vido.owl
type: Ontology
version IRI: vido.owl
default language: en
contributor: Barry Smith
contributor: Gustavo Carvalho
contributor: Regina Hurley
contributor: Sebastian Deusing
contributor: Shane Babcock
contributor: Sydney Cohen
contributor: Yongqun He
creator: John Beverley
license: http://creativecommons.org/licenses/by/4.0/
comment: The Virus Infectious Disease Ontology (VIDO) is an extension of the Infectious Disease Ontology (IDO). VIDO follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by specific viruses and associated virus diseases. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible.

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

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

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

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

in branch
type: AnnotationProperty
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

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

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

editor note
type: AnnotationProperty
editor preferred term: editor note
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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

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

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

definition source
type: AnnotationProperty
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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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

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

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

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

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

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

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

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

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

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

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

has ID digit count
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
term editor: Person:Alan Ruttenberg

has ID range allocated to
type: AnnotationProperty
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
term editor: Person:Alan Ruttenberg

has ID policy for
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

has ID prefix
type: AnnotationProperty
example of usage: Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
definition: Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
term editor: Person:Alan Ruttenberg

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

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

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

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

has axiom label
type: AnnotationProperty
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI

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

temporal interpretation
type: AnnotationProperty

shorthand
type: AnnotationProperty

label
type: AnnotationProperty

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

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

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

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

preceded by
type: ObjectProperty
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: 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
alternative term: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: precedes

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

occupies temporal region
type: ObjectProperty
domain: occurrent
range: temporal region
term editor: John Beverley
comment: Not sure if this has an IRI yet, so I supplied a placeholder.

results in
type: ObjectProperty

has_material_basis_in
type: ObjectProperty
range: material entity

has specified input
type: ObjectProperty
sub property of: has participant
inverse of: is specified input of
imported from: http://purl.obolibrary.org/obo/obi.owl

is specified input of
type: ObjectProperty
sub property of: participates in
definition: Participates in relation between a planned process and a continuant participating in that process that is not created during the process, where the presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
imported from: http://purl.obolibrary.org/obo/obi.owl

has specified output
type: ObjectProperty
sub property of: has participant
inverse of: is specified output of
imported from: http://purl.obolibrary.org/obo/obi.owl

is specified output of
type: ObjectProperty
sub property of: participates in
domain: continuant
range: planned process
definition: Participates in relation between a planned process and a continuant participating in that process where the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
imported from: http://purl.obolibrary.org/obo/obi.owl

inheres in
type: ObjectProperty
inverse of: bearer of
editor preferred term: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in

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

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

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

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

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

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

disposition of
type: ObjectProperty
sub property of: inheres in

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

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

regulates
type: ObjectProperty
type: TransitiveProperty
domain: process
range: process
definition: x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
term editor: Chris Mungall
term editor: David Hill
term editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
elucidation: false

negatively regulates
type: ObjectProperty
sub property of: regulates
definition: x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: negatively regulates (process to process)

positively regulates
type: ObjectProperty
sub property of: regulates
definition: x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: positively regulates (process to process)

has output
type: ObjectProperty
sub property of: has participant
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
term editor: Chris Mungall
alternative term: produces

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

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

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

viral disease
type: Class
equivalent class: Class
  intersection of: infectious disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: virus disorder
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: viral disease course
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: virus disorder
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
definition: Infectious disease inhering in a virus disorder that is a disorder due to the presence of the virus.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

infectious disease control objective specification
type: Class
subclass of: objective specification
definition: Objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population.
comment: http://purl.obolibrary.org/obo/apollo-sv.owl

infectious disease control strategy
type: Class
subclass of: plan specification
definition: Plan specification whose objective specification is an infectious disease control objective specification.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

disease transmission model
type: Class
subclass of: algorithm
definition: Algorithm that models the progress of a transmissible disease in a population.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

place closure control strategy
type: Class
subclass of: infectious disease control strategy
definition: Infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

case isolation control strategy
type: Class
subclass of: infectious disease control strategy
definition: Infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

vector control strategy
type: Class
subclass of: infectious disease control strategy
definition: Infectious disease control strategy that has a vector control action specification as part.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

quarantine control strategy
type: Class
subclass of: infectious disease control strategy
definition: Infectious disease control strategy whereby organisms who have had contact with infectious organisms but are not symptomatic or otherwise known to be infectious are prevented from having contact with other susceptible organisms.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

disease surveillance objective specification
type: Class
subclass of: objective specification
definition: Objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval.
comment: http://purl.obolibrary.org/obo/apollo-sv.owl

contact tracing
type: Class
subclass of: infectious disease control strategy
definition: Infectious disease control strategy that identifies and treats contacted organisms in a host population.
imported from: http://purl.obolibrary.org/obo/apollo-sv.owl

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

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

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

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

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

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

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

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

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

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

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

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

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

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.

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

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

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

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

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

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

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

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

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

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

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

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

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

temporal region
type: Class
subclass of: occurrent
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])

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

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

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

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

spatiotemporal region
type: Class
subclass of: occurrent
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.

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

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

disposition
type: Class
subclass of: realizable entity
disjoint with: role
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])

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

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])

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

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

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

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

quality
type: Class
subclass of: specifically dependent continuant
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])

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

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

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

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

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

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

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

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

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).

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

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

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

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

site
type: Class
subclass of: immaterial entity
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])

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

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

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

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

function
type: Class
subclass of: disposition
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.

process boundary
type: Class
subclass of: occurrent
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])

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

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).

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

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

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

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

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

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

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

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

process profile
type: Class
subclass of: process
disjoint with: history
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])

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

zero-dimensional temporal region
type: Class
subclass of: temporal region
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.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

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

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

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

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

anatomical entity
type: Class
subclass of: material entity
disjoint with: infection
disjoint with: immunodeficiency
definition: A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
editor note: Anatomical entities - like other material entities - may have immaterial parts.
imported from: caro.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
definition: Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.
imported from: http://purl.obolibrary.org/obo/chebi.owl

Axiom
annotated source: deoxyribonucleic acid
annotated property: definition
annotated target: Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.
editor note: This is a suggested revision to the ChEBI definition.
term editor: John Beverley

molecular entity
type: Class
subclass of: material entity
definition: Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc.
imported from: chebi.owl

biological role
type: Class
subclass of: Class
  intersection of: role
  intersection of: Restriction
    on property: realized in
    some values from: immune response
  intersection of: Restriction
    on property: inheres in
    some values from: Restriction
      on property: part of
      some values from: molecular entity
definition: Role inhering in a molecular entity or part of that entity, realized in biological processes.
imported from: http://purl.obolibrary.org/obo/chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
definition: Macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases.
imported from: http://purl.obolibrary.org/obo/chebi.owl

Axiom
annotated source: nucleic acid
annotated property: definition
annotated target: Macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases.
editor note: This is a suggested revision to the ChEBI definition.
term editor: John Beverley

ribonucleic acid
type: Class
subclass of: nucleic acid
definition: Nucleic acid composed of nucleotides containing ribose and linked by phosphodiester bonds.
imported from: http://purl.obolibrary.org/obo/chebi.owl

macromolecule
type: Class
subclass of: molecular entity
definition: Molecular entity of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
imported from: http://purl.obolibrary.org/obo/chebi.owl

protein
type: Class
subclass of: macromolecule
definition: A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
imported from: http://purl.obolibrary.org/obo/chebi.owl

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
definition: DNA consisting of two parallel strands joined by hydrogen bonds between complementary purines and pyrimidines.
imported from: http://purl.obolibrary.org/obo/chebi.owl

Axiom
annotated source: double-stranded DNA
annotated property: definition
annotated target: DNA consisting of two parallel strands joined by hydrogen bonds between complementary purines and pyrimidines.
editor note: This is a suggestion for the ChEBI definition of this term, since it currently lacks a definition.
term editor: John Beverley

cell
type: Class
subclass of: material entity
disjoint with: organism
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
definition: This should be an inferred subclass of BFO:object. -John
imported from: cl.owl

reagent
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: Restriction
    on property: has role
    some values from: reagent role
definition: Processed material bearing a reagent role.
imported from: http://purl.obolibrary.org/obo/ero.owl

antibody reagent
type: Class
subclass of: reagent
definition: Reagent that is comprised of immunoglobulins produced by B cells in response to an antigen.
imported from: http://purl.obolibrary.org/obo/ero.owl

viral plaque assay
type: Class
subclass of: assay
definition: Assay used to determine viral titers.
editor note: This term should be move from ERO to VIDO.
imported from: http://purl.obolibrary.org/obo/ero.owl

intervention
type: Class
subclass of: planned process
definition: Planned process used to influence one or more factors in a research study, and the independent variable in an interventional study wherein the influence is measured or evaluated.
imported from: http://purl.obolibrary.org/obo/ero.owl

serology assay
type: Class
subclass of: assay
definition: Assay analyzing blood serum and other bodily fluids, to detect the presence of serum antibodies.
imported from: http://purl.obolibrary.org/obo/ero.owl

immunoassay
type: Class
subclass of: assay
definition: Assay measuring the concentration of a substance in a material by exploiting binding between an analyte and a corresponding detection antibody.
imported from: http://purl.obolibrary.org/obo/ero.owl

generative stage
type: Class
subclass of: process
definition: Temporal subdivision of a developmental process.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

adaptive immune response
type: Class
subclass of: immune response
definition: Immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
imported from: go.owl

leukocyte mediated immunity
type: Class
subclass of: immune response
definition: Process involved in the carrying out of an immune response by a leukocyte.
imported from: go.owl

immune response
type: Class
subclass of: biological process
definition: Immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl

humoral immune response
type: Class
subclass of: immune response
definition: Immune response mediated through a body fluid.
imported from: go.owl

biological process
type: Class
subclass of: process
definition: Process specifically pertinent to the functioning of functionally integrated units.
imported from: go.owl

viral capsid
type: Class
subclass of: macromolecule
subclass of: Restriction
  on property: part of
  some values from: virion
definition: Protein surrounding virion nucleic acid in some virus particles.
definition: The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: viral capsid
annotated property: definition
annotated target: Protein surrounding virion nucleic acid in some virus particles.
editor note: This is a suggested revision to the GO definition and hierarchy placement.
term editor: John Beverley

viral envelope
type: Class
subclass of: macromolecule
definition: Macromolecule lipid bilayer of a virion surrounding capsid.
definition: The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: viral envelope
annotated property: definition
annotated target: Macromolecule lipid bilayer of a virion surrounding capsid.
editor note: This is a suggested revision to the GO definition and hierarchy placement.
term editor: John Beverley

virus uncoating stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
subclass of: Restriction
  on property: preceded by
  some values from: virus penetration stage
definition: Virus generative stage during which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus uncoating stage
annotated property: definition
annotated target: Virus generative stage during which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

virus attachment stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
definition: Virus generative stage during which a virion protein binds to molecules on the host surface or host cell surface projection.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus attachment stage
annotated property: definition
annotated target: Virus generative stage during which a virion protein binds to molecules on the host surface or host cell surface projection.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

virus synthesis stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
subclass of: Restriction
  on property: preceded by
  some values from: virus translation stage
definition: Virus developmental stage during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus synthesis stage
annotated property: definition
annotated target: Virus developmental stage during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

virus translation stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
subclass of: Restriction
  on property: preceded by
  some values from: virus uncoating stage
definition: Virus generative stage during which viral mRNA is translated into viral protein, using the host cellular machinery.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus translation stage
annotated property: definition
annotated target: Virus generative stage during which viral mRNA is translated into viral protein, using the host cellular machinery.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

virus transcription stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
subclass of: Restriction
  on property: preceded by
  some values from: virus translation stage
definition: Virus developmental stage during which a viral genome, or part of a viral genome, is transcribed within the host cell.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus transcription stage
annotated property: definition
annotated target: Virus developmental stage during which a viral genome, or part of a viral genome, is transcribed within the host cell.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

immunoglobulin complex
type: Class
subclass of: macromolecular complex
definition: Protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
imported from: go.owl

B cell receptor complex
type: Class
subclass of: macromolecular complex
definition: Immunoglobulin complex present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
imported from: go.owl

developmental process
type: Class
subclass of: biological process
definition: Biological process whose specific outcome is the progression of a functional, integrated, unit.
imported from: go.owl

macromolecular complex
type: Class
subclass of: material entity
definition: Stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
imported from: go.owl

T cell receptor complex
type: Class
subclass of: macromolecular complex
definition: Protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
imported from: go.owl

symbiotic process
type: Class
subclass of: biological process
definition: Process carried out by gene products in an organism or acellular structure that enables the entity to engage in a symbiotic relationship with an organism.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/go.owl

adhesion of symbiont to host
type: Class
subclass of: biological process
definition: Attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly.
imported from: go.owl

entry into host
type: Class
subclass of: biological process
definition: Penetration by an organism into the body, tissues, or cells of the host organism.
imported from: go.owl

entry into host through host barriers
type: Class
subclass of: entry into host
definition: Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism.
imported from: go.owl

innate immune response
type: Class
subclass of: immune response
definition: Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
imported from: go.owl

virus penetration stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
subclass of: Restriction
  on property: preceded by
  some values from: virus attachment stage
definition: Virus generative stage during which a virion or viral nucleic acid breaches the barriers of a host.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus penetration stage
annotated property: definition
annotated target: Virus generative stage during which a virion or viral nucleic acid breaches the barriers of a host.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

capsomere
type: Class
subclass of: macromolecule
subclass of: Restriction
  on property: part of
  some values from: viral capsid
definition: Protein subunit comprising viral capsid.
imported from: http://purl.obolibrary.org/obo/go.owl

negative regulation of biological process
type: Class
subclass of: biological regulation
definition: Process that stops, prevents, or reduces the frequency, rate or extent of a biological process.
imported from: go.owl

negative regulation of viral process
type: Class
subclass of: biological regulation
definition: Process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
imported from: go.owl

negative regulation of immune response
type: Class
subclass of: biological regulation
definition: Process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
imported from: go.owl

negative regulation of developmental process
type: Class
subclass of: biological regulation
definition: Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
imported from: go.owl

establishment of localization
type: Class
equivalent class: Restriction
  on property: preceded by
  some values from: pathogen transmission process
subclass of: biological process
subclass of: Restriction
  on property: part of
  some values from: pathogenesis
definition: Process that localizes a substance or cellular component via movement, tethering or selective degradation.
imported from: go.owl

biological regulation
type: Class
subclass of: process
definition: Process that modulates a measurable attribute of any biological process, quality or function.
imported from: go.owl

virus release stage
type: Class
subclass of: virus generative stage
subclass of: Restriction
  on property: part of
  some values from: virus replication
subclass of: Restriction
  on property: preceded by
  some values from: virus synthesis stage
definition: Virus generative stage involving dissemination of mature virus particles from the host cell, by cell lysis or the budding of virus particles from the cell membrane.
imported from: http://purl.obolibrary.org/obo/go.owl

Axiom
annotated source: virus release stage
annotated property: definition
annotated target: Virus generative stage involving dissemination of mature virus particles from the host cell, by cell lysis or the budding of virus particles from the cell membrane.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

objective specification
type: Class
subclass of: directive information content entity
definition: 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.
comment: http://purl.obolibrary.org/obo/iao.owl

action specification
type: Class
subclass of: directive information content entity
definition: Directive information entity that describes an action the bearer will take
comment: http://purl.obolibrary.org/obo/iao.owl

information content entity
type: Class
subclass of: generically dependent continuant

algorithm
type: Class
subclass of: plan specification
definition: Plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
imported from: http://purl.obolibrary.org/obo/iao.owl

plan specification
type: Class
subclass of: directive information content entity
definition: Directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
imported from: http://purl.obolibrary.org/obo/iao.owl

mycovirus
type: Class
subclass of: virus
subclass of: Class
  intersection of: virus
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
definition: Virus which infects and replicates within or on fungi.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

symbiont role
type: Class
subclass of: role
disjoint with: reservoir of pathogen role
disjoint with: pathogen portal of entry role
disjoint with: pathogen portal of exit role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: A role borne by an organism in symbiosis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

mutualist role
type: Class
subclass of: symbiont role
definition: Symbiont role borne by an organism in which both symbionts derive a growth, survival, or fitness advantage from symbiosis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

commensal role
type: Class
subclass of: symbiont role
definition: Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis, while the other symbiont is neither advantaged nor disadvantaged.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

parasite role
type: Class
subclass of: symbiont role
definition: Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

opportunistic infectious disposition
type: Class
subclass of: infectious disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: pathogen transmission process
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: Infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

primary infectious disposition
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: pathogen transmission process
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: Infectious disposition to become part of a disorder in immunocompetent organisms.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.

symbiont host role
type: Class
subclass of: Class
  intersection of: host role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
disjoint with: pathogen host role
definition: Host role borne by an organism whose extended organism provides an environment supportive for the survival, growth, maturation, or reproduction of an object contained as a proper part.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

definitive host role
type: Class
subclass of: symbiont host role
definition: Symbiont host role borne by an organism iwhose partner in symbiosis reaches developmental maturity or reproduces sexually in the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

intermediate host role
type: Class
subclass of: symbiont host role
definition: Symbiont host role borne by an organism whose partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

dead-end host role
type: Class
subclass of: symbiont host role
definition: Symbiont host role borne by an organism whose partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious agent host role
type: Class
equivalent class: Class
  intersection of: pathogen host role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
definition: Pathogen host role borne by an organism whose extended organism contains an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen host role
type: Class
equivalent class: Class
  intersection of: host role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
definition: Host role borne by an object having a pathogen as part or an borne by an organism having a pathogen as part of its extended organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

mechanical vector role
type: Class
subclass of: pathogen vector role
definition: A pathogen vector role borne by an organism in virtue of the fact that the pathogen does not multiply in or on the vector.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
has exact synonym: passive carrier

biological vector role
type: Class
subclass of: pathogen vector role
definition: A pathogen vector role borne by an organism in virtue of the fact that the pathogen multiplies in the vector.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

pathogen vehicle role
type: Class
equivalent class: Class
  intersection of: pathogen transporter role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Class
        complement of: organism
      intersection of: Restriction
        on property: location of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: indirect pathogen transmission process
subclass of: pathogen transporter role
definition: A pathogen transporter role borne by an entity in virtue of the fact that the entity is not a complete organism.
editor note: I don't understand the rdfs comment indicating drinking water bears the infected agent vehicle role, but neither of the subtypes. Presumably, if an infectious agent is present in drinking water, then it bears a fomite role. Drinking water is, in fact, a classic example. -John Beverley
editor note: I've expanded this definition and label to cover infectious agent pathogens and infectious structure pathogens. -John Beverley
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles.

biological vehicle role
type: Class
subclass of: pathogen vehicle role
definition: A pathogen vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Examples include blood, serum, tissue, or fresh produce.

fomite role
type: Class
subclass of: pathogen vehicle role
subclass of: Class
  complement of: organism
definition: An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

reservoir of pathogen role
type: Class
subclass of: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: location of
        some values from: pathogen
disjoint with: pathogen portal of entry role
disjoint with: pathogen portal of exit role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: Role borne by a material entity in which pathogens can persist, and from which they can be transmitted to hosts.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

virulence factor disposition
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: molecular entity
disjoint with: toxin disposition
disjoint with: adhesion disposition
disjoint with: invasion disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host.

toxin disposition
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: molecular entity
disjoint with: adhesion disposition
disjoint with: invasion disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

exotoxin disposition
type: Class
subclass of: toxin disposition
definition: Toxin disposition to damage cells or extracellular matrix by a direct enzymatic process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen portal of entry role
type: Class
subclass of: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: anatomical entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: part of
        some values from: pathogen transmission process
disjoint with: pathogen portal of exit role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: Role borne by an anatomical entity that serves as the site through which a pathogen enters a host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen portal of exit role
type: Class
subclass of: Class
  intersection of: role
  intersection of: Restriction
    on property: inheres in
    some values from: anatomical entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: part of
        some values from: pathogen transmission process
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: Role borne by an anatomical entity that serves as the site through which a pathogen exits a host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

primary infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: infectious disorder
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: Role borne by an infectious disorder whose host has another, distinct, infectious disorder - neither arising from the other through metastasis - which emerged after this infectious disorder was established due to increased host susceptibility to infectious disorders.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

secondary infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: infectious disorder
disjoint with: host role
disjoint with: source of infection role
definition: Role borne by an infectious disorder whose host has another, distinct, primary infectious disorder - neither arising from the other through metastasis - which emerged after the primary infectious disorder was established due to increased host susceptibility to infectious disorders.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious disease
type: Class
equivalent class: Class
  intersection of: disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: infectious disorder
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: infectious disease course
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: infectious disorder
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
subclass of: disease
definition: Disease whose physical basis is an infectious disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: tranmissible disease
imported from: http://purl.obolibrary.org/obo/ido.owl

adhesion disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: molecular entity
  intersection of: Restriction
    on property: realized in
    all values from: adhesion of symbiont to host
disjoint with: invasion disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition borne by a macromolecule that is the disposition to participate in adherence to a host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

invasion disposition
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: molecular entity
  intersection of: Restriction
    on property: realized in
    all values from: Restriction
      on property: positively regulates
      some values from: entry into host through host barriers
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition borne by a biological macromolecule that is the disposition to facilitate breach of and entry through host barriers.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: Invasion factor; invasin
imported from: http://purl.obolibrary.org/obo/ido.owl

protective resistance
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition inhering in an acellular structure or organism, with a part having a disposition to mitigate damage to the entity from invasive or internal threats, which is realized in one or more negative biological regulation process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide.

resistance to drug
type: Class
subclass of: protective resistance
disjoint with: resistance to pathogen
definition: Protective resistance that mitigates the damaging effects of a drug.
editor note: http://purl.obolibrary.org/obo/ido.owl
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

resistance to pathogen
type: Class
subclass of: protective resistance
subclass of: Restriction
  on property: inheres in
  some values from: organism
definition: Protective resistance that inheres in an organism and mitigates the damaging effects of a pathogen.
editor note: http://purl.obolibrary.org/obo/ido.owl
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

herd immunity to infectious organism
type: Class
equivalent class: Class
  intersection of: collective resistance disposition
  intersection of: Restriction
    on property: inheres in
    some values from: organism population
  intersection of: Restriction
    on property: realized in
    all values from: Restriction
      on property: realizes
      some values from: immunity to pathogen
subclass of: collective resistance disposition
definition: Collective resistance disposition that inheres in an organism population where the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts to susceptible individuals.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunity to pathogen
type: Class
subclass of: resistance to pathogen
definition: Resistance to pathogen that inheres in an organism due to immune system components in its extended organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

sterilizing immunity to infectious agent
type: Class
subclass of: immunity to pathogen
definition: Immunity to pathogen that results in elimination of the infectious agent from the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Sterilizing immunity is typically conferred by neutralizing antibodies.

pathogenic disposition
type: Class
equivalent class: Class
  intersection of: disposition
  intersection of: Restriction
    on property: realized in
    some values from: establishment of localization
  intersection of: Restriction
    on property: realized in
    some values from: appearance of disorder
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition borne by a material entity to establish localization in and result in formation of disorder in a host or immunocompetent members of the same species as the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: pathogenicity
imported from: http://purl.obolibrary.org/obo/ido.owl

invasive disposition
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: pathogen
  intersection of: Restriction
    on property: realized in
    all values from: entry into host through host barriers
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition borne by a pathogen that is the disposition to penetrate the epithelial barriers of an organism of another species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

zoonotic disposition
type: Class
subclass of: infectious disposition
definition: Infectious disposition to be transmitted from an infected, non-human host to a human host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

reverse zoonotic disposition
type: Class
subclass of: infectious disposition
definition: Infectious disposition to be transmitted from an infected, human host to a non-human host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.

collective disposition
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: object aggregate
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: This should be pushed up to: http://purl.obolibrary.org/obo/bfo.owl

immunosuppressed organism
type: Class
subclass of: organism
disjoint with: immunocompetent organism
definition: Organism that is experiencing immunosuppression.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunocompetent organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: immunocompetence
disjoint with: immunodeficient organism
definition: Organism that has immunocompetence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

contagiousness
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: pathogen host
  intersection of: Restriction
    on property: realized in
    all values from: horizontal pathogen transmission process
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition that inheres in a pathogen host and is a disposition to horizontally transmit that pathogen to organisms of the same species as the host, through casual contact, with a high likelihood of realization.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

colonized host
type: Class
equivalent class: Class
  intersection of: host
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: colony
definition: Host that contains a colony in or on its extended organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious pathogen transmissibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition: Quality that inheres in an infectious agent or infectious structure and is the likelihood that the agent or structure will undergo a horizontal transmission process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.

infectivity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in a pathogen and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: This quality is measured by the proportion of exposed who become infected.

virulence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition: Quality that inheres in a pathogen and is the degree to which realizations of the infectious disease caused by the pathogen become severe or fatal.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal.

susceptibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: material entity
definition: Quality that inheres in an entity and is the degree to which it can be harmed by another entity.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.

susceptibility to infectious agent
type: Class
subclass of: susceptibility
subclass of: Restriction
  on property: inheres in
  some values from: organism
disjoint with: drug susceptibility
definition: Susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

drug susceptibility
type: Class
subclass of: susceptibility
definition: Susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

drug susceptibility of infectious agent
type: Class
subclass of: drug susceptibility
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition: Drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

complex infection
type: Class
subclass of: infection
definition: Infection comprised of infectious organisms from different species.
term editor: John Beverley

extracellular infection
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Class
    intersection of: Class
      complement of: Restriction
        on property: located in
        some values from: cell
    intersection of: Restriction
      on property: has part
      some values from: pathogen
disjoint with: intracellular infection
definition: Infection in which pathogen parts persist in the extracellular space of the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

intracellular infection
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Class
    intersection of: Restriction
      on property: has part
      some values from: Class
        union of: infectious agent
        union of: infectious structure
    intersection of: Restriction
      on property: located in
      some values from: cell
subclass of: infection
disjoint with: bacteremia
disjoint with: viremia
definition: Infection in which pathogen parts persist inside host cells.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

systematic infection
type: Class
subclass of: infection
definition: Infection for which the infectious agents or structures that are part of the infection are distributed throughout the host.
term editor: John Beverley

local infection
type: Class
subclass of: infection
definition: Infection for which the infectious agents or structures that are part of the infection are limited to a relatively small area of the host's body.

acute infectious disease course
type: Class
subclass of: infectious disease course
definition: Infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious disease incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.

infection incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the number of organisms in the population that become infected with a pathogen during a specified period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.

infectious disease incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: cumulative incidence of infectious disease
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.

infection incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: cumulative incidence of infection
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.

infectious disease incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.

infection incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the infection incidence proportion per unit time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.

infectious disease prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.

infection prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the number of organisms in the population infected with a pathogen at a specified time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.

infectious disease lifetime prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.

pathogen seroprevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for a pathogen in their serum at a specified time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.

infectious disease mortality rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.

infectious disease endemicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic.

infectious disease sporadicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: Quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease.

infectious disease course
type: Class
equivalent class: Class
  intersection of: disease course
  intersection of: Restriction
    on property: has part
    some values from: virus replication
  intersection of: Restriction
    on property: realizes
    some values from: infectious disease
subclass of: disease course
definition: Disease course that is the realization of an infectious disease.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

long-term non-progressing infectious disease course
type: Class
subclass of: chronic infectious disease course
definition: Chronic infectious disease course that does not progress to severe stages for a long period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunization against infectious agent
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: has output
    some values from: Restriction
      on property:
        inverse of: has_material_basis_in
      some values from: immunity to pathogen
subclass of: process
definition: Process by which an organism acquires immunity to an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

active immunization against infectious agent
type: Class
subclass of: immunization against infectious agent
definition: Immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: inoculation
imported from: http://purl.obolibrary.org/obo/ido.owl

vaccination against infectious agent
type: Class
subclass of: active immunization against infectious agent
definition: Active immunization that begins with exposure of an organism to a vaccine .
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

variolation
type: Class
subclass of: active immunization against infectious agent
definition: Active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

passive immunization against infectious agent
type: Class
subclass of: immunization against infectious agent
definition: Immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious disease epidemic
type: Class
subclass of: process
definition: Process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious disease pandemic
type: Class
subclass of: infectious disease epidemic
definition: Infectious disease epidemic during which statistically significant increases of infectious disease incidences of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious disorder
type: Class
equivalent class: Class
  intersection of: disorder
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: extended organism
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: Disorder that is part of an organism whose extended organism has some infectious agent or structure as part, which participates in the formation of infection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

bacteremia
type: Class
equivalent class: Class
  intersection of: extracellular infection
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: bacteria
      intersection of: Restriction
        on property: located in
        some values from: blood
subclass of: extracellular infection
disjoint with: viremia
definition: Infection that has as part bacteria located in the blood.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

organism population
type: Class
subclass of: object aggregate
definition: ido.owl
definition: Aggregate of organisms of the same species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.

infected population
type: Class
subclass of: organism population
definition: ido.owl
definition: Organism population whose members have an infection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

diseased population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: infectious disease course
  intersection of: Restriction
    on property: has part
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: infectious disease course
definition: ido.owl
definition: Organism population in whose members an infectious disease is being realized.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: infectious agent
  intersection of: Restriction
    on property: has part
    all values from: infectious agent
definition: ido.owl
definition: Organism population whose members each have an infectious disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

susceptible population
type: Class
subclass of: organism population
definition: ido.owl
definition: Organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: at-risk population

normal resident microbiota population
type: Class
subclass of: organism population
definition: ido.owl
definition: Organism population whose members are participating in non-parasitic symbiosis with a particular host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: normal resident microflora population
comment: An infectious organism population (IDO:0000513) (1) that is not part of any infection (IDO:0000586), (2) whose members are participating in a process of symbiosis (GO:0044403) with the same host, and (3) whose members are organisms of types among the normal resident microbiota for the type of host organism.

incubation interval
type: Class
subclass of: one-dimensional temporal region
subclass of: Restriction
  on property: has part
  some values from: infection start temporal region
definition: One-dimensional temporal region beginning with the extablishment of an infectious agent or structure in a host and ending with the onset of symptoms in the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

communicability interval
type: Class
subclass of: one-dimensional temporal region
subclass of: Restriction
  on property: has part
  some values from: communicability start temporal region
subclass of: Restriction
  on property: preceded by
  some values from: latency interval
definition: One-dimensional temporal region during which a pathogen host bears a contagiousness disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

symbiont
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: symbiont role
definition: Organism bearing a symbiont role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

obligatory symbiont
type: Class
subclass of: symbiont
subclass of: Restriction
  on property: has role
  some values from: symbiont role
definition: Organism that can only reach developmental maturity, replicate, or persist in symbiosis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

mutualist
type: Class
equivalent class: Class
  intersection of: symbiont
  intersection of: Restriction
    on property: has role
    some values from: mutualist role
definition: Symbiont bearing a mutualist role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

commensal
type: Class
equivalent class: Class
  intersection of: symbiont
  intersection of: Restriction
    on property: has role
    some values from: commensal role
definition: Symbiont bearing a commensal role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

parasite
type: Class
equivalent class: Class
  intersection of: symbiont
  intersection of: Restriction
    on property: has role
    some values from: parasite role
definition: Symbiont bearing a parasite role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: pathogenic disposition
disjoint with: fomite
disjoint with: immunodeficiency
definition: Material entity bearing a pathogenic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

primary pathogen
type: Class
equivalent class: Class
  intersection of: pathogen
  intersection of: Restriction
    on property: has disposition
    some values from: primary infectious disposition
definition: Pathogen bearing a primary infectious disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: principal pathogen
imported from: http://purl.obolibrary.org/obo/ido.owl

host
type: Class
equivalent class: Class
  intersection of: object
  intersection of: Restriction
    on property: has role
    some values from: host role
definition: Object bearing a host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl This should be pushed to an upper-level ontology.

definitive host
type: Class
equivalent class: Class
  intersection of: host
  intersection of: Restriction
    on property: has role
    some values from: definitive host role
definition: Host bearing a definitive host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: primary host
imported from: http://purl.obolibrary.org/obo/ido.owl

intermediate host
type: Class
equivalent class: Class
  intersection of: host
  intersection of: Restriction
    on property: has role
    some values from: intermediate host role
definition: Host bearing an intermediate host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: secondary host
imported from: http://purl.obolibrary.org/obo/ido.owl

dead-end host
type: Class
equivalent class: Class
  intersection of: host
  intersection of: Restriction
    on property: has role
    some values from: dead-end host role
definition: Host bearing a dead-end host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: incidental host
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious agent host
type: Class
equivalent class: Class
  intersection of: pathogen host
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: infectious agent
  intersection of: Restriction
    on property: has role
    some values from: infectious agent host role
definition: Pathogen host bearing an infectious agent host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen host
type: Class
equivalent class: Class
  intersection of: host
  intersection of: Restriction
    on property: has role
    some values from: pathogen host role
definition: Host bearing a pathogen host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

asymptomatic infectious agent carrier
type: Class
equivalent class: Class
  intersection of: infectious agent host
  intersection of: Restriction
    on property: has role
    some values from: asymptomatic carrier role
definition: Infectious agent host bearing the infectious agent carrier role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen vehicle
type: Class
equivalent class: Class
  intersection of: pathogen transporter
  intersection of: Restriction
    on property: has role
    some values from: pathogen vehicle role
disjoint with: immunodeficiency
definition: Pathogen transporter bearing a pathogen vehicle role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

fomite
type: Class
equivalent class: Class
  intersection of: pathogen vehicle
  intersection of: Restriction
    on property: has role
    some values from: fomite role
disjoint with: organism
disjoint with: disorder
definition: Pathogen vehicle bearing a fomite role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious agent reservoir
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: infectious agent
  intersection of: Restriction
    on property: has role
    some values from: reservoir of pathogen role
disjoint with: immunodeficiency
definition: Material entity bearing a pathogen reservoir role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

virulence factor
type: Class
equivalent class: Class
  intersection of: macromolecule
  intersection of: Restriction
    on property: has disposition
    some values from: virulence factor disposition
definition: A macromolecule produced by a pathogen and that has a virulence factor disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

invasion factor
type: Class
equivalent class: Class
  intersection of: macromolecule
  intersection of: Restriction
    on property: has disposition
    some values from: invasion disposition
definition: Biological macromolecule that has an invasion disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: invasin
imported from: http://purl.obolibrary.org/obo/ido.owl

toxin
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has disposition
    some values from: toxin disposition
definition: Molecular entity that has a toxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

exotoxin
type: Class
equivalent class: Class
  intersection of: toxin
  intersection of: Restriction
    on property: has disposition
    some values from: exotoxin disposition
definition: Toxin bearing an exotoxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

enterotoxin
type: Class
equivalent class: Class
  intersection of: exotoxin
  intersection of: Restriction
    on property: has disposition
    some values from: enterotoxin disposition
subclass of: exotoxin
subclass of: Restriction
  on property: has disposition
  some values from: exotoxin disposition
definition: Exotoxin bearing an enterotoxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

endotoxin
type: Class
equivalent class: Class
  intersection of: toxin
  intersection of: Restriction
    on property: has disposition
    some values from: endotoxin disposition
subclass of: toxin
subclass of: Restriction
  on property: has disposition
  some values from: toxin disposition
definition: Toxin bearing an endotoxin disposition that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen portal of entry
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has part
    some values from: pathogen portal of entry site
  intersection of: Restriction
    on property: has role
    some values from: pathogen portal of entry role
definition: Anatomical entity bearing a pathogen portal of entry role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

pathogen portal of exit
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has part
    some values from: pathogen portal of exit site
  intersection of: Restriction
    on property: has role
    some values from: pathogen portal of exit role
subclass of: anatomical entity
definition: Anatomical entity bearing a pathogen portal of exit role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

adhesion factor
type: Class
equivalent class: Class
  intersection of: macromolecule
  intersection of: Restriction
    on property: has disposition
    some values from: adhesion disposition
definition: Biological macromolecule that has an adhesion disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: adhesin
alternative term: adhesion molecule
imported from: http://purl.obolibrary.org/obo/ido.owl

primary infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has role
    some values from: primary infection role
disjoint with: secondary infection
definition: Infectious disorder bearing a primary infection role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

secondary infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has role
    some values from: secondary infection role
definition: Infectious disorder bearing a secondary infection role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

zoonosis
type: Class
equivalent class: Class
  intersection of: infectious disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
subclass of: infectious disease
disjoint with: reverse zoonosis
definition: Infectious disease inhering in an infectious disorder composed of pathogens having zoonotic dispositions.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

subclinical infection
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: part of
    some values from: asymptomatic carrier
definition: Infection that is part of an asymptomatic carrier.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

resistant entity
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: protective resistance
subclass of: material entity
disjoint with: immunodeficiency
definition: Material entity bearing protective resistance.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

innate immunity to infectious agent
type: Class
subclass of: Class
  intersection of: immunity to pathogen
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: innate immune response
definition: Immunity to pathogen that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

humoral immunity to infectious agent
type: Class
subclass of: Class
  intersection of: immunity to pathogen
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: humoral immune response
definition: Immunity to pathogen that inheres in an organism in virtue of components of its circulating body fluid, e.g. blood, lymph, hemolymph.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: "Circulating body fluid" refers to blood, lymph, and hemolymph.

leukocyte-mediated immunity to infectious agent
type: Class
subclass of: immunity to pathogen
definition: Immunity to pathogen that inheres in an organism in virtue of its leukocytes.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

passive immunity to infectious agent
type: Class
subclass of: immunity to pathogen
definition: Immunity to pathogen that inheres in an organism in virtue of antibodies not produced by that organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

antibiotic resistance
type: Class
subclass of: resistance to drug
definition: Resistance to drug that mitigates the damaging effects of an antibiotic.
editor note: http://purl.obolibrary.org/obo/ido.owl
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

emerging pathogen
type: Class
subclass of: pathogen
definition: Pathogen whose infection incidence is increasing following its first introduction into a new host Species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

cytotoxin
type: Class
equivalent class: Class
  intersection of: toxin
  intersection of: Restriction
    on property: has disposition
    some values from: cytotoxin disposition
subclass of: toxin
subclass of: Restriction
  on property: has disposition
  some values from: toxin disposition
definition: Toxin bearing a cytotoxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

collective pathogenic disposition
type: Class
equivalent class: Class
  intersection of: collective disposition
  intersection of: Restriction
    on property: inheres in
    some values from: object aggregate
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: results in formation of
        some values from: disorder
subclass of: collective disposition
disjoint with: collective resistance disposition
definition: Collective disposition to initiate processes that result in a disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infection
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: extended organism
      intersection of: Restriction
        on property: has part
        some values from: Class
disjoint with: immunodeficiency
definition: Part of an organism that itself is part of an extended organism with a pathogen as part, which participates in the formation of the infection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

genetic resistance to pathogen
type: Class
subclass of: resistance to pathogen
definition: Resistance to pathogen that inheres in an organism due to an allele or combination of alleles in its genome.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another.

collective resistance disposition
type: Class
subclass of: collective disposition
definition: Collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunodeficient organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has part
    some values from: immunodeficiency
definition: Organism that has an immunodeficiency.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: immunocompromised organism
imported from: http://purl.obolibrary.org/obo/ido.owl

chronic infectious disease course
type: Class
subclass of: infectious disease course
definition: Infectious disease course that unfolds over a long period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immune population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: has disposition
        some values from: acquired immunity to infectious agent
  intersection of: Restriction
    on property: has part
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: has disposition
        some values from: acquired immunity to infectious agent
definition: ido.owl
definition: Organism population whose members have acquired immunity to an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

transmission interval
type: Class
subclass of: one-dimensional temporal region
definition: One-dimensional temporal region during which a transmission process occurs.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: This should be imported from: http://purl.obolibrary.org/obo/trans.owl

infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
definition: Organism that has an infectious disposition.
editor note: This is an inferred subclass of pathogen.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

process of establishing an infection
type: Class
subclass of: process
subclass of: Restriction
  on property: part of
  some values from: pathogenesis
subclass of: Restriction
  on property: preceded by
  some values from: establishment of localization in host
definition: Process by which an infectious agent or infectious structure, established in a host, becomes part of an infection in the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

colonization of host
type: Class
equivalent class: Class
  intersection of: establishment of localization in host
  intersection of: Restriction
    on property: has output
    some values from: colony
subclass of: establishment of localization in host
definition: Establishment of localization in host process in which an organism or acellular structure establishes a colony in or on a host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

establishment of a clinically abnormal colony
type: Class
subclass of: colonization of host
definition: Colonization of host process that results in a clinically abnormal colony.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

production
type: Class
subclass of: process
definition: Process in which an entity comes into being as a result of the process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

replication
type: Class
subclass of: production
definition: Production process in which a participant creates a copy of itself.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunosuppression
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: negatively regulates
    some values from: immune response
subclass of: process
definition: Process that attenuates an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

physiologic immunosuppression
type: Class
subclass of: immunosuppression
definition: Immunosuppression which unfolds as part of the natural self-regulation of an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathologic immunosuppression
type: Class
subclass of: immunosuppression
definition: Immunosuppression process which arises as the result of a disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

colony
type: Class
subclass of: organism population
definition: ido.owl
definition: Organism population persisting in a site it has colonized.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent colony
type: Class
equivalent class: Class
  intersection of: colony
  intersection of: Restriction
    on property: has part
    some values from: infectious agent
  intersection of: Restriction
    on property: has part
    all values from: infectious agent
subclass of: colony
definition: Colony whose members are infectious agents.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

immunodeficiency
type: Class
subclass of: disorder
disjoint with: source of infection
definition: Disorder of an immune system component that results in defective functioning of the immune system.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunocompetence
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: immune response
disjoint with: immunosuppressive disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition inhering in an organism that is the disposition to mount a normal immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

immunosuppressive disposition
type: Class
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: immunosuppression
disjoint with: transmissibility disposition
disjoint with: disease
definition: Disposition whose realization negatively regulates an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

acquired immunity to infectious agent
type: Class
equivalent class: Class
  intersection of: immunity to pathogen
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: Class
      union of: immunoglobulin complex
      union of: B cell receptor complex
      union of: T cell receptor complex
  intersection of: Restriction
    on property: realized in
    all values from: adaptive immune response
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: Class
      union of: immunoglobulin complex
      union of: B cell receptor complex
      union of: T cell receptor complex
definition: Immunity to pathogen that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: adaptive immunity to infectious agent
imported from: http://purl.obolibrary.org/obo/ido.owl

communicability
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has part
        some values from: horizontal pathogen transmission process
definition: Infectious disposition to be transmitted from one organism to another of the same species by horizontal transmission.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

establishment of localization in host
type: Class
equivalent class: Class
  intersection of: establishment of localization
  intersection of: Restriction
    on property: occurs in
    some values from: host
subclass of: establishment of localization
definition: Establishment of localization process in which a material entity reaches a site in or on a host in which it can survive, grow, multiply, or mature.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

appearance of disorder
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: results in formation of
    some values from: disorder
subclass of: Restriction
  on property: part of
  some values from: pathogenesis
definition: Process by which a disorder comes into existence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

acute infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property:
      inverse of: has_material_basis_in
    some values from: Restriction
      on property: realized in
      some values from: acute infectious disease course
definition: Infectious disorder that is the physical basis for an unfolding acute infectious disease course.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

chronic infection
type: Class
subclass of: infection
definition: Infection that persists for an extended period of time.
term editor: John Beverley

host role
type: Class
subclass of: role
subclass of: Class
  union of: Class
    intersection of: role
    intersection of: Restriction
      on property: inheres in
      some values from: Class
        intersection of: self-replicating organic structure
        intersection of: Restriction
  union of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
disjoint with: source of infection role
definition: Role borne by an acellular structure containing a material entity other than the structure, or organism whose extended organism contains a material entity other than the organism, realized in use of that structure or organism as a site of reproduction or replication.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: This should be pushed to: http://purl.obolibrary.org/obo/ogms.owl

hospital-acquired infection
type: Class
subclass of: Class
  intersection of: infection
  intersection of: Restriction
    on property: participates in
    some values from: Class
      intersection of: pathogenesis
      intersection of: Restriction
        on property: results in formation of
        some values from: infection
  intersection of: Restriction
    on property: located in
    some values from: hospital facility
disjoint with: community-acquired infection
definition: Infection resulting from a transmission process that unfolds in a hospital.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: nosocomial infection
imported from: http://purl.obolibrary.org/obo/ido.owl

community-acquired infection
type: Class
subclass of: infection
disjoint with: nursing-home acquired infection
definition: Infection resulting from a transmission process that did not unfold in a health care facility.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

neurotoxin
type: Class
equivalent class: Class
  intersection of: toxin
  intersection of: Restriction
    on property: has disposition
    some values from: neurotoxin disposition
subclass of: toxin
subclass of: Restriction
  on property: has disposition
  some values from: toxin disposition
definition: Toxin bearing a neurotoxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

metastatic infection
type: Class
subclass of: infection
definition: Infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
term editor: John Beverley

source of infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
definition: Role borne by a material entity that contains a site from which an infectious agent is transmitted.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

nursing-home acquired infection
type: Class
subclass of: infection
definition: Infection resulting from a transmission process that unfolds in a nursing home.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infectious human pathogen
type: Class
subclass of: pathogen
definition: Pathogen disposed to infect human hosts.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

acquired immunodeficiency
type: Class
subclass of: immunodeficiency
disjoint with: primary immunodeficiency
definition: Immunodeficiency that is not caused by a genetic predisposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl
comment: Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy).

simple infection
type: Class
subclass of: infection
definition: Infection comprised of infectious organisms or structures all of the same Species.

re-emerging pathogen
type: Class
subclass of: pathogen
definition: Pathogen whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

colonization of human
type: Class
subclass of: colonization of host
definition: Colonization of host in a human.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

primary immunodeficiency
type: Class
subclass of: immunodeficiency
definition: Immunodeficiency that exists in an organism because of a genetic predisposition.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
alternative term: congenital immunodeficiency
imported from: http://purl.obolibrary.org/obo/ido.owl

reverse zoonosis
type: Class
equivalent class: Class
  intersection of: infectious disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
subclass of: infectious disease
definition: Infectious disease inhering in an infectious disorder composed of pathogens bearing reverse zoonotic dispositions.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

opportunistic pathogen
type: Class
equivalent class: Class
  intersection of: pathogen
  intersection of: Restriction
    on property: has disposition
    some values from: opportunistic infectious disposition
definition: Pathogen with an opportunistic infectious disposition.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
alternative term: opportunist
imported from: http://purl.obolibrary.org/obo/ido.owl

transmissibility disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: disposition
  intersection of: Restriction
    on property: inheres in
    some values from: pathogen
  intersection of: Restriction
    on property: realized in
    all values from: pathogen transmission process
disjoint with: disease
definition: Disposition to undergo a transmission process.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
imported from: This should be pushed to: http://purl.obolibrary.org/obo/trans.owl

horizontal pathogen transmission process
type: Class
subclass of: pathogen transmission process
definition: Pathogen transmission process in which a pathogen is transmitted from one host to another of the same species, and the two hosts are not in a parent-child relationship.
definition: http://purl.obolibrary.org/obo/ido.owl

process that results in death
type: Class
subclass of: process
definition: Process that results in death.
term editor: Alex Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

susceptible organism
type: Class
subclass of: organism
subclass of: Class
  intersection of: organism
  intersection of: Class
    complement of: Restriction
      on property: has part
      some values from: infection
  intersection of: Class
    complement of: Restriction
      on property: bearer of
      some values from: resistance to pathogen
definition: Organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.
term editor: Alex Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

negative regulation of life-sustaining process
type: Class
subclass of: biological regulation
definition: Process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process.
term editor: Alex Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

source of infection
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: source of infection site
  intersection of: Restriction
    on property: has role
    some values from: source of infection role
subclass of: material entity
definition: Material entity bearing a source of infection role.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

infection incidence profile
type: Class
subclass of: process profile
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

infection incidence proportion profile
type: Class
subclass of: process profile
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

infection incidence rate profile
type: Class
subclass of: process profile
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

negative regulation of production
type: Class
subclass of: biological regulation
definition: Process that stops, prevents, or reduces the frequency, rate or extent of a production process.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

negative regulation of replication
type: Class
subclass of: negative regulation of production
definition: Process that stops, prevents, or reduces the frequency, rate or extent of a replication process.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen birth process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: pathogen birth temporal region
definition: Process boundary that marks the start of the life cycle of a pathogen.
term editor: Alex Diehl
term editor: John Beverley
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

pathogen death process boundary
type: Class
subclass of: Class
  intersection of: process boundary
  intersection of: Restriction
    on property: preceded by
    some values from: pathogen birth process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: pathogen death temporal region
definition: Process boundary that marks the end of the life cycle of a pathogen.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/ido.owl

fungicidal disposition
type: Class
subclass of: cidal agent disposition
definition: Disposition to kill fungi.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

bactericidal disposition
type: Class
subclass of: cidal agent disposition
definition: Disposition to kill bacteria.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

bacteriostatic disposition
type: Class
subclass of: static agent disposition
definition: Disposition to inhibit the reproduction of bacteria.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

parasiticidal disposition
type: Class
subclass of: cidal agent disposition
definition: Disposition to kill parasites.
editor note: We use parasite in the sense of organisms that are parasitic in humans.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

parasitostatic disposition
type: Class
subclass of: static agent disposition
definition: Disposition to inhibit the reproduction of parasites.
editor note: 'Parasite' is used in the sense of eukaryotic organisms that are parasitic in humans.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

bacteriostatic
type: Class
equivalent class: Class
  intersection of: static agent
  intersection of: Restriction
    on property: has disposition
    some values from: Class
      intersection of: bacteriostatic disposition
      intersection of: Restriction
        on property: realized in
        all values from: Restriction
subclass of: static agent
definition: Static agent bearing a bacteriostatic disposition.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

bactericidal
type: Class
equivalent class: Class
  intersection of: cidal agent
  intersection of: Restriction
    on property: has disposition
    some values from: bactericidal disposition
definition: Cidal agent with a bactericidal disposition that is realized in a process of killing bacteria.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infectious structure
type: Class
equivalent class: Class
  intersection of: self-replicating organic structure
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
definition: Self-replicating organic structure that has an infectious disposition.
editor note: This is an inferred subclass of pathogen.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

acellular self-replicating organic structure aggregate
type: Class
subclass of: self-replicating organic structure aggregate
definition: ido.owl
definition: Object aggregate that consists of acellular self-replicating organic structures.
term editor: John Beverley

pathogen birth temporal region
type: Class
subclass of: zero-dimensional temporal region
definition: Zero-dimensional temporal region occupied by a pathogen birth process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen death temporal region
type: Class
subclass of: Class
  intersection of: zero-dimensional temporal region
  intersection of: Restriction
    on property: preceded by
    some values from: pathogen birth temporal region
definition: Zero-dimensional temporal region occupied by a pathogen death process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

self-replicating organic structure
type: Class
subclass of: object
subclass of: Class
  complement of: Restriction
    on property: has part
    some values from: cell
example of usage: prions
example of usage: viruses
definition: Object consisting of an organic structure that is able to initiate replication of its structure in a host.
imported from: http://purl.obolibrary.org/obo/ido.owl
contributor: Yongqun He
term editor: John Beverley

cidal agent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: Class
      intersection of: cidal agent disposition
      intersection of: Restriction
        on property: realized in
        all values from: process that results in death
subclass of: material entity
disjoint with: static agent
definition: Material entity with a cidal agent disposition that is realized in a process of killing bacteria, fungi, parasites, or viruses.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

static agent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: Class
      intersection of: static agent disposition
      intersection of: Restriction
        on property: realized in
        all values from: Restriction
subclass of: material entity
definition: Material entity bearing a static agent disposition.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

static agent disposition
type: Class
subclass of: disposition
definition: Disposition to inhibit the reproduction of bacteria, fungi, or parasites, or inhibit the replication of viruses.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

cidal agent disposition
type: Class
subclass of: disposition
definition: Disposition to kill bacteria, fungi, parasites, or viruses.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infectious structure host
type: Class
equivalent class: Class
  intersection of: pathogen host
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: infectious structure
  intersection of: Restriction
    on property: has role
    some values from: infectious structure host role
definition: Pathogen host bearing an infectious structure host role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infectious structure host role
type: Class
equivalent class: Class
  intersection of: pathogen host role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
definition: Pathogen host role borne by an object or organism whose extended organism contains an infectious structure.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen transporter
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: pathogen transporter role
definition: Material entity bearing a pathogen transporter role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen transporter role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: location of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: indirect pathogen transmission process
definition: Role borne by a material entity in or on which a pathogen is located, from which the pathogen may be transmitted to a new host.
term editor: John Beverley

infectious agent generative stage
type: Class
subclass of: pathogen generative stage
definition: Pathogen generative stage that is a temporal subdivision of an infectious agent developmental process.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infectious structure generative stage
type: Class
subclass of: pathogen generative stage
definition: Pathogen generative stage that is a temporal subdivision of an infectious structure developmental process.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen generative stage
type: Class
subclass of: generative stage
definition: Generative stage that is a temporal subdivision of a pathogen developmental process.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

asymptomatic carrier role
type: Class
subclass of: pathogen host role
definition: Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the pathogen.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

asymptomatic carrier
type: Class
equivalent class: Class
  intersection of: pathogen host
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: infection
  intersection of: Restriction
    on property: has role
    some values from: asymptomatic carrier role
definition: Pathogen host with an infection as part but exhibits no signs or symptoms.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

asymptomatic infectious structure carrier
type: Class
equivalent class: Class
  intersection of: infectious structure host
  intersection of: Restriction
    on property: has role
    some values from: asymptomatic carrier role
definition: Infectious structure host bearing an asymptomatic carrier role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

symptomatic carrier role
type: Class
subclass of: pathogen host role
definition: Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has manifested symptoms of the infectious disease caused by the pathogen.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

symptomatic carrier
type: Class
equivalent class: Class
  intersection of: pathogen host
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: infection
  intersection of: Restriction
    on property: has role
    some values from: symptomatic carrier role
definition: Pathogen host with infection as part that exhibits symptoms.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

cytotoxin disposition
type: Class
subclass of: toxin disposition
definition: Toxin disposition realized in processes resulting in damage to host cells.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

neurotoxin disposition
type: Class
subclass of: toxin disposition
definition: Toxin disposition realized in damaging or interfering with the function of nerve tissue.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

endotoxin disposition
type: Class
subclass of: toxin disposition
definition: Toxin disposition that is a structural component of a pathogen and is realized only during cytolsis.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

enterotoxin disposition
type: Class
subclass of: exotoxin disposition
definition: Exotoxin disposition ithat is realized in a process of damaging intestinal mucosa cells.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

symptomatic infectious structure carrier
type: Class
equivalent class: Class
  intersection of: infectious structure host
  intersection of: Restriction
    on property: has role
    some values from: symptomatic carrier role
definition: Infectious structure host bearing a symptomatic carrier role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

symptomatic infectious agent carrier
type: Class
equivalent class: Class
  intersection of: infectious agent host
  intersection of: Restriction
    on property: has role
    some values from: symptomatic carrier role
definition: Infectious agent host bearing an infectious agent carrier role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infectious structure aggregate
type: Class
subclass of: self-replicating organic structure aggregate
definition: ido.owl
definition: Self-replicating organic structure aggregate whose members are infectious structures.
term editor: John Beverley

pathogen vector
type: Class
equivalent class: Class
  intersection of: pathogen transporter
  intersection of: Restriction
    on property: has role
    some values from: pathogen vector role
definition: Pathogen transporter bearing a pathogen vector role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

biological vector
type: Class
equivalent class: Class
  intersection of: pathogen vector
  intersection of: Restriction
    on property: has role
    some values from: biological vector role
definition: Pathogen vector bearing a biological vector role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

mechanical vector
type: Class
equivalent class: Class
  intersection of: pathogen vector
  intersection of: Restriction
    on property: has role
    some values from: mechanical vector role
definition: Pathogen vector bearing a mechanical vector role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

biological vehicle
type: Class
equivalent class: Class
  intersection of: pathogen vehicle
  intersection of: Restriction
    on property: has role
    some values from: biological vehicle role
definition: Pathogen vehicle bearing a biological vehicle role.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

establishment of localization in human host
type: Class
equivalent class: Class
  intersection of: establishment of localization in host
  intersection of: Restriction
    on property: occurs in
    some values from: homo sapiens
subclass of: establishment of localization in host
definition: Establishment of localization in or on a human host.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

latency interval
type: Class
subclass of: one-dimensional temporal region
subclass of: Restriction
  on property: part of
  some values from: incubation interval
subclass of: Restriction
  on property: has part
  some values from: infection start temporal region
definition: One-dimensional temporal region beginning with the establishing of an infection in a host and ending when the host becomes contagious.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infection start process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: infection start temporal region
definition: Process boundary that marks the start of an infection, latency process, and incubation process.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

latency end process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: preceded by
  some values from: latency start process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: latency end temporal region
definition: Process boundary marking the end of a latency period.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

incubation end process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: preceded by
  some values from: incubation start process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: incubation end temporal region
definition: Process boundary marking the end of an incubation period.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infection start temporal region
type: Class
subclass of: zero-dimensional temporal region
definition: Zero-dimensional temporal region occupied by an infection start process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

infection end temporal region
type: Class
subclass of: Class
  intersection of: zero-dimensional temporal region
  intersection of: Restriction
    on property: preceded by
    some values from: infection start temporal region
definition: Zero-dimensional temporal region occupied by an infection end process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

latency end temporal region
type: Class
subclass of: Class
  intersection of: zero-dimensional temporal region
  intersection of: Restriction
    on property: preceded by
    some values from: infection start temporal region
definition: Zero-dimensional temporal region occupied by a latency end process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

communicability end temporal region
type: Class
subclass of: Class
  intersection of: zero-dimensional temporal region
  intersection of: Restriction
    on property: preceded by
    some values from: communicability start temporal region
definition: Zero-dimensional temporal region occupied by a communicability end process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

incubation end temporal region
type: Class
subclass of: Class
  intersection of: zero-dimensional temporal region
  intersection of: Restriction
    on property: preceded by
    some values from: infection start temporal region
definition: Zero-dimensional temporal region occupied by an incubation end process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

communicability start temporal region
type: Class
subclass of: Class
  intersection of: zero-dimensional temporal region
  intersection of: Restriction
    on property: preceded by
    some values from: latency end temporal region
definition: Zero-dimensional temporal region occupied by a communicability start process boundary.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

latency start process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: infection start temporal region
definition: Process boundary marking the start of a latency interval.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

incubation start process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: infection start temporal region
definition: Process boundary marking the start of an incubation interval.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

communicability start process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: preceded by
  some values from: latency end process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: communicability start temporal region
definition: Process boundary marking the start of a communicability interval.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

communicability end process boundary
type: Class
subclass of: process boundary
subclass of: Restriction
  on property: preceded by
  some values from: communicability start process boundary
subclass of: Restriction
  on property: occupies temporal region
  some values from: communicability end temporal region
definition: Process boundary marking the end of a communicability interval.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

epitope role
type: Class
subclass of: biological role
definition: Biological role borne by a molecular entity that serves as the site on an antigen realized in immune system recognition and binding by antibodies.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen surveillance
type: Class
subclass of: surveillance process
definition: Surveillance process aiming to produce information about one or several objects, in the form of microorganisms, which have the role of pathogen.
imported from: http://purl.obolibrary.org/obo/ido.owl

vector surveillance
type: Class
subclass of: surveillance process
definition: Surveillance process aiming to produce information about one or several objects, in the form of arthropods, which have the role of serving as biological pathogen vectors.
imported from: http://purl.obolibrary.org/obo/ido.owl

acellular self-replicating organic structure
type: Class
subclass of: self-replicating organic structure
definition: Self-replicating organic structure comprised of acellular organic parts.
contributor: Yongqun He
creator: John Beverley

self-replicating organic structure aggregate
type: Class
subclass of: object aggregate
definition: Object aggregate that consists of self-replicating organic structures.
creator: John Beverley

virus
type: Class
subclass of: acellular self-replicating organic structure
definition: Acellular self-replicating organic structure with RNA or DNA genetic material which uses host metabolic resources for RNA or DNA replication.
editor note: The mass noun term label imported from the NCBITaxon "Viruses" has been replaced with the count noun "virus", to align with BFO.
imported from: ncbitaxon.owl

bacteria
type: Class
subclass of: organism
imported from: ncbitaxon.owl

single-stranded RNA retrovirus
type: Class
subclass of: virus
example of usage: Human Immunodeficiency Virus
definition: Virus with genetic material encoded in single-stranded RNA that replicates using reverse transcriptase to convert positive-sense RNA to DNA.
has exact synonym: Baltimore Classification Group VI
term editor: John Beverley

single-stranded DNA virus
type: Class
subclass of: virus
example of usage: Parvovirus
definition: Virus with genetic material encoded in single-stranded DNA and replicates using DNA polymerase.
has exact synonym: Baltimore Classification Group II
term editor: John Beverley

eukaryota
type: Class
subclass of: organism
imported from: ncbitaxon.owl

double-stranded DNA virus
type: Class
subclass of: virus
example of usage: Adenovirus
example of usage: Poxvirus
definition: Virus that has its genetic material encoded in double-stranded DNA and replicates using DNA polymerase.
has exact synonym: Baltimore Classification Group I
term editor: John Beverley

double-stranded DNA retrovirus
type: Class
subclass of: virus
example of usage: Hepatitus B Virus
definition: Virus with genetic material that is encoded in double-stranded DNA and replicates through single-stranded RNA intermediate.
has exact synonym: Baltimore Classification Group VII
has exact synonym: Pararetrovirus
term editor: John Beverley

positive-sense single-stranded RNA virus
type: Class
subclass of: virus
example of usage: Coronavirus
example of usage: Picornavirus
definition: Virus with genetic material encoded in single-stranded RNA that can be translated directly into proteins.
has exact synonym: Baltimore Classification Group IV
term editor: John Beverley

negative-sense single-stranded RNA virus
type: Class
subclass of: virus
example of usage: Rhabdovirus
definition: Virus with genetic material encoded in single-stranded RNA that can be translated into proteins only after transcription by RNA polymerase.
has exact synonym: Baltimore Classification Group V
term editor: John Beverley

double-stranded RNA virus
type: Class
subclass of: virus
example of usage: Reovirus
definition: Virus with genetic material encoded in double-stranded RNA.
has exact synonym: Baltimore Classification Group III
term editor: John Beverley

prion
type: Class
subclass of: acellular self-replicating organic structure
definition: Acellular self-replicating organic structure that consists of an abnormally folded protein which replicates by by transmitting its abnormal structure to other proteins.
term editor: John Beverley
comment: http://purl.obolibrary.org/obo/ncbitaxon.owl

homo sapiens
type: Class
subclass of: eukaryota
imported from: ncbitaxon.owl

planned process
type: Class
subclass of: process
definition: Process that realizes a plan which is the concretization of a plan specification.
imported from: http://purl.obolibrary.org/obo/obi.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is specified output of
    some values from: material processing
definition: Material entity that is created or changed during material processing.
imported from: http://purl.obolibrary.org/obo/obi.owl

assay
type: Class
subclass of: material processing
definition: Planned process with the objective to produce information about some evaluant.
imported from: http://purl.obolibrary.org/obo/obi.owl

reagent role
type: Class
subclass of: role
definition: Role inhering in a molecular entity when the molecular entity is used to produce a chemical reaction to detect, measure, or produce other substances.
imported from: http://purl.obolibrary.org/obo/obi.owl

material processing
type: Class
subclass of: planned process
definition: Planned process which results in physical changes in a specified input material.
imported from: http://purl.obolibrary.org/obo/obi.owl

antigen role
type: Class
subclass of: biological role
definition: Biological role inhering in some molecular entity, that stimulates an immune response when identified by the immune systems cells.
imported from: http://purl.obolibrary.org/obo/obi.owl
term editor: John Beverley

PCR product
type: Class
equivalent class: Class
  intersection of: double-stranded DNA
  intersection of: Restriction
    on property: is specified output of
    some values from: polymerase chain reaction
definition: Double stranded DNA that is the specified output of a polymerase chain reaction
imported from: http://purl.obolibrary.org/obo/obi.owl

polymerase chain reaction
type: Class
subclass of: Class
  intersection of: enzymatic amplification
  intersection of: Restriction
    on property: has specified input
    some values from: deoxyribonucleic acid
  intersection of: Restriction
    on property: has specified output
    some values from: PCR product
definition: Enzymatic amplification in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication.
imported from: http://purl.obolibrary.org/obo/obi.owl

reverse transcribed PCR
type: Class
subclass of: Class
  intersection of: enzymatic amplification
  intersection of: Restriction
    on property: has specified input
    some values from: ribonucleic acid
  intersection of: Restriction
    on property: has specified output
    some values from: PCR product
definition: Material processing amplifying cDNA during a PCR reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
imported from: http://purl.obolibrary.org/obo/obi.owl

organism
type: Class
subclass of: object
disjoint with: disorder
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: Object 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.
imported from: obi.owl

Axiom
annotated source: organism
annotated property: definition
annotated target: Object that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: This is a suggested revision to the OBI definition and hierarchy placement. Using OBI was a deliberate choice over CARO, for reasons discussed here: 10.31219/osf.io/5bx8c
term editor: John Beverley

enzymatic amplification
type: Class
subclass of: material processing
definition: Material processing using enzymes to increase the number of molecules of a material entity.
imported from: http://purl.obolibrary.org/obo/obi.owl

epitope
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: part of
    some values from: antigen
  intersection of: Restriction
    on property: has part
    some values from: epitope site
  intersection of: Restriction
    on property: has role
    some values from: epitope role
definition: Material entity bearing the epitope role.
imported from: http://purl.obolibrary.org/obo/obi.owl

antigen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: antigen role
definition: Material entity bearing an antigen role.
imported from: http://purl.obolibrary.org/obo/obi.owl

symptom
type: Class
subclass of: occurrent
definition: Process experienced by a patient which can only be experienced by the patient, that is hypothesized to be clinically relevant.
imported from: ogms.owl

disease
type: Class
subclass of: disposition
definition: Disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: ogms.owl

disorder
type: Class
subclass of: material entity
definition: Material entity that is a clinically abnormal part of an extended organism.
imported from: ogms.owl

disease course
type: Class
subclass of: process
definition: Totality of all processes through which a given disease instance is realized.
imported from: ogms.owl

extended organism
type: Class
subclass of: object aggregate
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: material entity
definition: Object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
imported from: ogms.owl

architectural structure
type: Class
subclass of: material entity
definition: Material entity that is a human made structure with firm connection between its foundation and the ground.
imported from: http://purl.obolibrary.org/obo/OMRSE

facility
type: Class
subclass of: architectural structure
definition: Architectural structure that bears some function.
imported from: http://purl.obolibrary.org/obo/OMRSE

hospital facility
type: Class
subclass of: healthcare facility
definition: Facility that is run by a hospital organization and is the bearer of a hospital function.
imported from: http://purl.obolibrary.org/obo/OMRSE

healthcare facility
type: Class
subclass of: facility
definition: Facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
imported from: http://purl.obolibrary.org/obo/OMRSE

pathogen transmission process
type: Class
subclass of: process
subclass of: Restriction
  on property: part of
  some values from: pathogenesis
definition: Process in which a pathogen is transmitted directly or indirectly to a new host.
editor note: TRANS includes a sibling class of 'indirect' labeled 'direct', and these terms mirror standard definitions of 'direct transmission' and 'indirect transmission' in the literature. However, in the literature and in TRANS the definitions seem confused. For example, direct transmission is claimed to involve direct contact, yet respiratory droplet spread from a host - which plausibly involves a vehicle - is counted as direct rather than indirect transmission. We will follow standard use in part, adopting indirect transmission, but not direct, and defining a term for contact transmission.
imported from: trans.owl

Axiom
annotated source: pathogen transmission process
annotated property: definition
annotated target: Process in which a pathogen is transmitted directly or indirectly to a new host.
editor note: This is a suggested revision of the TRANS definition.
term editor: John Beverley

indirect pathogen transmission process
type: Class
subclass of: pathogen transmission process
definition: Pathogen transmission process in which a pathogen is indirectly transferred to a host by intermediary vehicles or vectors.
imported from: trans.owl

Axiom
annotated source: indirect pathogen transmission process
annotated property: definition
annotated target: Pathogen transmission process in which a pathogen is indirectly transferred to a host by intermediary vehicles or vectors.
editor note: This is a suggested revision of the TRANS definition.
term editor: John Beverley

contact pathogen transmission process
type: Class
subclass of: pathogen transmission process
definition: Pathogen transmission process in which a pathogen is transferred to a host through surface-to-surface contact.
imported from: http://purl.obolibrary.org/obo/trans.owl

droplet pathogen transmission process
type: Class
subclass of: indirect pathogen transmission process
definition: Indirect pathogen transmission process in which a pathogen is transmitted from a host expelling respiratory droplets to another host.
imported from: http://purl.obolibrary.org/obo/trans.owl

blood
type: Class
subclass of: haemolymphatic fluid
definition: A fluid that is composed of blood plasma and erythrocytes.
imported from: uberon.owl

haemolymphatic fluid
type: Class
subclass of: bodily fluid
definition: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.

organism substance
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
imported from: http://purl.obolibrary.org/obo/uberon.owl

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.

bodily fluid
type: Class
subclass of: organism substance
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.

respiratory secretion
type: Class
subclass of: organism substance
definition: A portion of organism substance that secreted_by a respiratory system.
imported from: http://purl.obolibrary.org/obo/uberon.owl

sputum
type: Class
subclass of: respiratory secretion
definition: Matter ejected from the lungs, bronchi, and trachea, through the mouth.
imported from: http://purl.obolibrary.org/obo/uberon.owl

viremia
type: Class
equivalent class: Class
  intersection of: extracellular infection
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: virus
      intersection of: Restriction
        on property: located in
        some values from: blood
subclass of: extracellular infection
definition: Infection that has as part virus particles located in the blood.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

virion
type: Class
subclass of: virus
definition: Virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: vido.owl

viricide
type: Class
equivalent class: Class
  intersection of: cidal agent
  intersection of: Restriction
    on property: has disposition
    some values from: viricidal disposition
definition: Cidal agent with a viricidal disposition that is realized in a process of killing viruses.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/ido.owl

virostatic
type: Class
equivalent class: Class
  intersection of: static agent
  intersection of: Restriction
    on property: has disposition
    some values from: Class
      intersection of: virostatic disposition
      intersection of: Restriction
        on property: realized in
        all values from: Restriction
definition: Static agent bearing a virostatic disposition.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/vido.owl

virus replication
type: Class
subclass of: replication
subclass of: Restriction
  on property: occupies temporal region
  some values from: incubation interval
disjoint with: prion replication
definition: Replication process in which a virus containing some portion of genetic material inherited from a parent virus is replicated.
term editor: John Beverley
imported from: http://purl.obolibrary.org/obo/vido.owl

viricidal disposition
type: Class
equivalent class: Class
  intersection of: cidal agent disposition
  intersection of: Restriction
    on property: inheres in
    some values from: cidal agent
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: results in
        some values from: pathogen death process boundary
definition: Disposition to kill viruses.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

virostatic disposition
type: Class
equivalent class: Class
  intersection of: static agent disposition
  intersection of: Restriction
    on property: inheres in
    some values from: static agent
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: negatively regulates
        some values from: virus replication
definition: A disposition to inhibit the reproduction of viruses.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

virus aggregate
type: Class
subclass of: acellular self-replicating organic structure aggregate
definition: Acellular self-replicating organic structure aggregate whose members are viruses
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

viroid aggregate
type: Class
subclass of: acellular self-replicating organic structure aggregate
definition: Acellular self-replicating organic structure aggregate whose members are viroids.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

prion aggregate
type: Class
subclass of: Class
  intersection of: acellular self-replicating organic structure aggregate
  intersection of: Restriction
    on property: has member
    some values from: prion
definition: Acellular self-replicating organic structure aggregate whose members are prions.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

prion replication
type: Class
subclass of: replication
definition: Replication process in which a prion facilitates abnormal folding in proteins resulting in additional, identical, abnormally folded proteins.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

virus generative stage
type: Class
subclass of: infectious structure generative stage
definition: Infectious structure generative stage that is a temporal subdivision of a virus developmental process.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

viral disease course
type: Class
equivalent class: Class
  intersection of: infectious disease course
  intersection of: Restriction
    on property: realizes
    some values from: viral disease
subclass of: infectious disease course
definition: Infectious disease whose physical basis is a virus disorder that is clinically abnormal in virtue of the presence of the relevant virus population.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

virus disorder
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has part
    some values from: virus
  intersection of: Restriction
    on property:
      inverse of: has_material_basis_in
    some values from: Restriction
      on property: realized in
      some values from: viral disease course
subclass of: infectious disorder
definition: Infectious disorder that exists as a result of a process of formation of disorder initiated by a virus or virus population.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

virus host
type: Class
equivalent class: Class
  intersection of: infectious structure host
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: virus
definition: Infectious structure host whose extended organism has some virus part.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

subclinical virus infection
type: Class
equivalent class: Class
  intersection of: subclinical infection
  intersection of: Restriction
    on property: part of
    some values from: asymptomatic infectious structure carrier
  intersection of: Restriction
    on property: part of
    some values from: virus host
  intersection of: Restriction
    on property: has part
    some values from: virus
definition: Subclinical infection that is part of a virus host.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

respiratory droplet
type: Class
subclass of: respiratory secretion
imported from: Respiratory secretion composed of a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

respiratory droplet fomite
type: Class
equivalent class: Class
  intersection of: respiratory droplet
  intersection of: Restriction
    on property: has role
    some values from: fomite role
subclass of: respiratory droplet
definition: Respiratory droplet bearing a fomite role.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

respiratory droplet virus fomite
type: Class
equivalent class: Class
  intersection of: respiratory droplet fomite
  intersection of: Restriction
    on property: has part
    some values from: virus
  intersection of: Restriction
    on property: has role
    some values from: fomite role
definition: Respiratory droplet fomite with virus part.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

viral pathogenesis
type: Class
subclass of: Class
  intersection of: pathogenesis
  intersection of: Restriction
    on property: has part
    some values from: virus replication
definition: Pathogenesis process realization of a pathogenic disposition inhering in a virus or virus population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing a viral infection, and (4) appearance of a virus disorder.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

process of establishing viral infection
type: Class
subclass of: process of establishing an infection
definition: Process of establishing an infection in which a virus participates.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

virus adhesion susceptible cell
type: Class
equivalent class: Class
  intersection of: cell
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: molecular entity
      intersection of: Restriction
        on property: has disposition
        some values from: viral adhesion disposition
subclass of: cell
definition: Cell with an adhesion factor part bearing a viral adhesion disposition
imported from: vido.owl
term editor: John Beverley

viral adhesion disposition
type: Class
subclass of: Class
  intersection of: adhesion disposition
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: molecular entity
      intersection of: Restriction
        on property: part of
        some values from: virus
definition: Adhesion disposition borne by a macromolecule part of a virus that is the disposition to participate in a virus attachment process
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

viral load
type: Class
subclass of: quality
definition: Quality inhering in a portion of fluid that is the proportion of virions to volume of that portion of fluid
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

bacteriophage
type: Class
subclass of: Class
  intersection of: virus
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
definition: Virus which infects and replicates within or on bacteria or archea.
definition: http://purl.obolibrary.org/obo/vido.owl
editor note: This is an inferred subclass of pathogen.
term editor: John Beverley

virophage
type: Class
subclass of: Class
  intersection of: virus
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
definition: Virus which infects and replicates within or on viruses.
editor note: This is an inferred subclass of pathogen.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

establishment of localization in virus host
type: Class
equivalent class: Class
  intersection of: establishment of localization in host
  intersection of: Restriction
    on property: occurs in
    some values from: virus
subclass of: establishment of localization in host
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

oncovirus
type: Class
subclass of: virus
subclass of: Class
  intersection of: virus
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
definition: Virus that causes cancer in hosts.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

disordered virus
type: Class
subclass of: acellular self-replicating organic structure
definition: Acellular self-replicating organic structure having some arrangement of viral components (e.g. viral capsid, viral DNA/RNA), that is clinically abnormal.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

disordered prion
type: Class
subclass of: acellular self-replicating organic structure
definition: Acellular self-replicating organic structure having some arrangement of protein components, that is clinically abnormal.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

eclipse interval
type: Class
subclass of: one-dimensional temporal region
subclass of: Restriction
  on property: part of
  some values from: latency interval
imported from: One-dimensional temporal region beginning with the establishment of a virus in a host and ending with the first appearance of a virion following viral release.
imported from: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

epitope site
type: Class
subclass of: site
definition: Site part of an antigen that is recognized by immune system cells and to which antibodies attach.
term editor: John Beverley

viral disease pandemic
type: Class
subclass of: infectious disease pandemic
definition: Infectious disease pandemic in which multiple viral disease epidemics of the same type of viral disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents.
definition: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

viral disease epidemic
type: Class
subclass of: infectious disease epidemic
definition: Infectious disease epidemic in which there is a statistically significant increase in the viral disease incidence of a population.
definition: http://purl.obolibrary.org/obo/vido.owl
term editor: John Beverley

surveillance process
type: Class
subclass of: planned process
definition: Planned process with the objective to produce information about some evaluant with the purpose of, if justified by the information gathered, managing, directing, or protecting.
imported from: http://purl.obolibrary.org/obo/vsmo.owl

anatomical space
type: Class
subclass of: site
definition: Site generated by morphogenetic or physiologic processes that is bounded by an anatomical surface.
imported from: http://purl.obolibrary.org/obo/caro.owl
term editor: John Beverley

cell space
type: Class
equivalent class: Class
  intersection of: anatomical space
  intersection of: Restriction
    on property: part of
    some values from: cell
subclass of: anatomical space
definition: Anatomical space that is part of a cell.
imported from: http://purl.obolibrary.org/obo/caro.owl

fungistatic disposition
type: Class
subclass of: static agent disposition
definition: Disposition to inhibit the reproduction of fungi.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen portal of entry site
type: Class
subclass of: anatomical space
definition: Anatomical space through which a pathogen enters an organism.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen portal of exit site
type: Class
subclass of: anatomical space
definition: Anatomical space through which a pathogen exits an organism.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

site of infection
type: Class
equivalent class: Class
  intersection of: anatomical space
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: infection
definition: Anatomical space in which an infection is located.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

source of infection site
type: Class
subclass of: anatomical space
definition: Anatomical space in which an infection appears in a host organism.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

pathogen vector role
type: Class
equivalent class: Class
  intersection of: pathogen transporter role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Class
        intersection of: Restriction
  intersection of: Restriction
    on property: realized in
    all values from: indirect pathogen transmission process
subclass of: pathogen transporter role
definition: A pathogen transporter role that is borne by an organism active in the transfer of an infectious agent or infectious structure to an organism of another species in which it can realize its infectious disposition.
term editor: John Beverley
comment: The role is realized in a process that transfers an infectious organism from one location to another.

infectious disposition
type: Class
equivalent class: Class
  intersection of: pathogenic disposition
  intersection of: Restriction
    on property: realized in
    some values from: process of establishing an infection
  intersection of: Restriction
    on property: realized in
    some values from: pathogen transmission process
  intersection of: Restriction
    on property: inheres in
    some values from: pathogen
definition: Pathogenic disposition borne by a pathogen to be transmitted to a host and become part of an infection in that host or immunocompetent members of the same species as the host.
imported from: http://purl.obolibrary.org/obo/ido.owl
term editor: John Beverley

respiratory system disease
type: Class
subclass of: disease
definition: Disease that occurs in different organs functioning in respiration and consisting especially of the nose, nasal passages, nasopharynx, larynx, trachea, bronchi, and lungs.
imported from: http://www.ebi.ac.uk/efo/efo.owl

lower respiratory tract disease
type: Class
subclass of: respiratory system disease
definition: Respiratory system disease located in the lower respiratory tract.
imported from: http://www.ebi.ac.uk/efo/efo.owl

acute respiratory distress syndrome
type: Class
subclass of: respiratory system disease
definition: Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery.
imported from: http://www.ebi.ac.uk/efo/efo.owl

pathogenesis
type: Class
subclass of: process
definition: Process that generates the ability of a pathogen to induce disorder in an organism.
editor note: Process that is the realization of a pathogenic disposition inhering in an pathogen or pathogen population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing an infection, and (4) appearance of disorder.
imported from: http://purl.obolibrary.org/obo/go.owl
term editor: John Beverley

Axiom
annotated source: pathogenesis
annotated property: editor note
annotated target: Process that is the realization of a pathogenic disposition inhering in an pathogen or pathogen population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing an infection, and (4) appearance of disorder.
editor note: This is a suggested revision to the GO definition.
term editor: John Beverley

country
type: Class
subclass of: geopolitical entity
definition: A Geopolitical Entity that delimits a Government with effective internal and external sovereignty over the region and its population, and which is not dependent on or subject to any other power or Geopolitical Entity.
imported from: http://www.ontologyrepository.com/CommonCoreOntologies/

directive information content entity
type: Class
subclass of: information content entity
definition: Information Content Entity that consists of a set of propositions or images (as in the case of a blueprint) that prescribe some Entity.
imported from: http://www.ontologyrepository.com/CommonCoreOntologies/

geopolitical entity
type: Class
subclass of: geospatial region
definition: A geospatial region that delimits the authority of a formally constituted government to exercise its control within the bounded area.
imported from: http://www.ontologyrepository.com/CommonCoreOntologies/

geospatial region
type: Class
subclass of: site
definition: A site at or near the surface of the Earth.
imported from: http://www.ontologyrepository.com/CommonCoreOntologies

bfo-spec-label
definition source: Person:Alan Ruttenberg

BFO_0000134
elucidation: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
elucidation: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/080-003

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/081-003