studies [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865141/]
definition: the GWAS study that intend to repeat initial GWAS study's observation over a different population using a different design and methods by different investigation teams.

human study subject
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: Restriction
    on property: BFO_0000161
    some values from: study subject role
subclass of: Homo sapiens

human study subject group
type: Class
equivalent class: Class
  intersection of: BFO_0000027
  intersection of: Restriction
    on property: BFO_0000172
    some values from: human study subject
subclass of: BFO_0000027

human case group
type: Class
subclass of: human study subject group

human control group
type: Class
subclass of: human study subject group

human study subject group size
type: Class
subclass of: data item

odds ratio measurement
type: Class
subclass of: data transformation

logistic regression measurement
type: Class
subclass of: data transformation

odds ratio
type: Class
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: odds ratio measurement

human gene
type: Class
subclass of: gene

positive conclusion of genetic susceptibility
type: Class
subclass of: textual conclusion of genetic susceptibility
subclass of: Restriction
  on property: hasPvalue
  some values from: float
subclass of: Restriction
  on property: hasOddsRatio
  some values from: float
subclass of: Restriction
  on property: is positive supporting statistical evidence of
  some values from: genetic susceptibility
disjoint with: negative conclusion of genetic susceptibility
disjoint with: neutral conclusion of genetic susceptibility
definition: The textual conclusion from the paper that mentioned the genetic susceptibility of the genetic susceptibility factors that is statistically meaningful (statistically supported).

negative conclusion of genetic susceptibility
type: Class
subclass of: textual conclusion of genetic susceptibility
subclass of: Restriction
  on property: hasOddsRatio
  some values from: float
subclass of: Restriction
  on property: is negative statistical evidence of
  some values from: genetic susceptibility
subclass of: Restriction
  on property: hasPvalue
  some values from: float
disjoint with: neutral conclusion of genetic susceptibility
definition: The textual conclusion from the paper that mentioned the genetic susceptibility of a genetic susceptibility factors that is denied by statistical calculation.

neutral conclusion of genetic susceptibility
type: Class
subclass of: textual conclusion of genetic susceptibility
definition: The textual conclusion from the paper that mentioned the genetic susceptibility of a genetic susceptibility factors is neither deny nor support by statistical calculation.

susceptibility SNP
type: Class
equivalent class: Class
  intersection of: genetic susceptibility factor
  intersection of: Restriction
    on property: BFO_0000159
    some values from: SNP
subclass of: genetic susceptibility factor

genetic association with adverse event clinical trail
type: Class
equivalent class: Class
  intersection of: clinical trial
  intersection of: genetic association investigation
subclass of: genetic association investigation
comment: in this kind of study, the vaccination related adverse event is well controlled by selecting healthy or vaccinia naive individuals for enrollment to clinical trial. To analyze the genetic association with AE, the vaccinees experiencing AE will be used for case group, and others will be used fror control group.

two dimentional structure of genetic interval
type: Class
subclass of: two dimention structure of biological interval

three dimention structure of genetic interval
type: Class
subclass of: three dimention structure of biological interval

multiple sclerosis AE patient
type: Class
subclass of: Homo sapiens
subclass of: Restriction
  on property: actively participates in
  some values from: multiple sclerosis AE
subclass of: Restriction
  on property:
    inverse of: vaccine immunization for host
  some values from: Pandemrix

DRB1*15:01
type: Class
subclass of: allele of gene
subclass of: susceptibility allele
subclass of: Restriction
  on property: variant_of
  some values from: HLA DBR1 gene
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility to vaccine adverse event
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: multiple sclerosis AE patient
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Class
    intersection of: human vaccinee
    intersection of: Restriction
      on property:
        inverse of: vaccine immunization for host
      some values from: Pandemrix
type: NamedIndividual

HLA DBR1 gene
type: Class
subclass of: human gene

multiple sclerosis AE after Pandemrix vaccination
type: Class
subclass of: multiple sclerosis AE
subclass of: Restriction
  on property: is preceded by
  some values from: pandemrix vaccination
type: NamedIndividual

pandemrix vaccination
type: Class
subclass of: vaccination
subclass of: Restriction
  on property: has participant
  some values from: Pandemrix

T allele of rs1801133 SNP
type: Class
subclass of: alternative allele of SNP
subclass of: susceptibility allele of SNP
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility to vaccine adverse event
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Class
    intersection of: human vaccinee experiencing systematic adverse event
    intersection of: Restriction
      on property:
        inverse of: vaccine immunization for host
      some values from: Smallpox virus vaccine
subclass of: Restriction
  on property: isContainedIn
  some values from: MTHFR gene
type: NamedIndividual

G allele of rs9282763 SNP
type: Class
subclass of: alternative allele of SNP
subclass of: susceptibility allele of SNP
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility to vaccine adverse event
subclass of: Restriction
  on property: isContainedIn
  some values from: IRF1 gene
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Class
    intersection of: human vaccinee experiencing systematic adverse event
    intersection of: Restriction
      on property:
        inverse of: vaccine immunization for host
      some values from: Smallpox virus vaccine
type: NamedIndividual

A allele of rs839 SNP
type: Class
subclass of: alternative allele of SNP
subclass of: susceptibility allele of SNP
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Class
    intersection of: human vaccinee experiencing systematic adverse event
    intersection of: Restriction
      on property:
        inverse of: vaccine immunization for host
      some values from: Smallpox virus vaccine
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility to vaccine adverse event
subclass of: Restriction
  on property: isContainedIn
  some values from: IRF1 gene
type: NamedIndividual

T allele of rs2070874 SNP
type: Class
subclass of: alternative allele of SNP
subclass of: Restriction
  on property: isContainedIn
  some values from: IL4 gene

C allele of rs2243268 SNP
type: Class
subclass of: alternative allele of SNP
subclass of: Restriction
  on property: isContainedIn
  some values from: IL4 gene

A allele of rs2243290 SNP
type: Class
subclass of: alternative allele of SNP
subclass of: Restriction
  on property: isContainedIn
  some values from: IL4 gene

MTHFR gene
type: Class
subclass of: human gene

IRF1 gene
type: Class
subclass of: human gene

IL4 gene
type: Class
subclass of: human gene

haplotype 1 in IRF1 gene
type: Class
equivalent class: Class
  intersection of: haplotype
  intersection of: Restriction
    on property: hasContainedInterval
    some values from: G allele of rs9282763 SNP
  intersection of: Restriction
    on property: hasContainedInterval
    some values from: A allele of rs839 SNP
subclass of: haplotype
subclass of: susceptibility haplotype
subclass of: Restriction
  on property: hasContainedInterval
  some values from: A allele of rs839 SNP
subclass of: Restriction
  on property: hasContainedInterval
  some values from: G allele of rs9282763 SNP
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility to vaccine adverse event
subclass of: Restriction
  on property: isContainedIn
  some values from: IRF1 gene
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Class
    intersection of: human vaccinee experiencing systematic adverse event
    intersection of: Restriction
      on property:
        inverse of: vaccine immunization for host
      some values from: Smallpox virus vaccine
type: NamedIndividual

haplotype 2 in IL4 gene
type: Class
equivalent class: Class
  intersection of: haplotype
  intersection of: Restriction
    on property: hasContainedInterval
    some values from: T allele of rs2070874 SNP
  intersection of: Restriction
    on property: hasContainedInterval
    some values from: C allele of rs2243268 SNP
  intersection of: Restriction
    on property: hasContainedInterval
    some values from: A allele of rs2243290 SNP
subclass of: haplotype
subclass of: susceptibility haplotype
subclass of: Restriction
  on property: hasContainedInterval
  some values from: A allele of rs2243290 SNP
subclass of: Restriction
  on property: hasContainedInterval
  some values from: T allele of rs2070874 SNP
subclass of: Restriction
  on property: part of continuant at all times that whole exists
  some values from: Class
    intersection of: human vaccinee experiencing systematic adverse event
    intersection of: Restriction
      on property:
        inverse of: vaccine immunization for host
      some values from: Smallpox virus vaccine
subclass of: Restriction
  on property: BFO_0000127
  some values from: genetic susceptibility to vaccine adverse event
subclass of: Restriction
  on property: isContainedIn
  some values from: IL4 gene
subclass of: Restriction
  on property: hasContainedInterval
  some values from: C allele of rs2243268 SNP
type: NamedIndividual

human vaccinee
type: Class
equivalent class: Class
  intersection of: Homo sapiens
  intersection of: vaccinated organism
subclass of: vaccinated organism

human vaccinee experiencing systematic adverse event
type: Class
subclass of: human vaccinee
subclass of: Restriction
  on property: actively participates in
  some values from: systematic adverse event

systematic adverse event after smallpox vaccination
type: Class
subclass of: systematic adverse event
subclass of: Restriction
  on property: is preceded by
  some values from: smallpox vaccination
type: NamedIndividual

genetic susceptibility to adverse event following Pandemix vaccination
type: Class
subclass of: genetic susceptibility to vaccine adverse event
definition: a genetic susceptibility to adverse event that is proceded by a vaccination process.

genetic susceptibility to multiple scelorosis AE following Pandemix vaccination
type: Class
subclass of: genetic susceptibility to adverse event following Pandemix vaccination
definition: a genetic susceptibility to adverse event that is proceded by a vaccination process.

smallpox vaccination
type: Class
subclass of: vaccination

wheezing AE after influenza vaccination
type: Class
subclass of: wheezing AE
subclass of: Restriction
  on property: is preceded by
  some values from: influenza vaccination

influenza vaccination
type: Class
subclass of: vaccination

viability
type: Class
subclass of: quality of a single physical entity
definition: An organismal quality inhering in a bearer or a population by virtue of the bearer's ability or inability to survive and develop normally or the number of surviving individuals in a given population.
editor preferred term: viability
imported from: vo.owl
imported from: PATO

viable
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive and develop normally or the long term survival ability of a given population.
alternative term: live
editor preferred term: viable
imported from: vo.owl
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 term: quality of a single physical entity
imported from: vo.owl
imported from: PATO

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
editor preferred term: physical object quality
imported from: vo.owl
imported from: PATO

organismal quality
type: Class
subclass of: quality of a single physical entity
definition: A quality that inheres in an entire organism or part of an organism.
editor preferred term: organismal quality
imported from: vo.owl
imported from: PATO

virulence
type: Class
subclass of: organismal quality
definition: A quality inhering in a bearer by virtue of the bearer's pathogenicity.
editor preferred term: virulence
imported from: vo.owl
imported from: PATO

genetic material
type: Class
subclass of: material entity
definition source: adapted from 'genetic material' class definition in OBI ExpDesign.owl
definition: A nucleic acid macromolecule or submolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny.
alternative term: genetic nucleic acid
alternative term: genomic material
reo_requires_feedback_to: OBI - The concept of 'genetic material' was discussed in 2011 among OBI members, but a final definition or implementation was nver reached. There is a definition in OBO ExpDesign sandbox version, which was used to inform our definition and usage here. Further discussions with OBI will be required, however.
alternative term: genomic nucleic acid
imported from: reo.owl

region
type: Class
subclass of: generically dependent continuant
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
IAO id: SO:0000001
IAO subset: SOFA
alternative term: sequence
comment: This term is asserted as Quality in OBI, and OBI uses OBI's preferrable label: ' primary structure of sequence macromolecule'. In REO, this term is asserted as a 'generically dependent continuant'.
imported from: so.owl

SO:gene
type: Class
subclass of: biological_region
definition: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
IAO id: SO:0000704
IAO subset: SOFA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
IAO xref: http://en.wikipedia.org/wiki/Gene
alternative term: SO:gene
imported from: so.owl

SO:allele
type: Class
subclass of: biological_region
subclass of: Restriction
  on property: variant_of
  some values from: SO:gene
definition: An allele is one of a set of coexisting sequence variants of a gene.
IAO id: SO:0001023
alternative term: allelomorph
IAO xref: http://en.wikipedia.org/wiki/Allele
alternative term: SO:allele
imported from: so.owl

genome
type: Class
subclass of: BFO_0000027
subclass of: Restriction
  on property: BFO_0000111
  some values from: nucleic acid
definition: A genome is the sum of genetic material within a cell or virion.
IAO id: SO:0001026
IAO xref: http://en.wikipedia.org/wiki/Genome
imported from: so.owl

biological_region
type: Class
subclass of: region
definition: A region defined by its disposition to be involved in a biological process.
IAO id: SO:0001411
IAO subset: SOFA
alternative term: biological region
imported from: so.owl

vaccine
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: has function at some time
    some values from: Class
      intersection of: vaccine function
      intersection of: Restriction
        on property: is realized by
        some values from: vaccine immunization
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: vaccine preparation
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.
definition editor: YH, BP, BS, MC, LC, XZ, RS
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.
see also: MeSH: D014612
imported from: vo.owl

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: Class
    intersection of: organism
    intersection of: Restriction
      on property: has role at some time
      some values from: vaccine host role
subclass of: Restriction
  on property: has participant
  some values from: vaccine
definition editor: YH, BP
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
imported from: vo.owl

mineral salt vaccine adjuvant
type: Class
subclass of: vaccine adjuvant
see also: CVX: 119
definition editor: SGS, YH
definition: a vaccine adjuvant that is formed as a mineral salt.
imported from: vo.owl

adjuvant role
type: Class
subclass of: role
definition editor: YH,YL
definition: A role that inheres in a material entity that helps or enhances the effect of other agents, such as a drug or vaccine.
imported from: vo.owl

vaccine adjuvant role
type: Class
subclass of: adjuvant role
definition editor: YH
definition: an adjuvant role that inheres in a material entity which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen.
imported from: vo.owl

attenuated
type: Class
subclass of: virulence
definition editor: YH
imported from: vo.owl

vaccine component
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: part_of
    some values from: vaccine
subclass of: material entity
definition editor: YH
alternative term: cardinal part of vaccine
definition: a processed material that is output of the vaccine preparation and part of a vaccine.
has synonym: vaccine ingredient
imported from: vo.owl

vaccine function
type: Class
equivalent class: Class
  union of: preventive vaccine function
  union of: therapeutic vaccine function
subclass of: function
definition 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: vo.owl

company
type: Class
subclass of: organization
definition editor: YH
imported from: vo.owl

licensed vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: bearer_of
    some values from: licensed vaccine role
subclass of: vaccine
definition: A vaccine that is licensed for commercial use.
definition editor: YH
imported from: vo.owl

Pandemrix
type: Class
subclass of: Influenza virus vaccine
subclass of: Restriction
  on property: vaccine immunization for host
  some values from: Homo sapiens
subclass of: Restriction
  on property: has continuant part at all times
  some values from: sucrose vaccine stabilizer
subclass of: Restriction
  on property: is_manufactured_by
  has value: GlaxoSmithKline Biologicals
subclass of: Restriction
  on property: vaccine immunization against microbe
  some values from: H1N1 subtype
subclass of: Restriction
  on property: has continuant part at all times
  some values from: formaldehyde vaccine preservative
comment: ATC code J07BB02
alternative term: Pandemrix H1N1
definition: Pandemrix is an influenza vaccine for influenza pandemics, such as the H1N1 2009 flu pandemic colloquially called the swine flu. The vaccine was developed by GlaxoSmithKline and patented in September 2006.
curator note: TODO: the component 'egg protein' and 'sodium deoxycholate' is not added yet.
creator: YL
definition source: http://en.wikipedia.org/wiki/Pandemrix
imported from: vo.owl

vaccine additive role
type: Class
subclass of: role
definition editor: YL,YH
definition source: Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008
definition source: a role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity.
imported from: vo.owl

pathogen organism component in vaccine
type: Class
equivalent class: Class
  intersection of: vaccine component
  intersection of: Class
    union of: organism
    union of: Restriction
      on property: part_of
      some values from: organism
subclass of: vaccine component
definition editor: YH
definition: a vaccine component that originates from an organism such as a pathogen or a modified organism.
imported from: vo.owl

preventive vaccine function
type: Class
subclass of: vaccine function
subclass of: Restriction
  on property: is realized by
  some values from: vaccination
subclass of: Restriction
  on property: is realized by
  some values from: disorder prevention
subclass of: Restriction
  on property: is realized by
  some values from: induction of adaptive immune response to antigen
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.
definition editor: YH
alternative term: prophylactic vaccine function
imported from: vo.owl

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: vo.owl

active immunization
type: Class
subclass of: immunization
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
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.
definition editor: YH, XZ
imported from: vo.owl

vaccine immunization
type: Class
subclass of: active immunization
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
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: immunization objective
definition editor: YH, XZ
definition source: WEB: http://en.wikipedia.org/wiki/Immunization
alternative term: artificial active immunization
definition: artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.
imported from: vo.owl

induction of adaptive immune response to antigen
type: Class
subclass of: active immunization
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.
definition editor: YH, XZ
imported from: vo.owl

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.
definition editor: YH, XZ
imported from: vo.owl

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.
definition editor: YH, XZ
imported from: vo.owl

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.
definition editor: YH, XZ
imported from: vo.owl

therapeutic vaccine function
type: Class
subclass of: vaccine function
subclass of: Class
  union of: Restriction
    on property: is realized by
    some values from: induction of adaptive immune response to antigen
  union of: Restriction
    on property: is realized by
    some values from: modification of adaptive immune response to antigen
subclass of: Restriction
  on property: is realized by
  some values from: vaccination
subclass of: Restriction
  on property: is realized by
  some values from: disorder treatment
definition 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: vo.owl

thimerosal vaccine preservative
type: Class
equivalent class: Class
  intersection of: vaccine preservative
  intersection of: Restriction
    on property: has part
    some values from: thimerosal
subclass of: vaccine preservative
subclass of: Restriction
  on property: has role at some time
  some values from: vaccine preservative role
definition: vaccine preservative that has thimerosal as part.
definition editor: YH
imported from: vo.owl

vaccine adjuvant
type: Class
equivalent class: Class
  intersection of: vaccine additive
  intersection of: Restriction
    on property: has role at some time
    some values from: vaccine adjuvant role
subclass of: vaccine additive
definition editor: YH
definition: a vaccine component that is chemical substance added to vaccine and enhance and direct immune response to protective antigen. Many of vaccine adjuvants cause a range of serious side-effects.
imported from: vo.owl

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

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

viral vaccine
type: Class
equivalent class: Class
  intersection of: vaccine
  intersection of: Restriction
    on property: vaccine immunization against microbe
    some values from: Viruses
subclass of: vaccine
definition: A vaccine that protects against some viral disease.
definition editor: YH
see also: MeSH: D014765
imported from: vo.owl

whole pathogen organism as vaccine component
type: Class
equivalent class: Class
  intersection of: pathogen organism component in vaccine
  intersection of: Class
    intersection of: organism
    intersection of: Restriction
      on property: has role at some time
      some values from: immunization target role
subclass of: pathogen organism component in vaccine
comment: whole organism in vaccine is a organism component in vaccine that includes the whole organism such as a whole live attenuated organism.
definition editor: YH
imported from: vo.owl

licensed vaccine role
type: Class
subclass of: regulation-assigned role
definition editor: YH
definition: licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market.
imported from: vo.owl

Influenza virus vaccine
type: Class
equivalent class: Class
  intersection of: viral vaccine
  intersection of: Restriction
    on property: vaccine immunization against microbe
    some values from: Class
      union of: unidentified influenza virus
      union of: Influenzavirus A
      union of: Influenzavirus B
      union of: Influenzavirus C
subclass of: viral vaccine
definition: A viral vaccine that protects against infection with influenza virus.
definition editor: YH
see also: MeSH: D007252
alternative term: Influenza vaccine
imported from: vo.owl

Smallpox virus vaccine
type: Class
equivalent class: Class
  intersection of: viral vaccine
  intersection of: Restriction
    on property: vaccine immunization against microbe
    some values from: Variola virus
subclass of: viral vaccine
see also: MeSH: D012900
definition editor: YH
definition: A viral vaccine that protects against infection with Smallpox virus.
imported from: vo.owl

BCG vaccine
type: Class
subclass of: vaccine
subclass of: Restriction
  on property: has part
  some values from: whole pathogen organism as vaccine component
subclass of: Restriction
  on property: has quality at some time
  some values from: attenuated
subclass of: Restriction
  on property: has quality at some time
  some values from: viable
subclass of: Restriction
  on property: vaccine immunization for host
  some values from: Homo sapiens
definition editor: YH
see also: CVX: 19
alternative term: Bacillus Calmette Guerin
definition: BCG Vaccine is a Mycobacterium tuberculosis vaccine that is a live attenuated strain of Mycobacterium bovis (Bacillus Calmette Guerin; BCG).
imported from: vo.owl

vaccine additive
type: Class
equivalent class: Class
  intersection of: vaccine component
  intersection of: Restriction
    on property: bearer_of
    some values from: vaccine additive role
subclass of: vaccine component
definition source: Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 73.
definition: a vaccine component that is added to the immunogen by the vaccine manufacturer for a specific purpose. Additives include adjuvants, preservatives and stablizers, as well as materials that are added to affect pH and isotonicity.
definition editor: YH
imported from: vo.owl

vaccine preservative
type: Class
equivalent class: Class
  intersection of: vaccine additive
  intersection of: Restriction
    on property: has role at some time
    some values from: vaccine preservative role
subclass of: vaccine additive
alternative term: antimicrobial agent in vaccine
definition editor: YH
imported from: vo.owl

vaccine stabilizer
type: Class
equivalent class: Class
  intersection of: vaccine additive
  intersection of: Restriction
    on property: has role at some time
    some values from: vaccine stabilizer role
subclass of: vaccine additive
definition editor: YH
definition source: Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 75.
definition: a vaccine additive that helps to protect the vaccine from adverse conditions such as the freeze-drying process (for those vaccines that are freeze-dried) or heat.
imported from: vo.owl

aluminum vaccine adjuvant
type: Class
subclass of: mineral salt vaccine adjuvant
definition: a mineral salt vaccine adjuvant that is composed of aluminum salt.
definition editor: Aluminum vaccine adjuvant is a vaccine adjuvant that is composed of some aluminum compound.
definition editor: YH
imported from: vo.owl

vaccine preservative role
type: Class
subclass of: role
definition: a role inhers in a vaccine component that when added into a vccine formmulation, it can prevent the growth of bacteria or fungi that inadvertently may be introduced into the vaccine during administrating process or the manufacturing process.
definition source: P73 Chapter 6, Vaccine 5th edition by Plotkin, S. et al.
definition editor: YH,YL
comment: The CFR requires that, with certain defined exceptions, preservatives must be added to mulitdose vials of vaccine. (P73 Chapter 6, Vaccine 5th edition by Plotkin, S. et al.)
imported from: vo.owl

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: is realized by
  some values from: immunization
definition editor: YH, ZX
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).
imported from: vo.owl

immunization target role
type: Class
subclass of: role
definition editor: a role that represents a target (i.e., some disorder) of immunization.
definition editor: YH, ZX
imported from: vo.owl

formaldehyde vaccine preservative
type: Class
subclass of: vaccine preservative
subclass of: Restriction
  on property: has role at some time
  some values from: vaccine preservative role
subclass of: Restriction
  on property: has part
  some values from: formaldehyde
definition source: WEB: http://www.mja.com.au/public/issues/184_04_200206/eld10500_fm.pdf
definition: a vaccine preservative that contains formaldehyde.
definition editor: YH, SGS
imported from: vo.owl

vaccinated organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: vaccination
subclass of: organism
has synonym: Vaccinee
definition: an organism that is vaccinated with a vaccine
comment: YH, YL, MC
imported from: vo.owl

organism vaccinated with a licensed vaccine
type: Class
equivalent class: Class
  intersection of: vaccinated organism
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: vaccination
      intersection of: Restriction
        on property: has_specified_input
        some values from: licensed vaccine
subclass of: vaccinated organism
definition: a vaccinated organism that is vaccinated with a licensed vaccine
alternative term: vaccinee
definition editor: YH, YL, MC
imported from: vo.owl

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: vo.owl

vaccine stabilizer role
type: Class
subclass of: role
definition editor: YL
definition: a role inheres in vaccine component when added into vaccine's formulation, it tends to inhibit the reaction between two or more other vaccine substances in the final vaccine formulation; it also helps to protect the vaccine from adverse conditions such as the freeze-drying process or heat.
imported from: vo.owl

sugar vaccine stabilizer
type: Class
subclass of: vaccine stabilizer
definition: a vaccine stabilizer that is specifically made by a sugar.
definition editor: YH, YL
imported from: vo.owl

sucrose vaccine stabilizer
type: Class
subclass of: sugar vaccine stabilizer
definition: a vaccine stabilizer that is specifically made by a sucrose.
definition editor: YH, YL
imported from: vo.owl

author
type: Class
subclass of: material entity
definition: a human being that bears an author role.

biological macromolecule
type: Class
subclass of: biological molecule
subclass of: Restriction
  on property: hasBiomoleculeBoundary
  all values from: biomolecule boundary

biological molecule
type: Class
subclass of: material entity

biological small molecule
type: Class
subclass of: biological molecule

book
type: Class
subclass of: material entity
subclass of: Restriction
  on property: isWrittenBy
  some values from: author

coding RNA molecule
type: Class
subclass of: RNA molecule

CpG Island
type: Class
subclass of: gene regulatory element
comment: CpG islands are commonly defined as regions of DNA of at least 200 bp in length and that have a G+C content above 50% and a ratio of observed vs. expected CpGs close to or above 0.6. ( Ref. Gardiner-Garden and Fromer (1987) ). Sets of CG repeat elements, usually found upstream of transcribed regions of the genome.

Dexyribonuleic acid molecule
type: Class
equivalent class: Class
  intersection of: nucleic acid
  intersection of: Restriction
    on property: hasBiomoleculeBoundary
    some values from: biomolecule boundary
  intersection of: Restriction
    on property: hasPrimaryDNASequence
    some values from: DNA sequence
  intersection of: Restriction
    on property: hasBiomoleculeBoundary
    all values from: biomolecule boundary
  intersection of: Restriction
    on property: hasPrimaryDNASequence
    all values from: DNA sequence
disjoint with: RNA molecule

enhancer
type: Class
subclass of: gene regulatory element
description: An enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene cluster. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome. (http://en.wikipedia.org/wiki/Enhancer_(genetics))
definition: a set of short sequence elements which stimulate transcription of a gene and whose function is not critically dependent on their precise position or orientation.
definition source: Human Molecular Genetics3

genomic DNA
type: Class
subclass of: Dexyribonuleic acid molecule
comment: also gDNA

histone
type: Class
subclass of: protein

non codling RNA molecule
type: Class
subclass of: RNA molecule

nucleic acid
type: Class
equivalent class: Class
  union of: Dexyribonuleic acid molecule
  union of: RNA molecule
subclass of: polymer
disjoint with: polypeptide

polymer
type: Class
subclass of: biological macromolecule

polypeptide
type: Class
subclass of: polymer
subclass of: Restriction
  on property: isStructurePartOf
  some values from: protein
subclass of: Restriction
  on property: hasPrimarySequence
  some values from: amino acid sequence
subclass of: Restriction
  on property: hasPrimarySequence
  all values from: amino acid sequence

polypeptide coding gene
type: Class
subclass of: gene
disjoint with: pseudogene
disjoint with: RNA gene

primary transcript
type: Class
subclass of: transcript

promoter
type: Class
subclass of: gene regulatory element
description: In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA (towards the 3' region of the anti-sense strand, also called template strand and non-coding strand). Promoters can be about 100–1000 base pairs long. (http://en.wikipedia.org/wiki/Promoter_(genetics))
definition: a combination of short sequence elements, normally just upstream of a gene, to which RNA polymerase binds in order to initiate transcription of the gene.
definition source: Human Molecular Genetics3

protein
type: Class
subclass of: polymer

pseudogene
type: Class
subclass of: gene
disjoint with: RNA gene

RNA gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCodeFor
  all values from: RNA molecule
subclass of: Restriction
  on property: isCodeFor
  some values from: RNA molecule

RNA molecule
type: Class
subclass of: nucleic acid
subclass of: Restriction
  on property: hasPrimaryRNASequence
  all values from: RNA sequence
subclass of: Restriction
  on property: hasPrimaryRNASequence
  some values from: RNA sequence

STS non polymorphic marker
type: Class
subclass of: STS marker
subclass of: Restriction
  on property: hasMarkerRole
  all values from: genetic marker role
subclass of: Restriction
  on property: hasMarkerRole
  some values from: genetic marker role

transcript
type: Class
subclass of: RNA molecule
subclass of: Restriction
  on property: hasPrimaryRNASequence
  some values from: RNA sequence
subclass of: Restriction
  on property: hasPrimaryRNASequence
  all values from: RNA sequence
subclass of: Restriction
  on property: isTranscribedBy
  some values from: gene
comment: An RNA synthesized on a DNA or RNA template by an RNA polymerase.

complementary DNA
type: Class
subclass of: Dexyribonuleic acid molecule
comment: In genetics, complementary DNA (cDNA) is DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase.(wikipedia)

messenger RNA
type: Class
subclass of: transcript

Micro RNAs
type: Class
subclass of: RNA molecule
comment: short(22nt) RNA molecules encoded within normal genomes that have a role in regulation of gene expression and maybe also of chromatin structure. Sometimes called small temporal RNA(stRNA).

multicopy single-stranded DNA
type: Class
subclass of: Dexyribonuleic acid molecule

Mitochondrial DNA
type: Class
subclass of: Dexyribonuleic acid molecule
subclass of: Restriction
  on property: isStructurePartOf
  all values from: mitochondiral genome

ribosomal RNA
type: Class
subclass of: RNA molecule

transfer RNA
type: Class
subclass of: RNA molecule

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

metadata complete
type: Thing
type: curation status specification
type: NamedIndividual

organizational term
type: NamedIndividual
type: curation status specification

ready for release
type: NamedIndividual
type: curation status specification

metadata incomplete
type: NamedIndividual
type: curation status specification

uncurated
type: NamedIndividual
type: curation status specification

pending final vetting
type: NamedIndividual
type: curation status specification

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification

requires discussion
type: NamedIndividual
type: curation status specification

publication_PMID_22841884
type: NamedIndividual
type: publication about an investigation
is about: genetic association invesitgation 1

positive conclusion of genetic susceptibility_1
type: NamedIndividual
type: positive conclusion of genetic susceptibility
comment: The HLA DRB1*15:01 allele is responsible for genetic susceptibility to
is about: DRB1*15:01
is about: multiple sclerosis AE after Pandemrix vaccination

genetic association invesitgation 1
type: NamedIndividual
type: case-only study
has_specified_output: positive conclusion of genetic susceptibility_1

publication_PMID_18454680
type: NamedIndividual
type: publication about an investigation
is about: genetic adverse event association clinical trial 1
is about: genetic adverse event association clinical trial 2

genetic adverse event association clinical trial 1
type: NamedIndividual
type: genetic association with adverse event clinical trail
has_specified_output: positive conclusion 1 of genetic susceptibility_trial1

genetic adverse event association clinical trial 2
type: NamedIndividual
type: genetic association with adverse event clinical trail
has_specified_output: positive conclusion 1 of genetic susceptibility_trial2

positive conclusion 1 of genetic susceptibility_trial2
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.01
hasOddsRatio: 4.1
is positive supporting statistical evidence of: T allele of rs1801133 SNP
is positive supporting statistical evidence of: systematic adverse event after smallpox vaccination

positive conclusion 1 of genetic susceptibility_trial1
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 2.3
is about: T allele of rs1801133 SNP
is about: systematic adverse event after smallpox vaccination

positive conclusion 2 of genetic susceptibility_trial1
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 3.2
is about: G allele of rs9282763 SNP
is about: systematic adverse event after smallpox vaccination

positive conclusion 2 of genetic susceptibility_trial2
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 3.0
is about: G allele of rs9282763 SNP
is about: systematic adverse event after smallpox vaccination

positive conclusion 3 of genetic susceptibility_trial1
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 3.2
is about: A allele of rs839 SNP
is about: systematic adverse event after smallpox vaccination

positive conclusion 3 of genetic susceptibility_trial2
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 3.0
is about: A allele of rs839 SNP
is about: systematic adverse event after smallpox vaccination

positive conclusion 4 of genetic susceptibility_trial1
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 3.2
is about: haplotype 1 in IRF1 gene
is about: systematic adverse event after smallpox vaccination

positive conclusion 4 of genetic susceptibility_trial2
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.03
hasOddsRatio: 3.0
is about: haplotype 1 in IRF1 gene
is about: systematic adverse event after smallpox vaccination

positive conclusion 5 of genetic susceptibility_trial1
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.05
hasOddsRatio: 2.4
is about: haplotype 2 in IL4 gene
is about: systematic adverse event after smallpox vaccination

positive conclusion 5 of genetic susceptibility_trial2
type: NamedIndividual
type: positive conclusion of genetic susceptibility
hasPvalue: 0.06
hasOddsRatio: 3.8
is about: haplotype 2 in IL4 gene
is about: systematic adverse event after smallpox vaccination

GlaxoSmithKline Biologicals
type: NamedIndividual
type: company
definition editor: YH
has URI: http://www.gsk-bio.com/english/index.html