derives_from
type: AnnotationProperty
comment: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
has OBO namespace: ro_bfo_bridge
has OBO namespace: relationship
has alternative id: OBO_REL:0000015
domain: continuant
has definition: Definition
  label: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
has exact synonym: derived_from
type: ObjectProperty
type: TransitiveProperty
range: continuant
has definition: Definition
  label: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

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

term replaced by
type: AnnotationProperty
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
editor preferred term: term replaced by
has curation status: pending final vetting

Contributor
type: AnnotationProperty
comment: An entity responsible for making contributions to the content of the resource.
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.

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

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

has obsolescence reason
type: AnnotationProperty
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
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.
editor preferred term: has obsolescence reason

preceded_by
type: AnnotationProperty
comment: 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.
has OBO namespace: ro_bfo_bridge
has alternative id: OBO_REL:0000017
has OBO namespace: relationship
domain: occurrent
has definition: P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: occurrent
inverse of: precedes
has definition: P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

Creator
type: AnnotationProperty
comment: An entity primarily responsible for making the content of the resource.
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.

Subject and Keywords
type: AnnotationProperty
comment: The topic of the content of the resource.
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.

agent_in
type: AnnotationProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000022
has OBO namespace: ro_bfo_bridge
domain: continuant
type: ObjectProperty
range: occurrent
sub property of: participates_in

precedes
type: AnnotationProperty
has alternative id: OBO_REL:0000018
has OBO namespace: relationship
has OBO namespace: ro_bfo_bridge
domain: occurrent
type: ObjectProperty
type: TransitiveProperty
range: occurrent

Resource Identifier
type: AnnotationProperty
comment: An unambiguous reference to the resource within a given context.
description: Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).

Date
type: AnnotationProperty
comment: A date associated with an event in the life cycle of the resource.
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.

participates_in
type: AnnotationProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000020
has OBO namespace: ro_bfo_bridge
domain: continuant
type: ObjectProperty
range: occurrent

Title
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

inheres in
type: AnnotationProperty
label: inheres_in
editor note: This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant.
editor note: This relation belongs in BFO/RO, and will be in BFO 2
comment: This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on
has alternative id: OBO_REL:0000026
has OBO namespace: relationship
domain: specifically_dependent_continuant
has exact synonym: has_bearer
has definition: Definition
  label: A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation.
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm
type: ObjectProperty
type: FunctionalProperty
range: independent_continuant
has definition: Definition
  label: A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation.
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

Relation
type: AnnotationProperty
description: Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a related resource.

transformed_into
type: AnnotationProperty
comment: Obsoleted
has OBO namespace: relationship
has alternative id: OBO_REL:0000014
has OBO namespace: ro_bfo_bridge
domain: continuant
type: ObjectProperty
sub property of: ObsoleteProperty
range: continuant

derived_into
type: AnnotationProperty
has alternative id: OBO_REL:0000016
has OBO namespace: relationship
has OBO namespace: ro_bfo_bridge
domain: continuant
type: ObjectProperty
type: TransitiveProperty
range: continuant
inverse of: derives_from

has_participant
type: AnnotationProperty
comment: 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.
has alternative id: OBO_REL:0000019
has OBO namespace: ro_bfo_bridge
has OBO namespace: relationship
domain: occurrent
has definition: P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
range: continuant
inverse of: participates_in
has definition: P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

definition
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor: PERSON:Daniel Schober
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor preferred term: definition
has curation status: ready for release

expand expression to
type: AnnotationProperty
definition editor: Chris Mungall
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
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)"
editor preferred term: expand expression to

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

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

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

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

Language
type: AnnotationProperty
comment: A language of the intellectual content of the resource.
description: Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.

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

Resource Type
type: AnnotationProperty
comment: The nature or genre of the content of the resource.
description: Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.

has_quality
type: AnnotationProperty
definition: A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungall
has curation status: ready for release
domain: independent_continuant
type: ObjectProperty
sub property of: bearer_of
inverse of: quality of
range: quality
type: NamedIndividual
editor preferred term: has_quality

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

definition editor
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition editor: PERSON:Daniel Schober
editor preferred term: definition editor
has curation status: ready for release

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

has_specified_output
type: AnnotationProperty
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
editor preferred term: has_specified_output
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: PERSON: Alan Ruttenberg
domain: planned process
type: ObjectProperty
inverse of: is_specified_output_of
sub property of: has_participant
type: NamedIndividual

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

expand assertion to
type: AnnotationProperty
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
definition editor: Chris Mungall
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)"
editor preferred term: expand assertion to

transformation_of
type: AnnotationProperty
comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
has OBO namespace: ro_bfo_bridge
has alternative id: OBO_REL:0000013
has OBO namespace: relationship
domain: continuant
has definition: Definition
  label: Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: continuant
has definition: Definition
  label: Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

location_of
type: AnnotationProperty
has OBO namespace: ro_bfo_bridge
has alternative id: OBO_REL:0000009
has OBO namespace: relationship
domain: continuant
type: ObjectProperty
type: TransitiveProperty
range: continuant
inverse of: located_in

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

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

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

has_agent
type: AnnotationProperty
has alternative id: OBO_REL:0000021
has OBO namespace: ro_bfo_bridge
has OBO namespace: relationship
domain: occurrent
has definition: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
range: continuant
inverse of: agent_in
sub property of: has_participant
has definition: As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

Publisher
type: AnnotationProperty
comment: An entity responsible for making the resource available
description: Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.

Coverage
type: AnnotationProperty
description: Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
comment: The extent or scope of the content of the resource.

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

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

bearer_of
type: AnnotationProperty
comment: Examples: red eye bearer_of redness
has OBO namespace: relationship
has alternative id: OBO_REL:0000027
domain: independent_continuant
has exact synonym: has_inherer
has exact synonym: has_inherent
has definition: A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm
type: ObjectProperty
inverse of: inheres in
range: dependent_continuant
range: specifically_dependent_continuant
has definition: A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

located_in
type: AnnotationProperty
comment: 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
has OBO namespace: relationship
has alternative id: OBO_REL:0000008
has OBO namespace: ro_bfo_bridge
domain: continuant
has definition: Definition
  label: C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874
type: ObjectProperty
type: TransitiveProperty
range: continuant
has definition: Definition
  label: C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

is_realized_by
type: AnnotationProperty
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungall
definition: Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
alternative term: executed_during
alternative term: has_realization
alternative term: is_realized_as
editor preferred term: is_realized_by
has curation status: ready for release
domain: realizable_entity
type: ObjectProperty
range: processual_entity

Format
type: AnnotationProperty
comment: The physical or digital manifestation of the resource.
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).

Rights Management
type: AnnotationProperty
description: Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
comment: Information about rights held in and over the resource.

realizes
type: AnnotationProperty
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungal
definition: Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
example of usage: example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes.
alternative term: executes
alternative term: has_function_part
has curation status: ready for release
alternative term: involves_execution_of
alternative term: is_realization_of
domain: processual_entity
type: ObjectProperty
inverse of: realized_by
range: realizable_entity
type: Thing
type: NamedIndividual
editor preferred term: realizes

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

is about
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
definition editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting

mentions
type: ObjectProperty
editor note: 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
editor note: 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
definition: An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
definition editor: PERSON: Jonathan Rees
definition editor: Person: Alan Ruttenberg
has curation status: pending final vetting
sub property of: is about

denotes
type: ObjectProperty
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
definition: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
definition editor: person:Alan Ruttenberg
sub property of: is about

is quality measurement of
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
definition editor: Alan Ruttenberg
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
domain: measurement datum
sub property of: is about
range: quality

has coordinate unit label
type: ObjectProperty
type: FunctionalProperty
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
domain: cartesian spatial coordinate datum
range: length unit
sub property of: has_part

is duration of
type: ObjectProperty
definition editor: Person:Alan Ruttenberg
definition: relates a process to a time-measurement-datum that represents the duration of the process
has curation status: metadata complete
sub property of: is about
domain: time measurement datum
range: process

is quality measured as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
definition: inverse of the relation of is quality measurement of
has curation status: metadata complete
inverse of: is quality measurement of

is quality specification of
type: ObjectProperty
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition: a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
has curation status: metadata complete
sub property of: is about

quality is specified as
type: ObjectProperty
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition: inverse of the relation of is quality specification of
has curation status: metadata complete
inverse of: is quality specification of

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

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

results_in
type: ObjectProperty

capable_of
type: ObjectProperty
domain: independent_continuant
range: processual_entity

has_material_basis_in
type: ObjectProperty
range: material_entity

is_concretization_of
type: ObjectProperty
definition: a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends
range: generically_dependent_continuant
domain: specifically_dependent_continuant

is_specified_input_of
type: ObjectProperty
definition editor: PERSON:Bjoern Peters
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
range: planned process
inverse of: has_specified_input
sub property of: participates_in
type: NamedIndividual
editor preferred term: is_specified_input_of

is_concretized_as
type: ObjectProperty
definition: a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends
inverse of: is_concretization_of
domain: generically_dependent_continuant
range: specifically_dependent_continuant

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

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
range: objective specification
domain: planned process
inverse of: objective_achieved_by
type: Thing
type: NamedIndividual
editor preferred term: achieves_planned_objective

objective_achieved_by
type: ObjectProperty
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
editor note: definition needs clean up to indicate directionality
domain: objective specification
range: planned process
type: NamedIndividual
editor preferred term: objective_achieved_by

has_disposition
type: ObjectProperty
has OBO namespace: relationship
sub property of: bearer_of
range: disposition

has_function
type: ObjectProperty
definition editor: PERSON: Chris Mungall
definition: Relation between an independent continuant and a function.
comment: heart has_function to-pump-blood
imported from: http://purl.org/obo/owl/ro_proposed
has OBO namespace: relationship
has alternative id: OBO_REL:0000031
sub property of: bearer_of
range: function
has definition: Relation between an independent continuant and a function.
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

has_output
type: ObjectProperty
comment: Examples: secretory cells. Should this be has_function (export of ...)
has OBO namespace: relationship
has definition: C has_output C'
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

has_role
type: ObjectProperty
definition: A relation between a continuant C and a role R. The reciprocal relation of role_of.
has alternative id: OBO_REL:0000033
has OBO namespace: relationship
sub property of: bearer_of
range: role
has definition: A relation between a continuant C and a role R. The reciprocal relation of role_of.
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

negatively_regulates
type: ObjectProperty
has OBO namespace: relationship
sub property of: regulates
property chain axiom: part_of
has definition: A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process

positively_regulates
type: ObjectProperty
has OBO namespace: relationship
sub property of: regulates
has definition: A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process
property chain axiom: part_of

realized_by
type: ObjectProperty
comment: NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
definition: Relation between a realizable and a process. Reciprocal relation of realizes
has alternative id: OBO_REL:realized_as
has OBO namespace: relationship
has alternative id: OBO_REL:0000035
inverse of: realizes
domain: realizable_entity
range: processual_entity
has related synonym: executed_during
has definition: Relation between a realizable and a process. Reciprocal relation of realizes
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm
has exact synonym: has_realization
has definition: Relation between a realizable and a process. Reciprocal relation of realizes
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

realizes
type: ObjectProperty
comment: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
has OBO namespace: relationship
has alternative id: OBO_REL:0000034
has related synonym: executes
has definition: Definition
  label: Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm
has related synonym: involves_execution_of
has exact synonym: has_function_part
has exact synonym: is_realization_of

regulates
type: ObjectProperty
has OBO namespace: relationship
has definition: A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process
property chain axiom: part_of

results_in_formation_of
type: ObjectProperty
comment: Example: autophagic vacuole formation results_in_formation_of autophagic vacuole. macromolecular complex assembly results_in_formation_of a macromolecule. Note: essentially the same as biosynthesis, although in biosynthesis the assembly is via chemical reactions
has OBO namespace: relationship
sub property of: results_in
has exact synonym: results_in_creation_of
has exact synonym: results_in_assembly_of
has definition: Definition
  label: P results_in_formation_of C : any instance of P gives rise to a C from the parts of C. Formally: forall pP, exists some c such that c instantiates C at end-of p, and c has some parts c1, c2, ... such that the parts are connected at the end-of p and disconected at the start-of p
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

towards
type: ObjectProperty
definition: A relation between a relational quality and an independent continuant, subproperty of inheres that distinguishes the main bearers of a relational quality from additional dependents.
definition editor: GROUP:OBI:<http://obi.sourceforge.net>
definition editor: PERSON: Chris Mungall
imported from: ro proposed
sub property of: inheres in
type: NamedIndividual
editor preferred term: towards

unfolds_in
type: ObjectProperty
comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
has OBO namespace: relationship
domain: processual_entity
range: Class
  union of: material_entity
  union of: site
has definition: P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

adjacent_to
type: ObjectProperty
comment: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
has alternative id: OBO_REL:0000012
has OBO namespace: relationship
has definition: C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

contained_in
type: ObjectProperty
comment: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
has OBO namespace: relationship
has alternative id: OBO_REL:0000010
inverse of: contains
has definition: Definition
  label: C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

contains
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000011

has_improper_part
type: ObjectProperty
type: TransitiveProperty
comment: See reasons for obsoletion of improper_part_of
has OBO namespace: relationship
has alternative id: OBO_REL:0000024
sub property of: ObsoleteProperty
sub property of: has_part

has_integral_part
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000005
sub property of: has_part

has_part
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000003
inverse of: part_of
sub property of: topObjectProperty

has_proper_part
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000007
sub property of: has_part
inverse of: proper_part_of

improper_part_of
type: ObjectProperty
type: TransitiveProperty
comment: OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
has OBO namespace: relationship
has alternative id: OBO_REL:0000025
sub property of: ObsoleteProperty
inverse of: has_improper_part
sub property of: part_of
has definition: As for part_of, with the additional constraint that subject and object may be identical
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

integral_part_of
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000004
inverse of: has_integral_part
sub property of: part_of
has definition: C integral_part_of C' if and only if: C part_of C' AND C' has_part C
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

part_of
type: ObjectProperty
type: TransitiveProperty
comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
has OBO namespace: relationship
has alternative id: OBO_REL:0000002
editor note: There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
has definition: Definition
  label: For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

proper_part_of
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000006
has OBO namespace: relationship
sub property of: part_of
has definition: As for part_of, with the additional constraint that subject and object are distinct
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

relationship
type: ObjectProperty
comment: this relation was superfluous, so it has been obsoleted
has OBO namespace: relationship
sub property of: ObsoleteProperty
has definition: A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
  type: Definition
  has db xref: GOC:cjm
    type: DbXref
    has URI: http://purl.org/obo/owl/GOC#GOC_cjm

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: float

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

amplified virus preparation
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: virus amplification
  intersection of: Restriction
    on property: has_role
    some values from: specimen role
definition source: RBS:rbs
editor note: MC, 20101203: redefined as defined class after adding virus amplification process
definition: An amplified virus preparation is an organimal group representing a large number of copies of one or more viruses.

enriched cell fraction
type: Class
equivalent class: Class
  intersection of: cell fraction
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: enrichment process
subclass of: material_entity
definition source: RBS:rbs
definition: An enriched cell fraction is a cell fraction that has an increased concentration of one or more cell fraction components.
editor note: MC, 20101203: added enrichment process and cell fraction from GO and restrictions to make this a defined class

complementary ribonucleic acid role
type: Class
subclass of: role
definition source: RBS:rbs
definition: A complementary ribonucleic acid is a biological macromolecule role played by a RNA molecule that serves as a complementary copy (positive copy for negative stranded RNA and vice versa).

sequencing facility role
type: Class
subclass of: investigation agent role
definition source: RBS:rbs
definition: A sequencing laboratory role is a laboratory role played by a population that performs the assay process of nucleotide or amino acid sequenceing analysis.
editor note: MC, 08092009: moved as subclass of new mireoted term OBI_0000202, investigation agent role, which can be borne by either individuals or insitutions

influenza virion
type: Class
subclass of: virion
curator note: MC, 20100212: submitted tracker item to IDO at http://code.google.com/p/infectious-disease-ontology/issues/detail?id=25 to clarify definition of parent term virion
alternative term: influenza assembled virus
definition editor: person: Melanie Courtot
definition source: WEB: http://www.medterms.com/script/main/art.asp?articlekey=11558
alternative term: influenza virus particle
definition: A complete virus particle of influenza virus with its DNA or RNA core and protein coat as it exists outside the cell.

influenza hemagglutinin
type: Class
equivalent class: Class
  intersection of: hemagglutinin
  intersection of: Restriction
    on property: part_of
    some values from: influenza virion
definition: Influenza hemagglutinin is a type of hemagglutinin found on the surface of the influenza viruses. It is an antigenic glycoprotein. It is responsible for binding the virus to the cell that is being infected.
definition source: WEB: http://en.wikipedia.org/wiki/Hemagglutinin_%28influenza%29
editor note: MC, 20101201: added as subclass of hemagglutinin
definition editor: person: Melanie Courtot
alternative term: Influenza haemagglutinin
editor note: 20100203: submitted to PRO: http://sourceforge.net/tracker/?func=detail&atid=1135711&aid=2945554&group_id=266825

neuraminidase
type: Class
equivalent class: Class
  intersection of: protein
  intersection of: Restriction
    on property: has_function
    some values from: alpha-sialidase activity
definition: Neuraminidase enzymes are glycoside hydrolase enzymes (EC 3.2.1.18) that cleave the glycosidic linkages of neuraminic acids. Neuraminidase enzymes are a large family, found in a range of organisms. The most commonly known neuraminidase is the viral neuraminidase, a drug target for the prevention of influenza infection. The viral neuraminidases are frequently used as an antigenic determinants found on the surface of the Influenza virus. Some variants of the influenza neuraminidase confer more virulence to the virus than others. Neuraminidases, also called sialidases, catalyze the hydrolysis of terminal sialic acid residues from the newly formed virions and from the host cell receptors.[2] Sialidase activities include assistance in the mobility of virus particles through the respiratory tract mucus and in the elution of virion progeny from the infected cell.[3][4]
definition editor: person: Melanie Courtot
definition source: MC, 20101202: added definition
editor note: 20100203: submitted to PRO: http://sourceforge.net/tracker/?func=detail&aid=2945634&group_id=266825&atid=1135711
definition source: WEB: http://en.wikipedia.org/wiki/Neuraminidase

virus isolation
type: Class
subclass of: extraction
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: is_concretization_of
    some values from: virus isolation protocol
subclass of: Restriction
  on property: has_specified_output
  some values from: viral isolate
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://virology-online.com/general/Test1.htm
definition: a material separation to recover the virusfraction of an input material

haemadsorption
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: viral isolate
    intersection of: Restriction
      on property: has_part
      some values from: Class
        union of: Influenza A virus
        union of: Influenza B virus
        union of: Influenza C virus
example of usage: Influenza and parainfluenza viruses do not ordinarily induce CPE, however they possess haemagglutinins and thus the ability to absorb guinea pig RBCs as they bud from the cell. This phenomenon is known as haemadsorption. Commonly employed cell cultures include primary monkey kidney, LLC-MK2 and MDCK cells. The cell cultures are incubated with a suspension of guinea pig RBCs at 4oC or RT for 30 minutes. The unabsorbed RBCs are then removed and the cell sheet observed microscopically for the presence of haemadsorption.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://virology-online.com/general/Test1.htm
definition: the absorption of red blood cells by haemagglutinins

viral isolate
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: has_part
  some values from: Viruses
subclass of: Restriction
  on property: is_specified_output_of
  some values from: virus isolation

GenBank submission event
type: Class
subclass of: data transformation
definition source: URL:http://www.ncbi.nlm.nih.gov/Genbank/
definition: A data transformation event that encompasses the process of submitting new or updated sequence information or annotation to GenBank.

trypsin
type: Class
subclass of: protein
definition editor: PERSON: Melanie Courtot
editor note: Submitted to PRO, see https://sourceforge.net/tracker/?func=detail&atid=1135711&aid=3397087&group_id=266825
definition: Trypsin (EC 3.4.21.4) is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen.
definition source: WEB: http://en.wikipedia.org/wiki/Trypsin

disease severity
type: Class
subclass of: categorical measurement datum
definition source: URL:http://www.nationalasthma.org.au/html/strategy/camia/camia002.asp
definition: A disease phenotype that descrives the inherent severity of the disease independent of its management, including drug and other interventions.

tissue culture infectious dose 50
type: Class
subclass of: scalar measurement datum
definition source: URL:http://aleffgroup.com/AVISFMD/A010-fmd/mod2/0550-karber.html
editor note: MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum
alternative term: TCID50
definition: The quantity of virus in a specified suspension volume (e.g., 0.1 ml) that will infect 50% of a number (n) of cell culture microplate wells, or tubes

trypsin auxotrophic organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_quality
    some values from: Class
      intersection of: auxotrophic
      intersection of: Restriction
        on property: towards
        some values from: trypsin
subclass of: material_entity
definition: An organism that requires tryspin to grow
definition editor: PERSON: Melanie Courtot

immature
type: Class
subclass of: life stage
definition source: URL:http://elibrary.unm.edu/sora/JFO/v017n01/p0027-p0033.pdf
definition: A bird after completing the post-juvenal molt, but has not acquired the complete adult plumage. A life stage of any bird older than a nestling or chick that has not reached sexual maturity or its basic winter or first winter plumage.

cough
type: Class
subclass of: symptom
has db xref: SYMP:614
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cough
definition: An explosive expulsion of air from the lungs acting as a protective mechanism to clear the air passages or as a symptom of pulmonary disturbance.

intensity of body moult
type: Class
subclass of: measurement datum
definition: A intensity of body moult is a measurement datum that describes the intensity of the periodic replacement of epidermis (skin), pelage (hair, fur, wool), or other external layer. In some species, other body parts may be shed, for example, wings in some insects. Examples include old feathers in birds, old hairs in mammals (especially dogs and other canidae), old skin in reptiles, and the entire exoskeleton in arthropods.
has db xref: http://en.wikipedia.org/wiki/Moult
curator note: 20110823, MC: need to check on the unit for this. If it has a unit it should be asserted under scalar measurement datum
curator note: 20110823: this term initially refered only to bird in its definition. We may also need to create a moulting process.

virus passage date
type: Class
subclass of: date
subclass of: Restriction
  on property: is about
  some values from: virus passage
definition source: FLU:MK
definition: Date that the virus passage(s) took place.

annotation event
type: Class
subclass of: data transformation
definition source: URL:http://www.ncbi.nlm.nih.gov/projects/genome/guide/E132
definition: An annotation event is a data transformation event which encompasses adding biological information to genome sequence. This is a very complex task, and the process for doing this is rapidly evolving. Several groups are doing automated computational annotation of several genomes. Features that are added to the genome often include gene models, SNPs, and STSs.

GenBank name
type: Class
subclass of: data about a genbank entry

GenBank notes
type: Class
subclass of: data about a genbank entry

collection latitude GPS
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The GPS latitude coordinate where the sample was collected.

data about a laboratory
type: Class
subclass of: data item
definition source: RBS:rbs
editor note: MC, 20101118: this is a placeholder meant to be removed when we will have a laboratory, which will allow us to define current subclass using the is_about relation
editor note: MC, 08092009: moved from quality to GDC. Those are information entities. Need additional clean up. There is no laboratory role.
editor note: MC, 20101118: moved under data item and renamed data about a laboratory from "quality of a laboratory" Those should be outsourced towards the organization ontology.

neuraminidase typing
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: neuraminidase
definition: An assay which aims at determining the neuraminidase type of an influenza virus.
alternative term: N typing

juvenile
type: Class
subclass of: life stage
definition source: URL:http://elibrary.unm.edu/sora/JFO/v017n01/p0027-p0033.pdf
definition: A young bird out of the nest and able to take care of itself, but which has not completed the post-juvenal molt.

initial oxygen saturation
type: Class
subclass of: scalar measurement datum
definition source: URL:http://gyre.umeoce.maine.edu/data/gomoos/buoy/doc/buoy_system_doc/buoy_system/g6572.html
editor note: MC, 20101119: moved from quality to scalar measurement datum.
definition: Initial oxygen saturation is a scalar measurement datum that describes the initial volume of oxygen gas (STP) absorbed from humidity-saturated air at a total pressure of one atmosphere, per unit volume of the liquid at the temperature of measurement (units ml/l).

date
type: Class
subclass of: time measurement datum
definition source: URL:http://www.gnu.org/software/radius/manual/html_node/radius_36.html
definition: A date in the format: MON DD CCYY, where MON is the usual three-character abbreviation for month, DD is day of month (1-31), CCYY is the year, including the century. Date may also be reported as year CCYY. (DDMMYY).

fledgling
type: Class
subclass of: life stage

specimen identification number
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: inheres in
      some values from: specimen
editor note: MC, 20101118: removed dbxref to PATO_0001226, count. Updated from "sample number" to "specimen identification number" as per Burke's use case
definition source: GROUP: FLU
definition: The unique number inhering in and identifying the specimen

fatigue
type: Class
subclass of: symptom
has db xref: MP:0002899 'Mammalian phenotype'
has db xref: SYMP:0019177
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=fatigue
definition: Weariness or exhaustion from labor, exertion, or stress.

myalgia
type: Class
subclass of: symptom
has db xref: SYMP:0000626
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=myalgia
definition: Pain in one or more muscles.

virus pathogenicity after passage
type: Class
subclass of: Class
  intersection of: scalar measurement datum
  intersection of: Restriction
    on property: is about
    some values from: pathogenic disposition
subclass of: Restriction
  on property: is_specified_output_of
  some values from: virus passage
definition source: URL:http://www.pnas.org/cgi/content/abstract/97/13/6974
alternative term: virus passage level
editor note: MC, 20101119: moved from quality of specimen to scalar measurement datum
definition: A scalar measurement datum denoting the pathogenicity of a virus after several passages in cell culture.
editor note: MC, 20101201: updated definition and label

collection province
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The name of the geographic province where the collection occurred.

yearling
type: Class
subclass of: life stage
definition source: Flu:ls
definition: A bird that was observed the summer following its year of hatch.

sequence submission date
type: Class
subclass of: date
definition source: FLU:MK
definition: Date that the sequence was submitted (i.e. to GenBank).

GenBank district
type: Class
subclass of: data about a genbank entry

specimen collection date
type: Class
subclass of: date
subclass of: Restriction
  on property: is about
  some values from: specimen collection
definition source: FLU:MK
definition: Calendar date that the specimen was collected.

GenBank projected_timeline
type: Class
subclass of: data about a genbank entry

virus passage
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: pathogenic disposition
subclass of: Restriction
  on property: has_specified_input
  some values from: Viruses
definition: A virus passage is a transforming material transformation that involves the incubation of a pathogen (as a virus) in a tissue culture, a developing egg, or a living organism to increase the amount of pathogen or to alter its characteristics
definition source: WEB:http://www.merriam-webster.com/medical/passage

GenBank template_id
type: Class
subclass of: data about a genbank entry

vaccinated organism
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: vaccination against infectious agent
definition: An organism which has been vaccinated
comment: vaccination status is an IA about a vaccinated host
definition source: GROUP: FLU

collection district
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The name of the district where the sample was collected.

GenBank submission date
type: Class
subclass of: data about a genbank entry

sample quantity
type: Class
subclass of: scalar measurement datum
has db xref: PATO:0001226
definition source: GROUP: FLU
editor note: MC, 20101118: moved from specimen quality to scalar measurement datum
definition: The sample amount as measured in grams, milliliters or other standard unit of measurement.

RNA extraction protocol
type: Class
subclass of: extraction protocol
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: realized_by
      some values from: RNA extraction

viral RNA extraction
type: Class
subclass of: RNA extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Viruses
definition editor: PERSON: Melanie Courtot
editor note: A RNA extraction from a virus

primaries flight feather
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: part_of
  some values from: Aves
definition source: URL:http://volusia.org/birding/glossary.htm
definition: Large outermost flight feathers on wing. Can vary from 9-11, but the number remains constant within a species.

collection country
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The name of the country where the sample was collected.

lethal dose 50
type: Class
subclass of: scalar measurement datum
definition source: URL:http://www.virology.net/ATVGlossary.html
editor note: MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum
definition: The measure that describes the dosage of a drug or poison that is toxic to 50% of the organisms it is tested against.

specimen collector role
type: Class
subclass of: investigation agent role
subclass of: Restriction
  on property: realized_by
  some values from: specimen collection
definition: A specimen collector role is a study personnel role that is performed by a erson who collects the specimen from the environment.

strain taxonomy name
type: Class
subclass of: label
definition source: URL:http://www.niwa.cri.nz/rc/freshwater/fishatlas/glossary
editor note: MC: 20101119: moved from strain specimen quality to label. Not sure this term is required.
definition: The taxonomic name for a strain species, consisting of two words, the genus and species.

secondaries flight feather
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: part_of
  some values from: Aves
definition source: URL:http://volusia.org/birding/glossary.htm
definition: Flight feathers, smaller than the primaries, occurring in series along rear edge of wing between scapulars, inward of primaries.

GenBank subtype
type: Class
subclass of: data about a genbank entry
definition source: URL:http://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html
definition: The subtype is a quality that describes the subtype of organism from which sequence was obtained.

rural environment
type: Class
subclass of: environment
definition source: URL:http://en.wiktionary.org/wiki/rural
curator note: 20110826, MC: renamed from "rural" to "rural environment". Moved under environment.
definition: Rural environment is an environment that is characterized by sparsely-populated non-urban areas, such as found in farming communities or the countryside.

sequence coverage
type: Class
subclass of: measurement datum
definition source: wiki:http://en.wikipedia.org/wiki/Shotgun_sequencing
definition: Sequence coverage is the average number of reads representing a given nucleotide in the reconstructed sequence. It can be calculated from the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G. For example, a hypothetical genome with 2,000 base pairs reconstructed from 8 reads with an average length of 500 nucleotides will have 2x redundancy. This parameter also enables one to estimate other quantities, such as the percentage of the genome covered by reads (sometimes also called coverage).
editor note: MC, 20101201: old definition was "A sequencing specification that describes the average number of times a nucleotide position was sequenced to obtain a consensus." Moved from sequencing specification to measurement datum

virus passage history record
type: Class
subclass of: passage history record
subclass of: Restriction
  on property: is about
  some values from: virus passage
definition source: URL:http://www.pnas.org/cgi/content/abstract/97/13/6974
alternative term: virus passage number
definition: A virus passage history record is a passage history record that details the number of times a virus has been passaged in cell culture.
editor note: MC, 20111123: moved from quality of specimen to passage history record, and renamed accordingly (with addition of alt term)

Genbank reject date
type: Class
subclass of: data about a genbank entry

nucleic acid sequence
type: Class
subclass of: data item
editor note: has been scheduled for inclusion in OBI: nucleic acid sequence: A data item that is is a string of characters (e.g., A, G, C,T, U, N, R, Y, etc.) and represents the order of nucleotides found somewhere in nature or synthesized.

sequence submitter role
type: Class
subclass of: investigation agent role
definition source: RBS:rbs
definition: A sequence submitter role is a study personnel role that is repsponsible for sending sequence (DNA, RNA, Protein) data to a repository, usually GenBank.

collection sub-district
type: Class
subclass of: collection district
definition source: GROUP: FLU
definition: The name of the sub-district where collection occurred.

sequencing protocol
type: Class
subclass of: protocol
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: realized_by
      some values from: sequencing assay
editor note: MC, 20101201: updated label from sequencing specification to sequencing protocol to match position in hierarchy
definition: A protocol which specifies conditions, parameters and instructions to be used when performing sequencing assays
definition editor: PERSON: Melanie Courtot

GenBank length
type: Class
subclass of: data about a genbank entry
definition source: wiki:http://en.wikipedia.org/wiki/Length
definition: The length is a quality that describes measure of the nucleotide or amino acid sequence from beginning to end.

GenBank prep_date
type: Class
subclass of: data about a genbank entry

transmission environment
type: Class
equivalent class: Class
  intersection of: environment
  intersection of: Restriction
    on property:
      inverse of: unfolds_in
    some values from: transmission process
definition source: FLU:MK
curator note: 20110826, MC: trasnformed into a defined class. Subclasses rural and urban were renamde and asserted under environment
definition: A transmission environment is the environment in which the etiologic agent was harbored and spread from host to host.

extraction date
type: Class
subclass of: date
subclass of: Restriction
  on property: is about
  some values from: extraction
definition source: FLU:MK
definition: Calendar date that the sample was extracted.

lab isolation date
type: Class
subclass of: date
definition source: FLU:MK
definition: Date that the laboratory isolated the sample.

viral replication titer
type: Class
subclass of: scalar measurement datum
editor note: MC, 20101119: updated label from "replication titer" to "viral replication titer"
editor note: MC, 20101119: moved from quality to scalar mesurement dtum and updated defintiion accordingly
definition: A scalar measurement datum that denotes the virus replication level.

mature
type: Class
subclass of: life stage
definition source: URL:http://www.dfw.state.or.us/resources/hunting/upland_bird/projects/mtn-quail.asp
definition: A bird after hatch year.

bird wing length unflattened
type: Class
subclass of: length measurement datum
editor note: MC, 20101118: moved from winged organism anatomy to length measurement datum
definition source: GROUP: FLU
definition: The measured length of the bird wing as the wing is held without being flattened.

throat pain
type: Class
subclass of: symptom
has db xref: SYMP:505
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=sore%20throat
definition: Painful throat due to inflammation of the fauces and pharynx.

egg infectious dose 50
type: Class
subclass of: scalar measurement datum
definition source: :1938. L. Reed and H. Muench
editor note: MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum
definition: A strain specimen phenotype that describes the egg infectious dose 50 amount of a virus which is required to kill 50% of the eggs.

GenBank accession
type: Class
subclass of: data about a genbank entry
definition source: URL:http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/genejargon.shtml
definition: An accession number is a quality that describes the unique identifier assigned to the entire sequence record when the record is submitted to GenBank.

environment
type: Class
subclass of: site
editor note: MC, 20101202: moved under site and definition updated from "An environment is a spatial region having environmental qualities which may sustain an organism or a community of organisms."
definition: An environment is a site having environmental qualities which may sustain an organism or a community of organisms.
definition source: GROUP: FLU

nucleotide sequencer role
type: Class
subclass of: investigation agent role
subclass of: Restriction
  on property: realized_by
  some values from: sequencing assay
definition: A nucleotide sequencer role is a study personnel role that is performed by a person who determines the genetic sequence for a biomateral.

data about a collection location
type: Class
subclass of: data item
editor note: MC, 20101118: this is a placeholder meant to be removed when we will have the collection process, which will allow us to define current subclass using the is_about relation
editor note: MC, 20101118: renamed from collection location context

organism treated with antibiotics
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: administering substance in vivo
      intersection of: Restriction
        on property: has_specified_input
        some values from: antibiotic
subclass of: material_entity
editor note: 20110824, MC: renamed from "antibiotics administered" after adding correct restrictions. Note that even thought we say "organism treated with antibiotic" the sense of treated is not the one from OGMS:treatment - there doesn't have to be therapeutic intent.
definition: An organism which has been treated with antibiotics

bird length head to beak
type: Class
subclass of: length measurement datum
editor note: MC, 20101118: moved from winged organism anatomy to length measurement datum
definition source: GROUP: FLU
definition: The measured length from the birds head to beak.

genbank virion RNA submission event
type: Class
subclass of: GenBank submission event
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: ribonucleic acids
        intersection of: Restriction
editor note: MC, 20101207: I am trying to say logically that the info submitted is about the RNA sequence that has been obtained by sequencing the RNA that had been extracted from the virion
definition: A GenBank submission event in which the RNA sequence of a virion is submitted
definition editor: PERSON; Melanie Courtot

hemagglutinin titer
type: Class
subclass of: Restriction
  on property: is_specified_output_of
  some values from: hemagglutinin typing
subclass of: Class
  intersection of: scalar measurement datum
  intersection of: Restriction
    on property: is about
    some values from: hemagglutinin
definition source: URL:http://www.virology.net/ATVGlossary.html
definition: A measure of the amount or concentration of hemagluttanin in solution.
editor note: MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum

bird beak length
type: Class
subclass of: length measurement datum
editor note: MC, 20101118: moved from winged organism anatomy to length measurement datum
definition source: GROUP: FLU
definition: The measured length of the birds beaks.

runny nose
type: Class
subclass of: symptom
has db xref: SYMP:0000372
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=Rhinorrhea
definition: Excessive mucous secretion from the nose.

fever
type: Class
subclass of: symptom
has db xref: GO:0001660 'Gene ontology'
has db xref: SYMP:613
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=fever
definition: A rise of body temperature above the normal whether a natural response (as to infection) or artificially induced for therapeutic reasons.

nestling
type: Class
subclass of: life stage
definition source: URL:http://elibrary.unm.edu/sora/JFO/v059n03/p0235-p0238.html
definition: A young bird confined to the nest. Nestlings are infant birds having little or no feathering. They may be pink and naked, covered with down feathers, or covered with needle-like feathers (called pin feathers).

sample name
type: Class
subclass of: label
editor note: MC: 20101119: moved from strain specimen quality to label. Not sure this term is required.

extraction time
type: Class
subclass of: time measurement datum
definition source: FLU:MK
definition: A defined period when the sample was extracted.

GenBank lot
type: Class
subclass of: data about a genbank entry

laboratory address
type: Class
subclass of: data about a laboratory
definition source: URL:http://www.gnu.org/software/radius/manual/html_node/radius_36.html
definition: The address that describes the physical (geographic) location of the laboratory facility.

RNA amount shipped for sequencing
type: Class
subclass of: scalar measurement datum
definition editor: PERSON: Melanie Courtot
definition: The amount of RNA that has been sent to the lab for sequencing purposes
editor note: MC, 20101201: added definition for this term. Not sure how to deal with it though.

plaque forming units per size
type: Class
subclass of: scalar measurement datum
definition source: URL:http://en.wikipedia.org/wiki/Plaque_forming_units
editor note: MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum
definition: A plaque forming unit per size is a measure that is used in the assessment of the concentration of viruses in a sample.

GenBank modification date
type: Class
subclass of: data about a genbank entry

collection city
type: Class
subclass of: data about a collection location
definition source: URL:http://www.epa-echo.gov/echo/case_report_dd.html
definition: The name of the city, town, or village where the sample was collected.

GenBank created_by_person/group
type: Class
subclass of: data about a genbank entry

GenBank origin_lab
type: Class
subclass of: data about a genbank entry

bird wing length flat
type: Class
subclass of: length measurement datum
definition source: GROUP: FLU
editor note: MC, 20101118: moved from winged organism anatomy to length measurement datum
definition: The measured length of the bird wing as the wing is held flat.

collection longitude GPS
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The GPS longitude coordinate where the sample was collected.

specimen collection protocol
type: Class
subclass of: protocol
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: realized_by
      some values from: specimen collection
editor note: MC, 20101203: updated sample to specimen
definition source: GROUP: FLU
definition: The protocol specifying how to collect the specimen

hatch year
type: Class
subclass of: life stage
definition source: Flu:ls
definition: A bird in the first year after hatching.

hemagglutinin typing
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: measurement datum
      intersection of: Restriction
        on property: is about
        some values from: hemagglutinin
definition: An assay which aims at determining the hemagglutanin subtype of an influenza virus.
alternative term: HA typing
curator note: MC, 20101202: made it a defined class as there are several methods to identify the heagglutinin type as per http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T32-4C47KNC-5&_user=1022551&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1565330571&_rerunOrigin=google&_acct=C000050484&_version=1&_urlVersion=0&_userid=1022551&md5=c5d1a3bc08abe655acb70076b13e3a74&searchtype=a The haemagglutination-inhibition assay that is routinely used for subtyping and antigenic characterisation of influenza strains does not distinguish between A(H1N1) and A(H1N2) strains; therefore, alternative tests are required for typing the NA. The standard test used to determine neuraminidase type is a rather cumbersome and time-consuming procedure (approximately 18 h) which relies on inhibition, by antibody, of n-acetyl neuraminic acid release from a substrate such as fetuin (Aymard-Henry et al., 1973). Alternative methods of neuraminidase assay have been described, one for example relying on the agglutination of neuraminidase-treated erythrocytes by lectins (Fiszon and Hannoun, 1990 B Fiszon and C Hannoun, Comparison of neuraminidases of the same subtype but from different species using a new method of titration, J. Virol. Methods 27 (1990), pp. 79–90. Abstract | PDF (587 K) | View Record in Scopus | Cited By in Scopus (4)Fiszon and Hannoun, 1990)

laboratory name
type: Class
subclass of: data about a laboratory
definition source: wiki:http://en.wikipedia.org/wiki/Laboratory
definition: The name of the laboratory conducting the scientific research, experiments, analysis or sequencing may be performed.

nasal congestion
type: Class
subclass of: symptom
definition: A nasal congestion is a symptom that is characterized by the blockage of the nasal passages usually due to membranes lining the nose becoming swollen from inflamed blood vessels.
alternative term: stuffy nose

influenza virus antigenic data
type: Class
subclass of: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: viral hemagglutination inhibition assay
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: Influenza A virus
    union of: Influenza B virus
    union of: Influenza C virus
editor note: MC, 20101130: "Antibodies against the viral surface glycoprotein hemagglutinin (HA) provide protective immunity to influenza virus infection, and this protein is therefore the primary component of influenza vaccines. However, the antigenic structure of HA has changed significantly over time, a process known as antigenic drift (6), and in most years, the influenza vaccine has to be updated to ensure sufficient efficacy against newly emerging variants (7, 8). The World Health Organization coordinates a global influenza surveillance network, currently consisting of 112 national influenza centers and four collaborating centers for reference and research. This network routinely characterizes the antigenic properties of influenza viruses using a hemagglutination inhibition (HI) assay "
editor note: MC, 20101130: renamed antigenic data (from strain antigenic data) and moved under data item from strain specimen quality
definition: Data reflecting the antigenic properties of influenza viruses characterized using a hemagglutination inhibition (HI) assay
definition source: WEB: http://www.sciencemag.org/content/305/5682/371.full

sequence annotator role
type: Class
subclass of: investigation agent role
definition source: Flu:ls
definition: The sequence annotator role is a study personnel role of a scientist who assigns a set of characteristics to a sequence for the purpose of documenting relevant infromation from experimental results to aid in their interpretation.

Genbank isolation source
type: Class
subclass of: data about a genbank entry

extractor role
type: Class
subclass of: investigation agent role
definition: A extractor role is a study personnel role that is performed by a person who extracts genetic material from a biomaterial.

viral RNA segment
type: Class
subclass of: ribonucleic acids
definition editor: person: Melanie Courtot
definition: RNA molecule constituting the genome of viruses
alternative term: vRNA segment

principal investigator role
type: Class
subclass of: investigation agent role
definition source: OBI:0000103
definition: A person with the lead role on the project, as a scientist or engineer.

GenBank size
type: Class
subclass of: data about a genbank entry

treatment event
type: Class
subclass of: material combination
editor note: MC, 20101207: I believe this term reflects the biochemical treatment of a sample and is therefore not equivalent to ogms: treatment which is a treatment to alleviate a disorder

collection location name
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The name of the place where the sample was collected.

laboratory tracking number
type: Class
subclass of: specimen identification number
definition editor: PERSON: Melanie Courtot
editor note: MC, 20101119: moved from "data about a laboratory" to "specimen identification nmber". See http://groups.google.com/group/influenza-ontology/browse_thread/thread/91adb05b5e6b80aa?hl=en
definition: A laboratory specimen tracking number is a specimen identification number assigned to a specimen by a laboratory with the objective to uniquely identify and follow the specimen.

antiviral treatment date
type: Class
subclass of: date
subclass of: Restriction
  on property: is about
  some values from: antiviral treatment
definition source: FLU:MK
definition: Calendar date that antiviral treatment was administered.

GenBank center_project
type: Class
subclass of: data about a genbank entry

onset date
type: Class
subclass of: date
definition: Date when host first experienced clinical symptoms.
definition source: GROUP: FLU
editor note: MC, 20101119: moved from quality>output assessment > measure to date

collection time
type: Class
subclass of: time measurement datum
definition source: FLU:MK
definition: A defined period when the sample was collected.

GenBank gi
type: Class
subclass of: data about a genbank entry
definition source: URL:http://www.ncbi.nlm.nih.gov/Class/FieldGuide/glossary.html#G
definition: A GI number is a quality that is an identifier assigned to all sequences at the NCBI, which points to a specific version of a sequence record. GI stands for GenInfo, a database system at NCBI that preceded the Entrez system.

collection quantity
type: Class
subclass of: scalar measurement datum
definition: A collection quantity is a generically dependant continuant that specifies the quantity of material collected.

life stage
type: Class
subclass of: quality of organism
has db xref: PATO:0000261

virus isolation protocol
type: Class
subclass of: extraction protocol
definition source: GROUP: FLU
definition: Method by which virus is isolated.

quality of organism
type: Class
subclass of: quality

GenBank lib_name
type: Class
subclass of: data about a genbank entry

collection state
type: Class
subclass of: data about a collection location
definition source: GROUP: FLU
definition: The name of the state where the collection occurred.

sequence received date
type: Class
subclass of: date
definition source: FLU:MK
definition: Date that the laboratory received the sequence.

genomic sequencing
type: Class
subclass of: sequencing assay
editor note: MC, 20101207: we can't say that the output information is about the input material
editor note: MC, 20101207: moved under DNA sequencing
editor note: MC, 20101207: I think genomic sequencing is an assay that has specified input some DNA (genome?) and has specified output some genotype or ICE about a sequence

urban environment
type: Class
subclass of: environment
definition source: URL:http://wordnet.princeton.edu/perl/webwn?s=urban
curator note: 20110826, MC: renamed from "urban" to "urban environment". Moved under environment.
definition: Urban environment is an environment that is characterized by densely-populated areas, such as found in cities.

human social group
type: Class
subclass of: population
definition source: URL:en.wiktionary.org/wiki/social group
definition: A human social group is a material entitiy that is a collection of humans, who share certain characteristics, interact with one another, accept expectations and obligations as members of the group, and share a common identity.

amplification protocol
type: Class
subclass of: protocol
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: realized_by
      some values from: virus amplification

headache
type: Class
subclass of: symptom
has db xref: SYMP:504
definition source: URL:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=headache
definition: A pain in the head.

organism treated with antiviral drug
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: antiviral treatment
subclass of: material_entity
definition: An organism which has been treated with antiviral drugs.

extraction protocol
type: Class
subclass of: protocol
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: realized_by
      some values from: extraction

hospitalized host
type: Class
equivalent class: Class
  intersection of: host
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: hospitalization
subclass of: material_entity
definition: A host hospitalized is a condition that indicates whether or not an organism has been hospitalized.

GenBank bac_name
type: Class
subclass of: data about a genbank entry
definition source: URL:http://www.ncbi.nlm.nih.gov/Class/FieldGuide/glossary.html#B
definition: A bac_name is a quality that identifies the bacterial artifical chromosome (bac), a large insert cloning vector capable of handling large segments of cloned DNA, typically around 150 kb, which are used in the construction of genomic libraries for genome scale sequencing projects including human, mouse, Arabidopsis, and rice.

bird band identification number
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: is about
  some values from: Aves
subclass of: Restriction
  on property: is_concretized_as
  some values from: Class
    intersection of: specifically_dependent_continuant
    intersection of: Restriction
      on property: inheres in
      some values from: bird identification band
definition: A bird band identification number is a number identifies the individual (often the host) - analagous to a name in a human.
definition source: GROUP: FLU
editor note: MC, 20101118: moved from quality of organism to identification number

antiviral treatment
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: has_role
      some values from: host role
subclass of: Restriction
  on property: has_specified_input
  some values from: antiviral drug
definition source: URL:http://www.cdc.gov/flu/professionals/antivirals/indications.htm
definition: A treatment that specifies which, if any, antiviral treatment has been administered to a host.

data about a genbank entry
type: Class
subclass of: data item
editor note: MC, 20101118: renamed "data about a genbank entry" from "qualities of genbank" and moved under data item. We should create a genbank record and use the is_about relation to link both
editor note: MC, 20101118: this is a placeholder meant to be removed when we will have the class "genbank entry", which will allow us to define current subclass using the is_about relation
editor note: MC, 08092009: those need clean up

ligated ends molecule
type: Class
subclass of: processed material
definition: A ligated ends molecule is a biological macromolecule with overhanging nucleotides that assist in the ligation process.
editor note: MC, 20101118: moved under processed material and updated definition

post disease onset sample collection period
type: Class
subclass of: time measurement datum
definition source: GROUP: FLU
definition: The time period that comprises the sample collection period when the sample was collected following the disease onset.

adult
type: Class
subclass of: life stage
definition source: URL:http://www.okaponds.com/tips.htm
definition: A bird with definitive plumage or sexually mature. Adult birds are mature, independent birds who are fully feathered for flight and capable of surviving on their own (in regards to food, shelter, etc.

duration of illness
type: Class
subclass of: time measurement datum
definition source: GROUP: FLU
editor note: MC, 20101123: moved from quality of infectious disease to duration
definition: The number of days the patient was ill.

specimen barcode
type: Class
subclass of: specimen identification number
definition: A specimen barcode is a specimen identification number formatted as an optical machine-readable representation.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Barcode
editor note: MC, 20101118: moved from "quality of specimen" under specimen identification number.

antibody titer
type: Class
subclass of: scalar measurement datum
definition: A antibody titer is output of a measurement that describes the measure of antibodies in a biomaterial.

passage history record
type: Class
subclass of: data item
editor note: See http://groups.google.com/group/influenza-ontology/browse_thread/thread/12b3fb5ef0501b5b?hl=en
definition: A passage history record is a data item recording in sequential order the hosts in which the strain has been previously subcultured in.
definition source: PERSON: Burke Squires
definition editor: PERSON: Melanie Courtot

bird identification band
type: Class
subclass of: material_entity
subclass of: Restriction
  on property: bearer_of
  some values from: Restriction
    on property: is_concretization_of
    some values from: bird band identification number
definition: A plastic or metal ring attached usually to the ankle of the bird and bearing a band identification number
definition editor: MC, 20101201: added as bearer of band identification number as per Burke's email at http://groups.google.com/group/influenza-ontology/msg/8781d389ec670463?hl=en

hemagglutination disposition
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized_by
  some values from: induced hemagglutination
definition: A disposition to initiate an hemagglutination process
definition editor: PERSON: Melanie Courtot

hemagglutinin
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: bearer_of
    some values from: hemagglutination disposition
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Hemagglutinin
editor note: MC, 20101201: added as request to PRO tracker unanswered. See http://sourceforge.net/tracker/?func=detail&aid=2945554&group_id=266825&atid=1135711
definition: Hemagglutinin is a substance that causes red blood cells to agglutinate (has disposition hemagglutination)

enrichment process
type: Class
subclass of: processual_entity
definition: the process of increasing the concentration of a particule of interest in a sample
definition editor: PERSON: Melanie Courtot

antiviral drug
type: Class
subclass of: antiviral
subclass of: Restriction
  on property: is_specified_input_of
  some values from: treatment
definition: A drug used specifically for treating viral infections.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Antiviral_drug

virus amplification
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: specimen
subclass of: Restriction
  on property: has_specified_input
  some values from: Viruses
definition: A material processing aiming at increasing the number of viruses in a specimen
definition editor: PERSON: Melanie Courtot

neuraminidase inhibitor
type: Class
subclass of: function
definition editor: PERSON: Melanie Courtot
definition: The function of inhibiting the viral neuraminidase protein, thus preventing the virus from reproducing by budding from the host cell.
definition source: WEB: http://en.wikipedia.org/wiki/Neuraminidase_inhibitor

influenza neuraminidase
type: Class
equivalent class: Class
  intersection of: neuraminidase
  intersection of: Restriction
    on property: part_of
    some values from: influenza virion
definition: A type of neuraminidase found on the surface of influenza viruses that enables the virus to be released from the host cell.
curator note: MC, 20101202: When influenza virus replicates, it attaches to the cell surface using hemagglutinin, a molecule found on the surface of the virus which binds to sialic acid groups. Sialic acids are found on various glycoproteins at the host cell surface, and the virus exploits these groups to bind the host cell. In order for the virus to be released from the cell, neuraminidase must enzymatically cleave the sialic acid groups from host glycoproteins. As an integral part of influenza replication, blocking the synthesis of neuraminidase with neuraminidase inhibitors is an effective way to treat influenza.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Viral_neuraminidase

neuraminidase inhibitor drug
type: Class
subclass of: antiviral drug
subclass of: Restriction
  on property: has_function
  some values from: neuraminidase inhibitor
definition: A drug targeted at the influenza virus, which work by blocking the function of the viral neuraminidase protein, thus preventing the virus from reproducing by budding from the host cell.
definition editor: PERSON: Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Neuraminidase_inhibitor

specimen collection
type: Class
equivalent class: Class
  union of: collecting specimen from organism
  union of: environmental material collection
subclass of: processual_entity
definition editor: PERSON: Melanie Courtot
editor note: MC, 20101203: added this class to realize the concretization of the collection protocol
definition: the process of collecting a specimen, either from an organism or from an environment

geographical location
type: Class
subclass of: site
definition: A reference to a place on the Earth, by its name or by its geographical location.
imported from: GAZ

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI branch derived
definition source: OBI_0000349
definition editor: PlanAndPlannedProcess Branch
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
editor preferred term: conditional specification
has curation status: metadata complete

measurement unit label
type: Class
subclass of: label
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor preferred term: measurement unit label
has curation status: pending final vetting

objective specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor preferred term: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: pending final vetting

narrative object
type: Class
subclass of: information content entity
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition: A narrative object is an information content entity that is a set of propositions.
example of usage: Examples of narrative objects are reports, journal articles, and patents submission.
definition source: OBI_0000013
editor note: agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
definition source: group:OBI
editor preferred term: narrative object
definition editor: person:Chris Stoeckert
has curation status: uncurated

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

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

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Melanie Courtot
definition: Software is a plan specification which is a series of encoded instructions that can be directly executed by a processing unit or transformed in to a form that can be. For programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond to the tokenized version of the text stripped of comments.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
editor preferred term: software
has curation status: metadata complete

journal article
type: Class
subclass of: report
example of usage: Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
definition source: OBI_0000159
definition: a report that is published in a journal
definition source: group:OBI
editor preferred term: journal article
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
has curation status: metadata complete

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: is_concretization_of
    some values from: information content entity
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
definition: A quality of an information bearer that imparts the information content
definition editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The pattern in ink on a page of a paperback novel.
editor preferred term: information carrier
has curation status: pending final vetting

model number
type: Class
subclass of: symbol
definition: A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: Person: Alan Ruttenberg
editor note: manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
editor preferred term: model number
has curation status: pending final vetting

programming language
type: Class
subclass of: plan specification
definition: A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
definition source: OBI_0000058
example of usage: R, Perl, Java
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: programming language
has curation status: metadata complete

data item
type: Class
subclass of: information content entity
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
alternative term: data
editor preferred term: data item
has curation status: pending final vetting

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
definition editor: PERSON: Jonathan Rees
definition: a smallish, word-like datum...
editor preferred term: symbol

numeral
type: Class
subclass of: symbol
definition: A symbol that denotes a number.
definition editor: PERSON: Jonathan Rees
editor preferred term: numeral

information content entity
type: Class
subclass of: generically_dependent_continuant
subclass of: Restriction
  on property: is about
  some values from: entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
definition editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor preferred term: information content entity
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
has curation status: pending final vetting

integer numeral
type: Class
subclass of: numeral
definition editor: PERSON: Jonathan Rees
definition: a numeral that denotes an integer
editor preferred term: integer numeral

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
example of usage: 10 feet. 3 ml.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
has curation status: metadata complete

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable_entity
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
has curation status: metadata incomplete

time trigger
type: Class
subclass of: conditional specification
definition source: OBI branch derived
definition source: OBI_0000331
definition editor: PlanAndPlannedProcess Branch
definition: revisit?
editor preferred term: time trigger
has curation status: uncurated

dot plot
type: Class
subclass of: graph
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
example of usage: Dot plot of SSC-H and FSC-H.
definition source: OBI_0000123
editor preferred term: dot plot
definition source: group:OBI
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

graph
type: Class
subclass of: diagram
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
definition source: OBI_0000240
definition editor: PERSON: Lawrence Hunter
editor preferred term: graph
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson Lister
has curation status: pending final vetting

rule
type: Class
subclass of: conditional specification
editor note: MSI
definition source: OBI_0500021
definition source: PRS
definition editor: PRS
definition: a rule is an executable which guides, defines, restricts actions
example of usage: example to be added
editor preferred term: rule
has curation status: uncurated

contour plot
type: Class
subclass of: graph
example of usage: Contour plot of SSC-H, FSC-H, and FL1-H.
definition source: OBI_0000246
editor preferred term: contour plot
editor note: generically_dependent_continuants
definition source: group:Flow Cytometry community
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

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

software interpreter
type: Class
subclass of: algorithm
definition: An algorithm that takes, as input, some digital entity, and takes action driven by the information content of that algorithm
editor note: Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
definition source: OBI_0000199
example of usage: R program, Perl interpreter, Java virtual machine
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: software interpreter
has curation status: metadata complete

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

density plot
type: Class
subclass of: graph
definition: A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
example of usage: Density plot of SSC-H and FSC-H.
definition source: OBI_0000179
editor preferred term: density plot
definition source: group:Flow Cytometry community
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

report
type: Class
subclass of: document
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
definition source: GROUP: OBI
definition source: OBI_0000099
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Chris Stoeckert
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
editor preferred term: report
has curation status: pending final vetting

source code module
type: Class
subclass of: directive information entity
definition: A source code module is a directive information entity that specifies, using a programming language, some algorithm.
definition source: OBI_0000039
example of usage: The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
definition source: group:OBI
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: source code module
has curation status: uncurated

data format specification
type: Class
subclass of: directive information entity
editor note: 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
definition: A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
definition source: OBI branch derived
definition source: OBI_0000187
definition editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: metadata incomplete

data set
type: Class
subclass of: data item
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
definition source: OBI_0000042
editor preferred term: data set
definition source: group:OBI
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: metadata complete

image
type: Class
subclass of: figure
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
definition source: OBI_0000030
definition source: group:OBI
editor preferred term: image
definition editor: person:Alan Ruttenberg
definition editor: person:Allyson
definition editor: person:Chris Stoeckert
has curation status: ready for release

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

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has_part
  some values from: objective specification
subclass of: Restriction
  on property: has_part
  some values from: action specification
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
definition editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
editor preferred term: plan specification
has curation status: metadata complete

measurement datum
type: Class
subclass of: data item
editor note: 2/2/2009 is_specified_output of some assay?
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred term: measurement datum
definition editor: person:Chris Stoeckert
has curation status: metadata complete

version number
type: Class
subclass of: symbol
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
definition editor: GROUP: IAO
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
editor preferred term: version number
has curation status: uncurated

serial number
type: Class
subclass of: symbol
definition: A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
editor note: Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
editor preferred term: serial number
has curation status: uncurated

lot number
type: Class
subclass of: symbol
definition: A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
definition editor: GROUP: IAO
alternative term: batch number
editor preferred term: lot number
has curation status: uncurated

setting datum
type: Class
subclass of: data item
editor note: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
definition: A settings datum is a datum that denotes some configuration of an instrument.
editor note: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
has curation status: uncurated

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

material information bearer
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: bearer_of
    some values from: Restriction
      on property: is_concretization_of
      some values from: information content entity
definition: An information bearer is a material_entity in which a concretization of an information content entity inheres.
definition editor: GROUP: IAO
example of usage: a hard drive, a piece of paper with writing on it, a brain
editor preferred term: material information bearer
has curation status: metadata complete

histogram
type: Class
subclass of: graph
definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: histogram
has curation status: ready for release

heatmap
type: Class
subclass of: graph
definition: A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: heatmap
has curation status: ready for release

Venn diagram
type: Class
subclass of: graph
definition: A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
editor preferred term: Venn diagram
definition source: WEB: http://en.wikipedia.org/wiki/Venn_diagram
has curation status: ready for release

dendrogram
type: Class
subclass of: graph
definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
example of usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: dendrogram
has curation status: ready for release

scatter plot
type: Class
subclass of: graph
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
editor preferred term: scatter plot
alternative term: scattergraph
has curation status: ready for release

photograph
type: Class
subclass of: image
definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Joanne Luciano
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wiktionary.org/wiki/photograph
has curation status: ready for release

photographic print
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: bearer_of
    some values from: Restriction
      on property: is_concretization_of
      some values from: photograph
definition: A photographic print is a material entity upon which a photograph generically depends.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
editor preferred term: photographic print
has curation status: pending final vetting

obsolescence reason specification
type: Class
equivalent class: Class
  one of: other
  one of: terms merged
  one of: term imported
  one of: placeholder removed
  one of: failed exploratory term
  one of: term split
subclass of: data about an ontology part
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
editor note: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor preferred term: obsolescence reason specification
has curation status: pending final vetting

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

citation
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: document
definition editor: PERSON: Lawrence Hunter
example of usage: Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
definition: a textual entity intended to identify a particular publication
editor preferred term: citation
has curation status: pending final vetting

author identification
type: Class
subclass of: textual entity
definition: A textual entity intended to identify a particular author
example of usage: L. Hunter
definition editor: PERSON: Lawrence Hunter
editor preferred term: author identification
has curation status: pending final vetting

institutional identification
type: Class
subclass of: textual entity
definition: A textual entity intended to identify a particular institution
definition editor: PERSON: Lawrence Hunter
example of usage: University of Colorado Denver School of Medicine
editor preferred term: institutional identification
has curation status: pending final vetting

caption
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: figure
definition: A textual entity that describes a figure
example of usage: Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
definition editor: PERSON: Lawrence Hunter
editor preferred term: caption
has curation status: pending final vetting

document title
type: Class
subclass of: textual entity
definition: A textual entity that names a document
definition editor: PERSON: Lawrence Hunter
example of usage: Textual characteristics of traditional and Open Access scientific journals are similar
editor preferred term: document title
has curation status: pending final vetting

table
type: Class
subclass of: textual entity
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
definition editor: PERSON: Lawrence Hunter
editor preferred term: table
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting

table of abbreviations
type: Class
subclass of: table
definition: A table where the constituent texts are abbreviations and their expansions
example of usage: IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
definition editor: PERSON: Lawrence Hunter
editor preferred term: table of abbreviations
has curation status: pending final vetting

figure
type: Class
subclass of: information content entity
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
example of usage: Any picture, diagram or table
definition editor: PERSON: Lawrence Hunter
editor preferred term: figure
has curation status: metadata complete

diagram
type: Class
subclass of: figure
definition: A figure that expresses one or more propositions
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
definition editor: PERSON: Lawrence Hunter
editor preferred term: diagram
has curation status: metadata complete

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

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

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

patent
type: Class
subclass of: document
definition: A document that has been accepted by a patent authority
definition editor: PERSON: Lawrence Hunter
example of usage: US Patent 6,449,603
editor preferred term: patent
has curation status: metadata complete

document part
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part_of
  some values from: document
example of usage: An abstract, introduction, method or results section.
definition editor: PERSON: Lawrence Hunter
definition: an information content entity that is part of a document
editor preferred term: document part
has curation status: metadata complete

abstract
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document
definition: A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
definition editor: PERSON: Lawrence Hunter
example of usage: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
editor preferred term: abstract
has curation status: metadata complete

introduction to a publication about an investigation
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: objective specification
definition: A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
definition editor: PERSON: Lawrence Hunter
example of usage: Section labelled 'introduction' of a typical scientific journal article
alternative term: introduction
editor preferred term: introduction to a publication about an investigation
has curation status: metadata complete

methods section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design
definition: A part of a publication about an investigation that is about the study design of the investigation
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
editor preferred term: methods section
has curation status: metadata complete

results section
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: study design execution
definition: A part of a publication about an investigation that is about a study design execution
definition editor: PERSON: Lawrence Hunter
example of usage: The section labelled 'results' in a typical scientific journal article
editor preferred term: results section
has curation status: metadata complete

discussion section of a publication about an investigation
type: Class
subclass of: document part
definition: A part of a publication about an investigation that is about the study interpretation of the investigation
definition editor: PERSON: Lawrence Hunter
alternative term: discussion section
editor preferred term: discussion section of a publication about an investigation
has curation status: metadata complete

references section
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: citation
definition: A part of a document that has citations as parts
definition editor: PERSON: Lawrence Hunter
example of usage: The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
editor preferred term: references section
has curation status: metadata complete

author list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: author identification
example of usage: Lawrence Hunter and Kevin Brettonel Cohen
definition editor: PERSON: Lawrence Hunter
editor preferred term: author list
definition: part of a document that enumerates the authors of the document
has curation status: metadata complete

institution list
type: Class
subclass of: document part
subclass of: Restriction
  on property: has_part
  some values from: institutional identification
definition editor: PERSON: Lawrence Hunter
example of usage: The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
editor preferred term: institution list
definition: part of a document that has parts that are institution identifications associated with the authors of the document
has curation status: metadata complete

author contributions section
type: Class
subclass of: document part
definition: A part of a publication that is about the specific contributions of each author
example of usage: LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
definition editor: PERSON: Lawrence Hunter
editor preferred term: author contributions section
has curation status: metadata complete

acknowledgements section
type: Class
subclass of: document part
definition editor: PERSON: Lawrence Hunter
definition: Part of a publication that is about the contributions of people or institutions other than the authors.
example of usage: The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
editor preferred term: acknowledgements section
has curation status: metadata complete

footnote
type: Class
subclass of: document part
subclass of: Restriction
  on property: is about
  some values from: document part
definition: A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
definition editor: PERSON: Lawrence Hunter
example of usage: The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
alternative term: endnote
editor preferred term: footnote
has curation status: metadata complete

supplementary material to a document
type: Class
subclass of: document part
definition editor: PERSON: Lawrence Hunter
alternative term: appendix
definition: part of a document that is segregated from the rest of the document due to its size
alternative term: supplementary material
editor preferred term: supplementary material to a document
has curation status: metadata complete

table of contents
type: Class
subclass of: table
definition: A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter
editor preferred term: table of contents
has curation status: pending final vetting

table of figures
type: Class
subclass of: table
definition: A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
definition editor: PERSON: Lawrence Hunter
editor preferred term: table of figures
has curation status: pending final vetting

running title
type: Class
subclass of: document title
definition: A shorter version of a document title
definition editor: PERSON: Lawrence Hunter
editor preferred term: running title
has curation status: pending final vetting

copyright section
type: Class
subclass of: document part
definition: A document part that describes legal restrictions on making or distributing copies of the document
definition editor: PERSON: Lawrence Hunter
example of usage: This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
editor preferred term: copyright section
has curation status: metadata complete

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: zero_dimensional_region
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
definition editor: Alan Ruttenberg
has curation status: metadata complete

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero_dimensional_region
    intersection of: Restriction
      on property: part_of
      some values from: one_dimensional_region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero_dimensional_region
    intersection of: Restriction
      on property: part_of
      some values from: two_dimensional_region
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero_dimensional_region
    intersection of: Restriction
      on property: part_of
      some values from: three_dimensional_region
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
definition editor: Alan Ruttenberg
has curation status: uncurated

length measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Restriction
  on property: is quality measurement of
  some values from: length
subclass of: Restriction
  on property: has measurement unit label
  some values from: length unit
definition: A scalar measurement datum that is the result of measurement of length quality
definition editor: Alan Ruttenberg
has curation status: metadata incomplete

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
definition editor: Alan Ruttenberg
definition source: Barry Smith, Werner Ceusters
example of usage: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: mass unit
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measurement of mass quality
definition editor: Person:Alan Ruttenberg
has curation status: metadata incomplete

hypothesis textual entity
type: Class
subclass of: textual entity
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A textual entity that expresses an assertion that is intended to be tested.
definition editor: Person:Alan Ruttenberg
editor preferred term: hypothesis textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: process
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition: A scalar measurement datum that is the result of measuring a temporal interval
definition editor: Person:Alan Ruttenberg
has curation status: metadata incomplete

postal address
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is about
  some values from: geographical location
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59

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

data item extraction from journal article
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  some values from: journal article
definition: a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
definition editor: Person:Alan Ruttenberg
has curation status: metadata complete

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
definition editor: Bjoern Peters
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
definition: a planned process in which a document is created or added to by including the specified input in it.
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
has curation status: pending final vetting

line graph
type: Class
subclass of: graph
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
definition source: GROUP:OBI
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
alternative term: line chart
editor preferred term: line graph
has curation status: ready for release

assigning a centrally registered identifier
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_participant
  some values from: CRID symbol
subclass of: Restriction
  on property: has_participant
  some values from: CRID registry
example of usage: A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
definition editor: Person:Alan Ruttenberg
definition editor: Person:Bjoern Peters
definition editor: Person:Melanie Courtot
definition: a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
has curation status: metadata complete

associating information with a CRID in the CRID registry
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: CRID symbol
subclass of: Restriction
  on property: has_participant
  some values from: CRID registry
definition: A planned process in which a CRID registry associates an information content entity with a CRID symbol
definition editor: PERSON:Alan Ruttenberg
has curation status: metadata complete

CRID symbol
type: Class
subclass of: symbol
definition: A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
editor note: IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
definition source: Original proposal from Bjoern, discussions at IAO calls
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
example of usage: PMID:12345, 12345 in a database column which has header "pubmedID"

CRID
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has_part
  some values from: CRID symbol
alternative term: Centrally Registered IDentifier
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
example of usage: Entries in a Column of which the header is "Pubmed ID"
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
definition source: Original proposal from Bjoern, discussions at IAO calls
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
example of usage: PMID:12345
example of usage: The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
example of usage: The following sentence contains a CRID: "The article with Pubmed ID: 19918065".

CRID registry
type: Class
subclass of: data set
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
editor note: IAO call, 20101124: PubMed registry is an instance of CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
has curation status: metadata incomplete

looking up a CRID
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: CRID symbol
subclass of: Restriction
  on property: has_participant
  some values from: CRID registry
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
has curation status: metadata complete

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: metadata incomplete

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has_part
  some values from: time stamped measurement datum
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
definition editor: Alan Ruttenberg
alternative term: experimental time series
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete

symbiont role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates_in
      some values from: symbiosis, encompassing mutualism through parasitism
disjoint with: pathogen role
disjoint with: infectious agent transporter role
disjoint with: reservoir of infectious agent role
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition editor: Alexander Diehl
definition editor: Albert Goldfain
comment: The role is realized in symbiosis.
definition: A role borne by an organism in symbiosis.
definition editor: Lindsay Cowell

mutualist role
type: Class
subclass of: symbiont role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates_in
      some values from: mutualism
definition: A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis.
definition editor: Alexander Diehl
comment: The role is realized in processes that result in the growth, survival, or fitness advantage of either organism.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

commensal role
type: Class
subclass of: symbiont role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates_in
      some values from: commensalism
definition editor: Alexander Diehl
comment: The role is realized in processes that result in the commensal's growth, survival, or fitness advantage.
definition: A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis, but the other symbiont is neither advantaged nor disadvantaged.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

parasite role
type: Class
subclass of: symbiont role
comment: In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen.
comment: The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction.
definition: A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

infectious agent role
type: Class
subclass of: pathogen role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: infectious agent
    intersection of: Restriction
      on property: located_in
      some values from: host
definition: A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

pathogen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: pathogen
disjoint with: infectious agent transporter role
disjoint with: reservoir of infectious agent role
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic 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 pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles.

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_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: has_part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has_part
        some values from: transmission process
      intersection of: Restriction
        on property: has_part
        some values from: Class
definition editor: Albert Goldfain
definition: An infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).
alternative term: opportunitistic pathogenic disposition

primary infectious disposition
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: has_part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has_part
        some values from: transmission process
      intersection of: Restriction
        on property: has_part
        some values from: Class
subclass of: infectious disposition
definition editor: Alexander Diehl
comment: A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease."
definition editor: Lindsay Cowell
comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
definition editor: Albert Goldfain
definition: An infectious disposition to become part of a disorder in organisms that have intact defenses.

symbiont host role
type: Class
subclass of: host role
subclass 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: extended organism
        intersection of: Restriction
disjoint with: pathogen host role
comment: The role is realized in processes in which the host makes the relevant environmental resources available to its partner in symbiosis. A bearer of a symbiont host role is bearer also of a symbiont role.
definition editor: Lindsay Cowell
definition: A host role borne by an organism in virtue of the fact that its extended organism contains a second organism and provides an environment supportive for the survival, growth, maturation, or reproduction of that organism.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: The relevant environmental resources may include nutrient resources, warmth, or moisture.

definitive host role
type: Class
subclass of: symbiont host role
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host.
comment: The role is realized in developmental and reproduction processes of the host's partner in symbiosis.
alternative term: primary host role

intermediate host role
type: Class
subclass of: symbiont host role
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The role is realized in developmental processes of the host's partner in symbiosis.
definition editor: Albert Goldfain
definition: A symbiont host role borne by an organism in virtue of the fact that its 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.
alternative term: secondary host role

paratenic host role
type: Class
subclass of: symbiont host role
comment: The role is realized in developmental processes of the host's partner in symbiosis.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, but the host is not required for continuation of the partner's life cycle.
definition editor: Albert Goldfain

dead-end host role
type: Class
subclass of: symbiont host role
definition: A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
alternative term: incidental host role

parasite host role
type: Class
subclass of: symbiont host role
subclass 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: extended organism
        intersection of: Restriction
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced.
comment: The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction.
comment: The partner in symbiosis bears the parasite role.
definition editor: Lindsay Cowell

infectious agent host role
type: Class
subclass of: pathogen host role
subclass 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: extended organism
        intersection of: Restriction
definition: A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role.

pathogen host role
type: Class
subclass of: host role
subclass 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: extended organism
        intersection of: Restriction
definition editor: Albert Goldfain
comment: Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen.

infectious agent carrier role
type: Class
subclass of: infectious agent host role
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent.

infectious agent 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: infectious agent
  intersection of: Restriction
    on property: realized_by
    all values from: Suggested label: indirect pathogen transmission process
disjoint with: reservoir of infectious agent role
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition editor: Lindsay Cowell
definition: A role borne by a material entity in virtue of the fact that an infectious agent is located in or on the entity and the entity has the capability to transfer (either actively or passively) the infectious agent from one location to another.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: The role is realized in a process that transfers an infectious organism from one location to another.

infectious agent vector role
type: Class
equivalent class: Class
  intersection of: infectious agent transporter role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: location_of
        some values from: infectious agent
  intersection of: Restriction
    on property: realized_by
    all values from: Suggested label: indirect pathogen transmission process
subclass of: infectious agent transporter role
definition editor: Alexander Diehl
definition: An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious.
comment: The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

mechanical vector of infectious agent role
type: Class
subclass of: infectious agent vector role
subclass of: Class
  intersection of: infectious agent vector role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: location_of
        some values from: Class
  intersection of: Restriction
    on property: realized_by
    all values from: Suggested label: indirect pathogen transmission process
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent does not multiply in or on the vector.

biological vector of infectious agent role
type: Class
subclass of: infectious agent vector role
subclass of: Class
  intersection of: infectious agent vector role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: location_of
        some values from: Class
  intersection of: Restriction
    on property: realized_by
    all values from: Suggested label: indirect pathogen transmission process
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in or on the vector.

infectious agent vehicle role
type: Class
equivalent class: Class
  intersection of: infectious agent 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: infectious agent
  intersection of: Restriction
    on property: realized_by
    all values from: Suggested label: indirect pathogen transmission process
subclass of: infectious agent transporter role
definition editor: Albert Goldfain
comment: Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles.
definition: An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

biological vehicle of infectious agent role
type: Class
subclass of: infectious agent vehicle role
definition editor: Albert Goldfain
comment: Examples include blood, serum, tissue, or fresh produce.
definition editor: Alexander Diehl
definition: An infectious agent 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.
definition editor: Lindsay Cowell

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

reservoir of infectious agent role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material_entity
    intersection of: Restriction
      on property: location_of
      some values from: infectious agent
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic 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 a material entity in virtue of the fact that it is a habitat in which infectious agents can persist and multiply and from which they can be transmitted in virtue of prevailing practices of potential hosts.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: If the material entity bearing the reservoir role is an organism, then this organism also bears the host role. The organism may also bear the vector role.
definition editor: Lindsay Cowell
comment: The role is realized in a process that has as part life and multiplication processes of an infectious agent and a transmission process.

virulence factor disposition
type: Class
subclass of: disposition
subclass 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: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
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: disposition
subclass of: Restriction
  on property: inheres in
  some values from: molecular entity
disjoint with: adhesion disposition
disjoint with: invasion disposition
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Alexander Diehl
definition: A 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.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

exotoxin disposition
type: Class
subclass of: toxin disposition
definition editor: Albert Goldfain
comment: The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix.
definition: A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

infectious agent portal of entry role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: anatomical entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: part_of
        some values from: transmission process
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic 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 anatomical entity in virtue of the fact that it serves as the site through which an infectious agent enters a host.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: The role is realized in a process by which an infectious agent enters a host.
definition editor: Lindsay Cowell

infectious agent portal of exit role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: anatomical entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: part_of
        some values from: transmission process
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host.
comment: The role is realized in a process by which an infectious agent exists a host.

disinfectant 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: has_disposition
        some values from: antimicrobial disposition
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: Restriction
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
comment: The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity.
definition editor: Alexander Diehl
definition: A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to a non-living entity.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

antiseptic 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: has_disposition
        some values from: antimicrobial disposition
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: Restriction
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity.
definition: A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to an anatomical entity of a living organism.
definition editor: Albert Goldfain

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 editor: Alexander Diehl
comment: The role is realized in a process by which the infectious disorder is established in the host.
definition: A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

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
comment: The role is realized in a process by which the infectious disorder is established in the host.
definition: A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

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: 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
  intersection of: Restriction
    on property: realized_by
    all values from: infectious disease course
subclass of: disease
comment: The disposition is realized in an infectious disease course.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A disease whose physical basis is an infectious disorder.
definition editor: Lindsay Cowell
alternative term: tranmissible disease

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_by
    all values from: adhesion to host
disjoint with: invasion disposition
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
comment: The disposition is realized in an adherence to host process.
definition editor: Lindsay Cowell
definition: A disposition borne by a biological macromolecule that is the disposition to participate in adherence to host.
definition editor: Albert Goldfain
definition editor: Alexander Diehl

invasion 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_by
    all values from: Restriction
      on property: positively_regulates
      some values from: entry into host through host barriers
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Alexander Diehl
definition: A disposition borne by a biological macromolecule that is the disposition to facilitate breach of host epithelial barriers or entry into and survival in host cells.
definition editor: Lindsay Cowell
comment: A molecule with the invasion disposition is referred to as an invasion factor or invasin.
definition editor: Albert Goldfain

antimicrobial disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: Restriction
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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to kill or inhibit the development or reproduction of microorganisms.
definition editor: Alexander Diehl
definition editor: Albert Goldfain
comment: The disposition is realized in the killing or growth inhibition of microorganisms.
definition editor: Lindsay Cowell
comment: Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic.

antiviral disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: negative regulation of viral reproduction
        union of: Restriction
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A disposition to kill or inhibit the lifecycle of viruses.
definition editor: Albert Goldfain

antifungal disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: Restriction
disjoint with: antibacterial disposition
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
definition: A disposition to kill or inhibit the development or reproduction of fungal organisms.
definition editor: Albert Goldfain
definition editor: Alexander Diehl

antibacterial disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: Restriction
disjoint with: antiparasitic 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
alternative term: antibiotic disposition
definition: A disposition to kill or inhibit the reproduction of bacteria.
definition editor: Albert Goldfain

antiparasitic disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Class
        union of: Restriction
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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans.
definition: A disposition to kill or inhibit the development or reproduction of eukaryotic parasites.

protective resistance
type: Class
subclass of: disposition
subclass 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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
comment: This mitigation sometimes takes the form of protection. CCR5 mutations protect T cells from HIV invasion. If a patient's tumor is resistant to chemotherapy, then the patient is resistant to something beneficial, but the tumor is resistant to something damaging. In this case protective resistance inheres in the tumor's cells and in the tumor, but not in the patient. In some cases, the quality that confers the protective resistance will confer other dispositions that damage the entity, such as is the case with sickle cell trait.
definition editor: Alexander Diehl
comment: The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant.
definition editor: Lindsay Cowell
definition: A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity.
definition editor: Albert Goldfain

resistance to drug
type: Class
subclass of: protective resistance
disjoint with: resistance to infectious agent
definition editor: Albert Goldfain
definition: A protective resistance that mitigates the damaging effects of a drug.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
alternative term: drug resistance

resistance to infectious agent
type: Class
subclass of: protective resistance
subclass of: Restriction
  on property: inheres in
  some values from: organism
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent.
definition 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_by
    all values from: Restriction
      on property: realizes
      some values from: immunity to infectious agent
subclass of: collective resistance disposition
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts in the population to susceptible individuals in the population and thereby mitigating the damaging effects of the infectious agent on the population.

immunity to infectious agent
type: Class
subclass of: resistance to infectious agent
definition: A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
comment: We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response.
definition editor: Albert Goldfain
alternative term: protective immunity to infectious agent

sterilizing immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An immunity to infectious agent that results in elimination of the infectious agent from the host.
comment: Sterilizing immunity is typically conferred by neutralizing antibodies.

pathogenic disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: results_in_formation_of
        some values from: disorder
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
comment: The disposition is realized in processes that create a disorder.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
definition: A disposition to initiate processes that result in a disorder.
definition editor: Albert Goldfain
alternative term: pathogenicity

invasive disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: infectious agent
  intersection of: Restriction
    on property: realized_by
    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: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Albert Goldfain
definition: A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

infectious disposition
type: Class
subclass of: pathogenic disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: has_part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has_part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has_part
        some values from: transmission process
definition: A pathogenic disposition that inheres in an organism and is the disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, and (3) to become part of a disorder in the host.
definition editor: Lindsay Cowell
comment: The disposition is realized in a process that has as part a transmission process, an establishment in host process, and a process in which an entity becomes part of a disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an entity with an infectious disposition and to undergo processes intiated by that entity that result in a disorder.
definition editor: Albert Goldfain
definition editor: Alexander Diehl

zoonotic disposition
type: Class
subclass of: infectious disposition
definition editor: Albert Goldfain
comment: An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host.

reverse zoonotic disposition
type: Class
subclass of: infectious disposition
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
comment: An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.
definition editor: Alexander Diehl
definition: An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host.

collective disposition
type: Class
subclass of: disposition
subclass of: Restriction
  on property: inheres in
  some values from: object_aggregate
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
comment: "... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition.
definition editor: Lindsay Cowell
definition: A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection.
definition editor: Albert Goldfain
comment: The disposition is realized in a process that has as part realizations of some of the individual dispositions.
definition editor: Alexander Diehl

immunosuppressed organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: participates_in
    some values from: Class
      union of: pathologic immunosuppression
      union of: pregnancy-induced immunosuppression
subclass of: organism
disjoint with: immunocompetent organism
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism that is experiencing pregnancy-induced or pathologic immunosuppression.
definition editor: Lindsay Cowell

immunocompetent organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_disposition
    some values from: immunocompetence
subclass of: organism
disjoint with: immunodeficient organism
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism that has immunocompetence.
definition editor: Lindsay Cowell

contagiousness
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: infectious agent host
  intersection of: Restriction
    on property: realized_by
    all values from: horizontal pathogen transmission process
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
comment: Highly contagious infections, those with a relatively high likelihood of spread, are referred to as contagious and are those for which spread is likely as a result of data-to-day activities of the host.
definition editor: Alexander Diehl
definition editor: Albert Goldfain
comment: The disposition is realized in a horizontal transmission process.
definition: A disposition that inheres in a host of infectious agent and is a disposition to transmit infectious agents to organisms of the same Species through casual contact with a high likelihood of realization.

colonized host
type: Class
equivalent class: Class
  intersection of: organism
  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
subclass of: organism
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An organism that contains a colony in or on its extended organism.

infected organism
type: Class
equivalent class: Class
  intersection of: organism
  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
subclass of: organism
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism that has an infection in or on its extended organism.

co-infected organism
type: Class
subclass of: infected organism
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism that has two infections with distinct Species of infectious agents.

infectious agent transmissibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition editor: Alexander Diehl
comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process.

infectivity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: This quality is measured by the proportion of exposed who become infected.
definition: A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
definition editor: Albert Goldfain

virulence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
definition editor: Alexander Diehl
definition: A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

susceptibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: material_entity
comment: Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.
definition: A quality that inheres in an entity and is the degree to which it can be harmed by another entity.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl

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 editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.

drug susceptibility
type: Class
subclass of: susceptibility
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug.
definition editor: Alexander Diehl

drug susceptibility of infectious agent
type: Class
subclass of: drug susceptibility
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A 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.

complex infection
type: Class
subclass of: infection
comment: DL needs 'different species'
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infection comprised of infectious organisms from different Species.
alternative term: mixed infection
alternative term: polymicrobial infection

extracellular infection
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: has_part
    some values from: Class
      intersection of: infectious agent
      intersection of: Class
        complement of: Restriction
subclass of: infection
disjoint with: intracellular infection
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host.

intracellular infection
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: has_part
    some values from: Class
      intersection of: infectious agent
      intersection of: Restriction
        on property: located_in
        some values from: cell
subclass of: infection
disjoint with: viremia
disjoint with: bacteremia
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection for which the infectious agents that are part of the infection persist inside host cells.

systemic infection
type: Class
subclass of: infection
disjoint with: local infection
comment: DL needs 'distributed throughout'
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection for which the infectious agents that are part of the infection are distributed throughout the host.

local infection
type: Class
subclass of: infection
disjoint with: bacteremia
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: DL needs 'relatively small area'
definition: An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body.
definition editor: Lindsay Cowell

focal infection
type: Class
subclass of: local infection
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection.

acute infectious disease course
type: Class
subclass of: infectious disease course
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.

infectious disease incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Alexander Diehl
definition editor: Albert Goldfain
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.
definition editor: Lindsay Cowell
definition: A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time.

infection incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Albert Goldfain
definition editor: Alexander Diehl
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.
definition: A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time.
definition editor: Lindsay Cowell

infectious disease incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
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.
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time in whom the infectious disease begins during the specified period of time.
definition editor: Lindsay Cowell
alternative term: cumulative incidence of infectious disease

infection incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
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.
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time in whom the infectious disease begins during the specified period of time.
alternative term: cumulative incidence of infection

infectious disease incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Lindsay Cowell
definition: A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
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.
definition editor: Albert Goldfain
definition editor: Alexander Diehl

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

infectious disease prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
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.
definition editor: Albert Goldfain
definition: A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.

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

infectious agent seroprevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Albert Goldfain
definition editor: Alexander Diehl
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.
definition editor: Lindsay Cowell
definition: A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time.

infectious disease mortality rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
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.
definition: A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time.

infectious disease endemicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir.
definition editor: Albert Goldfain
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 endemic level
type: Class
subclass of: infectious disease prevalence
definition editor: Alexander Diehl
comment: Infectious disease endemic level is relational to previous prevalences of the disease.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infectious disease prevalence that is typical for an infectious disease in an organism population.

infectious disease endemic rate
type: Class
subclass of: infectious disease incidence rate
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease.
definition editor: Albert Goldfain
definition: An infectious disease incidence rate that is typical for an infectious disease in an organism population.

infectious disease hyper-endemicity
type: Class
subclass of: infectious disease endemicity
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population.
comment: Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally.

infectious disease sporadicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence.
comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease.
definition editor: Alexander Diehl

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

long-term non-progressing infectious disease course
type: Class
subclass of: chronic infectious disease course
definition: A chronic infectious disease course that does not progress to severe stages for a long period of time.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

immunization against infectious agent
type: Class
equivalent class: Class
  intersection of: processual_entity
  intersection of: Restriction
    on property: has_output
    some values from: Restriction
      on property:
        inverse of: has_material_basis_in
      some values from: immunity to infectious agent
subclass of: processual_entity
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A process by which an organism acquires immunity to an infectious agent.

active immunization against infectious agent
type: Class
subclass of: immunization against infectious agent
definition editor: Albert Goldfain
definition: An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
alternative term: inoculation

vaccination against infectious agent
type: Class
subclass of: active immunization against infectious agent
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An active immunization that begins with exposure of an organism to a vaccine.
definition editor: Lindsay Cowell

variolation
type: Class
subclass of: active immunization against infectious agent
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox.
definition editor: Lindsay Cowell

passive immunization against infectious agent
type: Class
subclass of: immunization against infectious agent
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent.
editor note: Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus.
definition editor: Lindsay Cowell

infectious disease epidemic
type: Class
subclass of: processual_entity
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
definition editor: Alexander Diehl
editor note: For a particular instance of infectious disease epidemic, signficance is determined based on the infectious disease incidence that is typical for an infectious disease for the particular population and time period.
alternative term: infectious disease outbreak

infectious disease pandemic
type: Class
subclass of: processual_entity
definition: A process in which multiple infectious disease epidemics 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.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

infectious disorder
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: disorder
subclass of: infection
subclass of: disorder
disjoint with: immunodeficiency
disjoint with: anatomical entity
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: An infection that is clinically abnormal.

viremia
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: has_part
    some values from: Class
      intersection of: infectious agent
      intersection of: Viruses
subclass of: extracellular infection
disjoint with: bacteremia
definition editor: Lindsay Cowell
comment: DL needs FMA term.
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An infection that has as part virus particles located in the blood.

bacteremia
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: has_part
    some values from: Class
      intersection of: infectious agent
      intersection of: Bacteria
subclass of: extracellular infection
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: DL needs FMA term.
definition editor: Albert Goldfain
definition: An infection that has as part bacteria located in the blood.

virion
type: Class
subclass of: Viruses
definition editor: Melanie Courtot
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules.

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

infected population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has_part
    some values from: infected organism
  intersection of: Restriction
    on property: has_part
    all values from: infected organism
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism population whose members have an infection.

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 editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism population in whose members an infectious disease is being realized.

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 editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An organism population whose members each have an infectious disposition.

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

normal resident microbiota population
type: Class
subclass of: organism population
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism population whose members are particpating in non-parasitic symbiosis with a particular host.
definition editor: Lindsay Cowell
alternative term: normal resident microflora population

incubation period
type: Class
subclass of: temporal_interval
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?).

communicability period
type: Class
subclass of: temporal_interval
definition: A continuous temporal interval during which contagiousness inhering in the bearer of a host role.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain

symbiont
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: symbiont role
subclass of: organism
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism bearing a symbiont role.

obligatory symbiont
type: Class
subclass of: symbiont
subclass of: Restriction
  on property: has_role
  some values from: symbiont role
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism that can only reach developmental maturity, replicate, or persist in symbiosis.

mutualist
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: mutualist role
subclass of: symbiont
definition editor: Albert Goldfain
definition: An organism bearing a mutualist role.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

commensal
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: commensal role
subclass of: symbiont
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism bearing a commensal role.
definition editor: Lindsay Cowell

parasite
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: parasite role
subclass of: symbiont
definition: A organism bearing a parasite role.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

pathogen
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: pathogenic disposition
subclass of: material_entity
disjoint with: fomite
disjoint with: disinfectant
disjoint with: antiseptic
disjoint with: immunodeficiency
disjoint with: anatomical entity
definition: A material entity with a pathogenic disposition.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

primary pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_disposition
    some values from: primary infectious disposition
subclass of: infectious agent
definition editor: Alexander Diehl
alternative term: principal pathogen
definition editor: Albert Goldfain
definition: An infectious agent with a primary infectious disposition.
definition editor: Lindsay Cowell

host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: host role
subclass of: organism
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism bearing a host role.
definition editor: Lindsay Cowell

definitive host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: definitive host role
subclass of: host
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism bearing a definitive host role.
alternative term: primary host

intermediate host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: intermediate host role
subclass of: host
definition editor: Alexander Diehl
definition: A organism bearing an intermediate host role.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
alternative term: secondary host

paratenic host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: paratenic host role
subclass of: host
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism bearing a paratenic host role.

dead-end host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: dead-end host role
subclass of: host
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An organism bearing a dead-end host role.
alternative term: incidental host

parasite host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: parasite host role
subclass of: host
definition editor: Albert Goldfain
definition: An organism bearing a parasite host role.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

infectious agent host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent host role
subclass of: pathogen host
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism bearing an infectious agent host role.

pathogen host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: pathogen host role
subclass of: host
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An organism bearing a pathogen host role.

infectious agent carrier
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent carrier role
subclass of: infectious agent host
definition editor: Albert Goldfain
definition: An organism bearing the infectious agent carrier role.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

infectious agent vector
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent vector role
subclass of: organism
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An organism bearing an infectious agent vector role.

mechanical vector of infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: mechanical vector of infectious agent role
subclass of: infectious agent vector
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infectious agent vector bearing a mechanical vector of infectious agent role.
definition editor: Lindsay Cowell

biological vector of infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: biological vector of infectious agent role
subclass of: infectious agent vector
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infectious agent vector bearing a biological vector of infectious agent role.
definition editor: Lindsay Cowell

vehicle of infectious agent
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent vehicle role
subclass of: material_entity
disjoint with: immunodeficiency
definition editor: Alexander Diehl
definition: A material entity bearing an infectious agent vehicle role.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

fomite
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: fomite role
subclass of: vehicle of infectious agent
disjoint with: organism
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Alexander Diehl
definition: A material entity bearing a fomite role.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

infectious agent reservoir
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: reservoir of infectious agent role
subclass of: material_entity
disjoint with: immunodeficiency
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A material entity bearing an infectious agent reservoir role.
definition editor: Alexander Diehl

virulence factor
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has_disposition
    some values from: virulence factor disposition
subclass of: molecular entity
definition editor: Albert Goldfain
comment: DL: Needs 'product of' relation. It is a product of this process: production and has_participant some (has_role some pathogen and has_disposition some 'virulence factor disposition')
definition: A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

invasion factor
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has_disposition
    some values from: invasion disposition
subclass of: molecular entity
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: A biological macromolecule that has an invasion disposition.
definition editor: Albert Goldfain
alternative term: invasin

toxin
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has_disposition
    some values from: toxin disposition
subclass of: molecular entity
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: A molecular entity that has a toxin disposition.

exotoxin
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has_disposition
    some values from: exotoxin disposition
subclass of: toxin
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: A molecular entity bearing an exotoxin disposition.
definition editor: Albert Goldfain

enterotoxin
type: Class
subclass of: exotoxin
subclass of: Restriction
  on property: has_disposition
  some values from: exotoxin disposition
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa.

endotoxin
type: Class
subclass of: toxin
subclass of: Restriction
  on property: has_disposition
  some values from: toxin disposition
definition: A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
definition editor: Lindsay Cowell
comment: IDO Error endotoxin role => endotoxin disposition
definition editor: Albert Goldfain
definition editor: Alexander Diehl

infectious agent portal of entry
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent portal of entry role
subclass of: anatomical entity
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An anatomical entity bearing an infectious agent portal of entry role.
definition editor: Lindsay Cowell

infectious agent portal of exit
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent portal of exit role
subclass of: anatomical entity
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: An anatomical entity bearing an infectious agent portal of exit role.

disinfectant
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: disinfectant role
subclass of: antimicrobial
disjoint with: infection
disjoint with: organism
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A material entity bearing a disinfectant role.

antiseptic
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: antiseptic role
subclass of: antimicrobial
disjoint with: infection
disjoint with: organism
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Alexander Diehl
definition: A material entity bearing an antiseptic role.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

adhesion factor
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has_disposition
    some values from: adhesion disposition
subclass of: molecular entity
definition editor: Alexander Diehl
definition: A biological macromolecule that has an adhesion disposition.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
alternative term: adhesin
alternative term: adhesion molecule

antimicrobial
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: antimicrobial disposition
subclass of: material_entity
disjoint with: infection
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Lindsay Cowell
definition: A material entity with an antimicrobial disposition.
definition editor: Alexander Diehl
definition editor: Albert Goldfain

antiviral
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: antiviral disposition
subclass of: material_entity
disjoint with: infection
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A material entity bearing an antiviral disposition.

antifungal
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: antifungal disposition
subclass of: material_entity
disjoint with: infection
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: A material entity bearing an antifungal disposition.
definition editor: Alexander Diehl

antiparasitic
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: antiparasitic disposition
subclass of: material_entity
disjoint with: infection
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A material entity bearing an antiparasitic disposition.

antibiotic
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: antibacterial disposition
subclass of: material_entity
disjoint with: infection
disjoint with: disorder
disjoint with: anatomical entity
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A material entity bearing an antiviral disposition.

microbicide
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: Class
      intersection of: antimicrobial disposition
      intersection of: Restriction
        on property: realized_by
        all values from: Restriction
subclass of: antimicrobial
definition: A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
comment: DL needs 'process of killing microorganisms'
definition editor: Alexander Diehl
alternative term: microbicidal [entity]

viricide
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: Class
      intersection of: antiviral disposition
      intersection of: Restriction
        on property: realized_by
        all values from: death
subclass of: antiviral
definition: A material entity with an antiviral disposition that is realized in a process of killing viruses.
definition editor: Lindsay Cowell
comment: DL needs 'process of killing viruses'
definition editor: Albert Goldfain
definition editor: Alexander Diehl

microbistatic
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_disposition
    some values from: Class
      intersection of: antimicrobial disposition
      intersection of: Restriction
        on property: realized_by
        all values from: Class
subclass of: antimicrobial
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms.
comment: DL needs 'process of inhibiting the growth of microorganisms'

primary infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has_role
    some values from: primary infection role
subclass of: infectious disorder
disjoint with: secondary infection
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An infection bearing the primary infection role.

secondary infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has_role
    some values from: secondary infection role
subclass of: infectious disorder
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An infection bearing the secondary infection role.

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 editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition.

aymptomatic host of infectious agent
type: Class
subclass of: infectious agent host
subclass of: Restriction
  on property: has_role
  some values from: infectious agent host role
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism that is host to an infectious agent has no symptoms of the infectious disease associated with the infectious agent.
definition editor: Lindsay Cowell

subclinical infection
type: Class
subclass of: infection
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An infection that is part of an asymptomatic host.
definition editor: Lindsay Cowell

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 editor: Albert Goldfain
definition: A material entity that has a resistance disposition.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

chronic carrier of infectious agent
type: Class
subclass of: infectious agent carrier
subclass of: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_role
    some values from: infectious agent carrier role
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism who has been bearer of the infectious agent carrier role for an extended period of time.
definition editor: Lindsay Cowell

symptomatic host of infectious agent
type: Class
subclass of: infectious agent host
subclass of: Restriction
  on property: has_role
  some values from: infectious agent host role
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent

innate immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized_by
    all values from: innate immune response
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: The disposition is realized in an innate immune response.
definition: An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens.

humoral immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized_by
    all values from: humoral immune response
comment: "Circulating body fluid" refers to blood, lymph, and hemolymph.
definition editor: Albert Goldfain
comment: The disposition is realized in a humoral immune response.
definition editor: Alexander Diehl
definition: An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid.
definition editor: Lindsay Cowell

leukocyte-mediated immunity to infectious agent
type: Class
equivalent class: Class
  intersection of: immunity to infectious agent
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: leukocyte
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: leukocyte
  intersection of: Restriction
    on property: realized_by
    all values from: leukocyte mediated immunity
subclass of: immunity to infectious agent
definition: An immunity to infectious agent that inheres in an organism in virtue of its leukocytes.
comment: The disposition is realized in a leukocyte-mediated immune response.
alternative term: cell-mediated immunity to infectious agent
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl

passive immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism.
definition editor: Lindsay Cowell
comment: Passive immunity results from a passive immunization.
comment: The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus.
comment: The disposition is realized in a neutralizing process carried out by the antibodies.

antibiotic resistance
type: Class
subclass of: resistance to drug
definition: A resistance to drug that mitigates the damaging effects of an antibiotic.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl

long-term non-progressor
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property:
      inverse of: unfolds_in
    some values from: long-term non-progressing infectious disease course
subclass of: organism
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An organism experiencing a long-term non-progressing infectious disease course.

emerging pathogen
type: Class
subclass of: infectious agent
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An infectious agent whose infection incidence is increasing following its first introduction into a new host Species.

cytotoxin
type: Class
subclass of: toxin
subclass of: Restriction
  on property: has_disposition
  some values from: toxin disposition
definition editor: Alexander Diehl
definition: A molecular entity with a toxin disposition, the realization of which damages host cells.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

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_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: results_in_formation_of
        some values from: disorder
subclass of: collective disposition
disjoint with: collective resistance disposition
definition editor: Alexander Diehl
definition: A collective disposition to initiate processes that result in a disorder.
definition editor: Lindsay Cowell
comment: The disposition is realized in processes that create a disorder.
definition editor: Albert Goldfain

infection
type: Class
subclass of: material_entity
subclass of: Class
  intersection of: Restriction
    on property: has_part
    some values from: infectious agent
  intersection of: Restriction
    on property: part_of
    some values from: extended organism
disjoint with: immunodeficiency
disjoint with: anatomical entity
definition editor: Alexander Diehl
comment: The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A part of an extended organism that itself has as part a population of one or more infectious agents and that is (1) clinically abnormal in virtue of the presence of this infectious agent population, or (2) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent popuation.

genetic resistance to infectious agent
type: Class
subclass of: resistance to infectious agent
definition editor: Albert Goldfain
definition editor: Alexander Diehl
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.
definition editor: Lindsay Cowell
definition: A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome.

collective resistance disposition
type: Class
subclass of: collective disposition
definition: A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

immunodeficient organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_part
    some values from: immunodeficiency
subclass of: organism
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An organism that has an immunodeficiency.
alternative term: immunocompromised organism

chronic infectious disease course
type: Class
subclass of: infectious disease course
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infectious disease course that unfolds over a long period of time.
definition editor: Lindsay Cowell
alternative term: persistent infectious disease course

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 editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism population whose members have acquired immunity to an infectious agent.

transmission period
type: Class
subclass of: temporal_interval
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: A continuous temporal interval during which a transmission process occurs.

direct host exposure to infectious agent
type: Class
subclass of: host exposure to infectious agent
definition editor: Bjoern Peters
definition: A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent.

potential host of infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_disposition
    some values from: Restriction
      on property: realized_by
      some values from: Restriction
        on property: realizes
        some values from: infectious agent host role
subclass of: organism
definition editor: Alexander Diehl
definition: An organism that has the capability to bear a host of infectious agent role.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_disposition
    some values from: infectious disposition
subclass of: pathogen
subclass of: organism
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An organism that has an infectious disposition.

host exposure to environment containing infectious agent
type: Class
subclass of: host exposure to infectious agent
definition: A process in which a potential host of an infectious agent is exposed to an environment in which the infectious agent is present and physical contact between the two can occur, but such contact is not planned.
definition editor: Bjoern Peters

host living with infected household contact
type: Class
subclass of: host exposure to environment containing infectious agent
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Bjoern Peters
definition: A host exposure to environment with infectious agent where the environment is a household that also has an infected host
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern
definition editor: Albert Goldfain

host living in endemic area
type: Class
subclass of: host exposure to environment containing infectious agent
definition: A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern
definition editor: Bjoern Peters
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain

release of infectious human pathogen in laboratory
type: Class
subclass of: host exposure to environment containing infectious agent
definition editor: Alexander Diehl
definition editor: Bjoern Peters
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: A host exposure to environment with infectious agent where the exposure is accidental; the environment is a laboratory, and the infectious agent is infectious in humans.
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

host coming into contact with vector of infectious agent
type: Class
subclass of: host exposure to environment containing infectious agent
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Bjoern Peters
definition: A host exposure to environment with infectious agent where the environment contains an infectious agent vector.
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

host exposure to substance that might have infectious agent
type: Class
subclass of: host exposure to environment containing infectious agent
definition editor: Alexander Diehl
definition: A host exposure to environment with infectious agent where the environment contains a material entity that has been assessed to confer a risk of infection.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern
definition editor: Bjoern Peters

process of establishing an infection
type: Class
subclass of: processual_entity
definition: A process by which an infectious agent, established in a host, becomes part of an infection in the host.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

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 editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An establishment in host process in which an organism establishes itself in a host.
editor note: Establishment of one organism in the extended organism of another (the host) involves at least one of (1) movement of the organism to a location within the host in which the organism can persist, or (2) adherence or attachment of the organism to part of the host.

establishment of a clinically abnormal colony
type: Class
subclass of: colonization of host
definition editor: Albert Goldfain
definition: A colonization of host process that results in a clinically abnormal colony.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

production
type: Class
subclass of: process
definition: A process in which an entity comes into being as a result of the process.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

replication
type: Class
subclass of: production
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A production process in which a participant creates a copy of itself.
definition editor: Albert Goldfain

colonization of human anterior nares
type: Class
subclass of: colonization of human
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A colonization of human process in which the colonized site is the anterior nares.

immunosuppression
type: Class
equivalent class: Class
  intersection of: processual_entity
  intersection of: Restriction
    on property: negatively_regulates
    some values from: immune response
subclass of: processual_entity
definition editor: Alexander Diehl
definition: A process that attenuates an immune response.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

physiologic immunosuppression
type: Class
subclass of: immunosuppression
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An immunosuppression which unfolds as part of the natural self-regulation of an immune response.

pathologic immunosuppression
type: Class
subclass of: immunosuppression
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An immunosuppression process which arises as the result of a disorder.
editor note: Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition.

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

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 editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A colony whose members are infectious agents.

immunodeficiency
type: Class
subclass of: disorder
disjoint with: source of infection
disjoint with: anatomical entity
definition: A disorder of an immune system component that results in defective functioning of the immune system.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
comment: DL needs immune system component (FMA?) and defective functioning (OGMS?)

immunocompetence
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized_by
    all values from: immune response
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
comment: The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response.
definition editor: Albert Goldfain
definition: A disposition that is the ability to mount a normal immune response.

immunosuppressive disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material_entity
  intersection of: Restriction
    on property: realized_by
    all values from: immunosuppression
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: A disposition whose realization negatively regulates an immune response.

acquired immunity to infectious agent
type: Class
equivalent class: Class
  intersection of: immunity to infectious agent
  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: has_material_basis_in
    all 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_by
    all values from: adaptive immune response
subclass of: immunity to infectious agent
comment: The disposition is realized in an immune response in which such antigen receptors participate.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An immunity to infectious agent 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.
alternative term: adaptive immunity to infectious agent
alternative term: immune memory

disposition to form a non-parasitic colony
type: Class
subclass of: disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: A disposition to colonize an organism and participate in mutualism or commensalism with that organism.
definition editor: Alexander Diehl

communicability
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: realized_by
    all values from: Class
      intersection of: processual_entity
      intersection of: Restriction
        on property: has_part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has_part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has_part
        some values from: horizontal pathogen transmission process
subclass of: infectious disposition
definition editor: Alexander Diehl
comment: The disposition is realized in a direct, horizontal transmission process between members of the same Species.
definition editor: Albert Goldfain
definition: An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission.
definition editor: Lindsay Cowell

establishment of localization in host
type: Class
equivalent class: Restriction
  on property: unfolds_in
  some values from: host
subclass of: establishment of localization
editor note: Requested addition of this term to the GO.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature.
comment: An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA.

appearance of disorder
type: Class
equivalent class: Restriction
  on property: results_in_formation_of
  some values from: disorder
subclass of: processual_entity
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A process by which a disorder comes into existence.

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_by
      some values from: acute infectious disease course
subclass of: infectious disorder
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: An infectious disorder that is the physical basis for an unfolding acute infectious disease course.

chronic infection
type: Class
subclass of: infection
comment: DL needs 'extended period of time'
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition: An infection that persists for an extended period of time.
alternative term: persistent infection

host role
type: Class
subclass of: role
subclass 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: extended organism
        intersection of: Restriction
disjoint with: source of infection role
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
definition editor: Alexander Diehl

hospital-acquired infection
type: Class
subclass of: infection
disjoint with: community-acquired infection
comment: DL needs 'hospital' (OGMS?)
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection resulting from a transmission process that unfolds in a hospital.
definition editor: Lindsay Cowell
alternative term: nosocomial infection

community-acquired infection
type: Class
subclass of: infection
disjoint with: nursing-home acquired
comment: DL needs 'health care facility'
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An infection resulting from a transmission process that did not unfold in a health care facility.

neurotoxin
type: Class
subclass of: toxin
subclass of: Restriction
  on property: has_disposition
  some values from: toxin disposition
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue.

metatstatic infection
type: Class
subclass of: infection
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
comment: DL needs 'another infection in a non-adjacent location'

source of infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material_entity
definition: A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted.
comment: The role is realized in a process that has as part a transmission process and a process by which the infectious agent or one of its offspring becomes part of a disorder in the host.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

sepsis
type: Class
subclass of: processual_entity
definition: A process that is a systemic inflammatory response to infection.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain

severe sepsis
type: Class
subclass of: sepsis
definition editor: Albert Goldfain
definition: A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ.
definition editor: Alexander Diehl
definition editor: Lindsay Cowell

nursing-home acquired
type: Class
subclass of: infection
comment: DL needs nursing home (OGMS?)
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection resulting from a transmission process that unfolds in a nursing home.
definition editor: Lindsay Cowell

infectious human pathogen
type: Class
subclass of: infectious agent
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition: An infectious agent with a capability to infect human hosts.

acquired immunodeficiency
type: Class
subclass of: immunodeficiency
disjoint with: primary immunodeficiency
comment: Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy).
definition editor: Albert Goldfain
definition: An immunodeficiency that is not caused by a genetic predisposition.
definition editor: Lindsay Cowell
definition editor: Alexander Diehl

simple infection
type: Class
subclass of: infection
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alexander Diehl
comment: needs 'species'
definition: An infection comprised of infectious organisms all of the same Species.

re-emerging pathogen
type: Class
subclass of: infectious agent
definition editor: Lindsay Cowell
definition editor: Alexander Diehl
definition editor: Albert Goldfain
definition: An infectious agent 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.

pregnancy-induced immunosuppression
type: Class
subclass of: immunosuppression
definition editor: Alexander Diehl
definition: An immunosuppression induced by progesterone and other factors upregulated in pregnant women.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain

candidiasis
type: Class
subclass of: infection
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection that has as part organisms of the Genus Candida.
comment: DL needs NCBI taxonomy term.
definition editor: Lindsay Cowell

trichomoniasis
type: Class
subclass of: infection
comment: DL needs NCBI taxonomy terms.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition: An infection that has as part organisms of the Species Trichomonas vaginalis.
definition editor: Lindsay Cowell

leptospirosis
type: Class
subclass of: infection
definition editor: Albert Goldfain
definition: An infection that has as part organisms of the Genus Leptospira.
definition editor: Lindsay Cowell
comment: DL needs NCBI Taxonomy term.
definition editor: Alexander Diehl

Shigellosis
type: Class
subclass of: infection
definition: An infection located in the bowel and that has as part organisms of the Genus Shigella.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
comment: DL needs NCBI taxonomy term.
definition editor: Alexander Diehl

amebiasis
type: Class
subclass of: infection
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
definition: An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica
comment: DL needs NCBI taxonomy term.

colonization of human
type: Class
subclass of: colonization of host
definition editor: Alexander Diehl
definition: A colonization of host process in which the host is of Species Homo sapiens.
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

primary immunodeficiency
type: Class
subclass of: immunodeficiency
definition editor: Albert Goldfain
definition editor: Lindsay Cowell
definition: An immunodeficiency that exists in an organism because of a genetic predisposition.
alternative term: congenital immunodeficiency
definition editor: Alex Diehl

colonization of human perineum
type: Class
subclass of: colonization of human
definition editor: Albert Goldfain
definition editor: Alex Diehl
definition: A colonization of human process in which the colonized site is a perineum.
definition editor: Lindsay Cowell

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 editor: Albert Goldfain
definition: An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition.
definition editor: Alex Diehl
definition editor: Lindsay Cowell

opportunistic pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has_disposition
    some values from: opportunistic infectious disposition
subclass of: infectious agent
definition: An infectious agent with an opportunistic infectious disposition.
definition editor: Lindsay Cowell
definition editor: Albert Goldfain
definition editor: Alex Diehl
alternative term: opportunist

transmissibility disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: pathogen
  intersection of: Restriction
    on property: realized_by
    all values from: transmission process
disjoint with: disease
definition editor: Lindsay Cowell
comment: The disposition is realized in a transmission process.
definition editor: Albert Goldfain
definition: A disposition to undergo a transmission process.
definition editor: Alex Diehl

horizontal pathogen transmission process
type: Class
subclass of: transmission process
definition editor: Lindsay Cowell
definition: A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship.

process that results in death
type: Class
subclass of: processual_entity
definition: A process that results in death.
definition editor: Lindsay Cowell
definition editor: Alex Diehl

host exposure to infectious agent
type: Class
subclass of: processual_entity
definition editor: Bjoern Peters
definition: A process in which a potential host of an infectious agent is exposed to an infectious agent.

susceptible organism
type: Class
subclass of: organism
definition editor: Alex Diehl
definition editor: Lindsay Cowell
definition: An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.

life-sustaining process
type: Class
subclass of: biological_process
definition editor: Lindsay Cowell
definition editor: Alex Diehl
definition: A process which is necessary for the survival of an organism.

negative regulation of life-sustaining process
type: Class
equivalent class: Restriction
  on property: negatively_regulates
  some values from: life-sustaining process
subclass of: biological regulation
definition editor: Lindsay Cowell
definition editor: Alex Diehl
definition: Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process.

source of infection
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: source of infection role
subclass of: material_entity
definition: A material entity bearing a source of infection role.
definition editor: Alex Diehl
definition editor: Albert Goldfain
definition editor: Lindsay Cowell

transition to clinical abnormality
type: Class
subclass of: processual_entity
definition: A process by which a part of an organism or something contained in an organism becomes clinically abnormal.

planned process
type: Class
subclass of: processual_entity
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor preferred term: planned process
imported from: obi.owl

material supplier role
type: Class
subclass of: service provider role
definition: a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
editor preferred term: material supplier role
imported from: obi.owl

processed material
type: Class
subclass of: material_entity
definition: Is a material entity that is created or changed during material processing.
editor preferred term: processed material
imported from: obi.owl

investigation
type: Class
subclass of: planned process
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
editor preferred term: investigation
imported from: obi.owl

assay
type: Class
subclass of: planned process
definition: A planned process with the objective to produce information about some evaluant
editor preferred term: assay
imported from: obi.owl

diagnosis textual entity
type: Class
subclass of: textual entity
definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
editor preferred term: diagnosis textual entity
imported from: obi.owl

material processing
type: Class
subclass of: planned process
definition: A planned process which results in physical changes in a specified input material
editor preferred term: material processing
imported from: obi.owl

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized_by
  all values from: investigation
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material_entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen creation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
definition editor: GROUP: Role Branch
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition source: OBI
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
definition: a role borne by a material entity that is gained during a specimen creation process and that is realized by use of the specimen in an investigation
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
editor preferred term: specimen role
has curation status: ready for release
imported from: obi.owl
type: NamedIndividual

population
type: Class
subclass of: material_entity
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor preferred term: population
imported from: obi.owl

investigation agent role
type: Class
subclass of: role
editor preferred term: investigation agent role
definition: Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing.
imported from: obi.owl

protocol
type: Class
subclass of: plan specification
definition: a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
editor preferred term: protocol
imported from: obi.owl

cloning vector role
type: Class
subclass of: role
definition: a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
editor preferred term: cloning vector role
imported from: obi.owl

enzyme
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Class
    union of: protein
    union of: ribonucleic acids
    union of: protein complex
    union of: Restriction
      on property: has_part
      some values from: protein
    union of: Restriction
      on property: has_part
      some values from: ribonucleic acids
    union of: Restriction
      on property: has_part
      some values from: protein complex
  intersection of: Restriction
    on property: has_function
    some values from: catalytic activity
subclass of: material_entity
definition source: GROUP:OBI
editor note: MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
has curation status: pending final vetting
definition editor: person: Melanie Courtot
definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
type: Thing
type: NamedIndividual
editor preferred term: enzyme

study design execution
type: Class
subclass of: planned process
definition: a planned process that realizes the concretization of a study design
editor preferred term: study design execution
imported from: obi.owl

DNA sequencing
type: Class
subclass of: sequencing assay
editor preferred term: DNA sequencing
definition: DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
imported from: obi.owl

material combination
type: Class
subclass of: material processing
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor preferred term: material combination
imported from: obi.owl

specimen creation
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: has_specified_output
    some values from: specimen
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen creation objective
subclass of: planned process
definition editor: Bjoern Peters
definition: a planned process with the objective of obtaining specimen.
editor preferred term: specimen creation
has curation status: metadata incomplete
imported from: obi.owl
type: NamedIndividual

specimen creation objective
type: Class
subclass of: objective specification
definition: A specimen creation objective is to obtain a material entity for potential use as an input during an investigation
editor preferred term: specimen creation objective
imported from: obi.owl

complementary nucleotide probe role
type: Class
subclass of: role
definition: A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
editor preferred term: complementary nucleotide probe role
imported from: obi.owl

viral hemagglutination inhibition assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: neuraminidase
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: hemagglutinin
definition: a highly sensitive procedure for the measurement of soluble antigens in biologic specimens; the amount of hemagglutination reflects the amount of free antibody present after reaction with the specimen and thus varies inversely with amount of antigen in the specimen.
editor preferred term: viral hemagglutination inhibition assay
imported from: obi.owl

induced hemagglutination
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: realizes
  some values from: hemagglutination disposition
definition: The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
editor preferred term: induced hemagglutination
imported from: obi.owl

categorical measurement datum
type: Class
subclass of: measurement datum
definition: A measurement datum that is reported on a categorical scale
editor preferred term: categorical measurement datum
imported from: obi.owl

service provider role
type: Class
subclass of: role
definition: is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
editor preferred term: service provider role
imported from: obi.owl

sequence data
type: Class
subclass of: measurement datum
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
editor preferred term: sequence data
imported from: obi.owl

genotype information
type: Class
subclass of: data item
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor preferred term: genotype information
imported from: obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material_entity
disjoint with: disorder
imported from: OBI
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: An organism is material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor preferred term: organism
imported from: obi.owl

specimen
type: Class
equivalent class: Class
  intersection of: material_entity
  intersection of: Restriction
    on property: has_role
    some values from: specimen role
subclass of: material_entity
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition: A material entity that has the specimen role.
definition source: GROUP: OBI Biomaterial Branch
editor preferred term: specimen
has curation status: ready for release
imported from: obi.owl
type: NamedIndividual

cell culture
type: Class
subclass of: processed material
definition: a cell culture is a material entity consisting of a population of cells that is maintained in vitro
editor preferred term: cell culture
imported from: obi.owl

data transformation
type: Class
subclass of: planned process
definition: A data transformation is a process which produces output data from input data
editor preferred term: data transformation
imported from: obi.owl

extraction
type: Class
subclass of: material component separation
definition: A material separation in which a desired component of an input material is separated from the remainder
editor preferred term: extraction
alternative term: isolation event
imported from: obi.owl

study design
type: Class
subclass of: plan specification
definition: A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor preferred term: study design
imported from: obi.owl

collecting specimen from organism
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen creation objective
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
definition source: IEDB
definition editor: PERSON:Bjoern Peters
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
editor preferred term: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release
imported from: obi.owl
type: NamedIndividual

killing
type: Class
subclass of: material processing
definition: A protocol application in which an organism is intentionally put to death
editor preferred term: killing
imported from: obi.owl

administering substance in vivo
type: Class
subclass of: material combination
definition: A process by which a substance is intentionally given to an organism
editor preferred term: administering substance in vivo
imported from: obi.owl

environmental material collection
type: Class
subclass of: processual_entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen creation objective
definition editor: Bjoern Peters, Alan Ruttenberg
definition source: IEDB
example of usage: Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
editor preferred term: environmental material collection
definition: environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
has curation status: metadata incomplete
imported from: obi.owl
type: NamedIndividual

material component separation
type: Class
subclass of: material processing
definition: a material processing in which components of an input material become segregated in space
editor preferred term: material component separation
imported from: obi.owl

material portioning
type: Class
subclass of: material processing
definition: a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
editor preferred term: material portioning
imported from: obi.owl

establishing cell culture
type: Class
subclass of: material processing
definition: establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
editor preferred term: establishing cell culture
imported from: obi.owl

sequencing assay
type: Class
subclass of: assay
editor preferred term: sequencing assay
definition: the use of a chemical or biochemical means to infer the sequence of a biomaterial
imported from: obi.owl

RNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: is_concretization_of
    some values from: RNA extraction protocol
subclass of: Restriction
  on property: has_specified_output
  some values from: ribonucleic acids
definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
editor preferred term: RNA extraction
imported from: obi.owl

nucleic acid extraction
type: Class
subclass of: extraction
definition: a material separation to recover the nucleic acid fraction of an input material
editor preferred term: nucleic acid extraction
imported from: obi.owl

symptom
type: Class
subclass of: entity
subclass of: quality
editor preferred term: symptom
definition: A quality of a patient that is observed by the patient and is hypothesized by the patient to be a realization of a disease.
definition: A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease.
imported from: ogms.owl

disease
type: Class
subclass of: disposition
editor preferred term: disease
definition: A 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
editor preferred term: disorder
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
imported from: ogms.owl

disease course
type: Class
subclass of: processual_entity
editor preferred term: disease course
definition: The totality of all processes through which a given disease instance is realized.
imported from: ogms.owl

extended organism
type: Class
subclass of: object_aggregate
editor preferred term: extended organism
definition: An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
imported from: ogms.owl

treatment
type: Class
subclass of: processual_entity
editor preferred term: treatment
definition: A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
imported from: ogms.owl

health care process
type: Class
subclass of: processual_entity
definition: A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process
editor preferred term: health care process
imported from: ogms.owl

health care encounter
type: Class
subclass of: health care process
definition: A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
editor preferred term: health care encounter
imported from: ogms.owl

hospitalization
type: Class
subclass of: health care encounter
editor preferred term: hospitalization
definition: TODO
imported from: ogms.owl

protein
type: Class
subclass of: peptide
editor preferred term: protein
imported from: pr.owl

anatomical entity
type: Class
subclass of: material_entity
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
editor preferred term: anatomical entity
imported from: CARO

peptide
type: Class
subclass of: molecular entity
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
editor preferred term: peptide
imported from: CHEBI

deoxyribonucleic acids
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.
editor preferred term: deoxyribonucleic acids
imported from: CHEBI

molecular entity
type: Class
subclass of: material_entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor preferred term: molecular entity
imported from: CHEBI

nucleic acid
type: Class
subclass of: molecular entity
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.
editor preferred term: nucleic acid
imported from: CHEBI

ribonucleic acids
type: Class
subclass of: nucleic acid
definition: Naturally occurring polyribonucleotides.
editor preferred term: ribonucleic acids
imported from: CHEBI

messenger RNA
type: Class
subclass of: ribonucleic acids
definition: An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation.
editor preferred term: messenger RNA
imported from: CHEBI

cell
type: Class
subclass of: anatomical entity
subclass of: material_entity
definition: Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
editor preferred term: cell
imported from: CL

leukocyte
type: Class
subclass of: cell
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
editor preferred term: leukocyte
imported from: CL

influenza
type: Class
subclass of: infectious disease
definition: A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness.
editor preferred term: influenza
imported from: DOID

biome
type: Class
subclass of: material_entity
definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation.
editor preferred term: biome
imported from: ENVO

habitat
type: Class
subclass of: site
definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms.
editor preferred term: habitat
imported from: ENVO

Lung
type: Class
subclass of: anatomical entity
definition: Lobular organ which has as its parts alveoli connected to the tracheobronchial tree. Examples: There are only two instances, right lung and left lung.
editor preferred term: Lung
imported from: FMA

reproduction
type: Class
subclass of: biological_process
definition: The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.
editor preferred term: reproduction
imported from: GO

cell fraction
type: Class
subclass of: material_entity
definition: A generic term for parts of cells prepared by disruptive biochemical techniques.
editor preferred term: cell fraction
imported from: GO

adaptive immune response
type: Class
subclass of: immune response
definition: An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
editor preferred term: adaptive immune response
imported from: GO

leukocyte mediated immunity
type: Class
subclass of: immune response
definition: Any process involved in the carrying out of an immune response by a leukocyte.
editor preferred term: leukocyte mediated immunity
imported from: GO

molecular_function
type: Class
subclass of: function
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
editor preferred term: molecular_function
imported from: GO

catalytic activity
type: Class
subclass of: molecular_function
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
editor preferred term: catalytic activity
imported from: GO

RNA-directed RNA polymerase activity
type: Class
subclass of: RNA polymerase activity
definition: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template.
editor preferred term: RNA-directed RNA polymerase activity
imported from: GO

immune response
type: Class
subclass of: biological_process
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
editor preferred term: immune response
imported from: GO

humoral immune response
type: Class
subclass of: immune response
definition: An immune response mediated through a body fluid.
editor preferred term: humoral immune response
imported from: GO

biological_process
type: Class
subclass of: processual_entity
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
editor preferred term: biological_process
imported from: GO

death
type: Class
subclass of: biological_process
definition: A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
editor preferred term: death
imported from: GO

alpha-sialidase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the hydrolysis of alpha-glycosidic linkages in oligo- or poly(sialic) acids.
editor preferred term: alpha-sialidase activity
imported from: GO

immunoglobulin complex
type: Class
subclass of: macromolecular complex
definition: A 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.
editor preferred term: immunoglobulin complex
imported from: GO

B cell receptor complex
type: Class
subclass of: macromolecular complex
definition: An immunoglobulin complex that is 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.
editor preferred term: B cell receptor complex
imported from: GO

ribonucleoprotein complex
type: Class
subclass of: molecular entity
definition: A macromolecular complex containing both protein and RNA molecules.
editor preferred term: ribonucleoprotein complex
imported from: GO

RNA polymerase complex
type: Class
subclass of: protein complex
subclass of: Restriction
  on property: has_function
  some values from: RNA polymerase activity
definition: Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits.
editor preferred term: RNA polymerase complex
imported from: GO

RNA-directed RNA polymerase complex
type: Class
subclass of: RNA polymerase complex
subclass of: Restriction
  on property: has_function
  some values from: RNA-directed RNA polymerase activity
definition: A protein complex that possesses RNA-directed RNA polymerase activity.
editor preferred term: RNA-directed RNA polymerase complex
imported from: GO

developmental process
type: Class
subclass of: biological_process
definition: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
editor preferred term: developmental process
imported from: GO

macromolecular complex
type: Class
subclass of: material_entity
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
editor preferred term: macromolecular complex
imported from: GO

RNA polymerase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template.
editor preferred term: RNA polymerase activity
imported from: GO

growth
type: Class
subclass of: biological_process
definition: The increase in size or mass of an entire organism, a part of an organism or a cell.
editor preferred term: growth
imported from: GO

T cell receptor complex
type: Class
subclass of: macromolecular complex
definition: A 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.
editor preferred term: T cell receptor complex
imported from: GO

cytokinesis by binary fission
type: Class
subclass of: reproduction
definition: A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells; the process by which prokaryotic cells divide.
editor preferred term: cytokinesis by binary fission
imported from: GO

organelle
type: Class
subclass of: material_entity
definition: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
editor preferred term: organelle
imported from: GO

protein complex
type: Class
subclass of: material_entity
definition: Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
editor preferred term: protein complex
imported from: GO

symbiosis, encompassing mutualism through parasitism
type: Class
subclass of: multi-organism process
definition: An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont organism. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs.
editor preferred term: symbiosis, encompassing mutualism through parasitism
imported from: GO

adhesion to host
type: Class
subclass of: biological_process
definition: The attachment of an organism to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
editor preferred term: adhesion to host
imported from: GO

entry into host
type: Class
subclass of: multi-organism process
definition: Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
editor preferred term: entry into host
imported from: GO

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. The host is defined as the larger of the organisms involved in a symbiotic interaction.
editor preferred term: entry into host through host barriers
imported from: GO

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.
editor preferred term: innate immune response
imported from: GO

negative regulation of viral reproduction
type: Class
subclass of: biological regulation
definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts.
editor preferred term: negative regulation of viral reproduction
imported from: GO

negative regulation of immune response
type: Class
subclass of: biological regulation
definition: Any 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.
editor preferred term: negative regulation of immune response
imported from: GO

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).
editor preferred term: negative regulation of developmental process
imported from: GO

establishment of localization
type: Class
subclass of: biological_process
imported from: Gene Ontology: http://purl.org/obo/owl/GO
definition: The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
editor preferred term: establishment of localization
imported from: GO

multi-organism process
type: Class
subclass of: biological_process
definition: Any process by which an organism has an effect on another organism of the same or different species.
editor preferred term: multi-organism process
imported from: GO

biological regulation
type: Class
subclass of: processual_entity
definition: Any process that modulates the frequency, rate or extent of any biological process, quality or function.
editor preferred term: biological regulation
imported from: GO

mutualism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism
definition: An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other.
editor preferred term: mutualism
imported from: GO

commensalism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism
definition: An interaction between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected.
editor preferred term: commensalism
imported from: GO

Muridae
type: Class
subclass of: Muroidea
editor preferred term: Muridae
imported from: NCBITaxon

Mus
type: Class
subclass of: Murinae
editor preferred term: Mus
imported from: NCBITaxon

Mus musculus
type: Class
subclass of: organism
subclass of: Mus
editor preferred term: Mus musculus
imported from: NCBITaxon

Viruses
type: Class
subclass of: organism
imported from: NCBITaxon

Orthomyxoviridae
type: Class
subclass of: ssRNA negative-strand viruses
editor preferred term: Orthomyxoviridae
imported from: NCBITaxon

Influenza A virus
type: Class
subclass of: organism
subclass of: Influenzavirus A
editor preferred term: Influenza A virus
imported from: NCBITaxon

Influenza B virus
type: Class
subclass of: organism
subclass of: Influenzavirus B
editor preferred term: Influenza B virus
imported from: NCBITaxon

Influenza C virus
type: Class
subclass of: organism
subclass of: Influenzavirus C
editor preferred term: Influenza C virus
imported from: NCBITaxon

Teleostomi
type: Class
subclass of: Gnathostomata
editor preferred term: Teleostomi
imported from: NCBITaxon

Euteleostomi
type: Class
subclass of: Teleostomi
editor preferred term: Euteleostomi
imported from: NCBITaxon

Mustelinae
type: Class
subclass of: Mustelidae
editor preferred term: Mustelinae
imported from: NCBITaxon

Influenzavirus A
type: Class
subclass of: Orthomyxoviridae
editor preferred term: Influenzavirus A
imported from: NCBITaxon

Influenzavirus B
type: Class
subclass of: Orthomyxoviridae
editor preferred term: Influenzavirus B
imported from: NCBITaxon

Influenzavirus C
type: Class
subclass of: Orthomyxoviridae
editor preferred term: Influenzavirus C
imported from: NCBITaxon

Bacteria
type: Class
subclass of: organism
imported from: NCBITaxon

Homo/Pan/Gorilla group
type: Class
subclass of: Hominidae
editor preferred term: Homo/Pan/Gorilla group
imported from: NCBITaxon

Archaea
type: Class
subclass of: organism
imported from: NCBITaxon

Eukaryota
type: Class
subclass of: organism
imported from: NCBITaxon

Laurasiatheria
type: Class
subclass of: Eutheria
editor preferred term: Laurasiatheria
imported from: NCBITaxon

Euarchontoglires
type: Class
subclass of: Eutheria
editor preferred term: Euarchontoglires
imported from: NCBITaxon

Glires
type: Class
subclass of: Euarchontoglires
editor preferred term: Glires
imported from: NCBITaxon

Simiiformes
type: Class
subclass of: Haplorrhini
editor preferred term: Simiiformes
imported from: NCBITaxon

Hominoidea
type: Class
subclass of: Catarrhini
editor preferred term: Hominoidea
imported from: NCBITaxon

Tetrapoda
type: Class
subclass of: Sarcopterygii
editor preferred term: Tetrapoda
imported from: NCBITaxon

Amniota
type: Class
subclass of: Tetrapoda
editor preferred term: Amniota
imported from: NCBITaxon

Theria
type: Class
subclass of: Mammalia
editor preferred term: Theria
imported from: NCBITaxon

Sauria
type: Class
subclass of: Sauropsida
editor preferred term: Sauria
imported from: NCBITaxon

Fungi/Metazoa group
type: Class
subclass of: Eukaryota
editor preferred term: Fungi/Metazoa group
imported from: NCBITaxon

Metazoa
type: Class
subclass of: Fungi/Metazoa group
editor preferred term: Metazoa
imported from: NCBITaxon

Bilateria
type: Class
subclass of: Eumetazoa
editor preferred term: Bilateria
imported from: NCBITaxon

Coelomata
type: Class
subclass of: Bilateria
editor preferred term: Coelomata
imported from: NCBITaxon

Deuterostomia
type: Class
subclass of: Coelomata
editor preferred term: Deuterostomia
imported from: NCBITaxon

Sciurognathi
type: Class
subclass of: Rodentia
editor preferred term: Sciurognathi
imported from: NCBITaxon

Carnivora
type: Class
subclass of: Laurasiatheria
editor preferred term: Carnivora
imported from: NCBITaxon

Muroidea
type: Class
subclass of: Sciurognathi
editor preferred term: Muroidea
imported from: NCBITaxon

ssRNA negative-strand viruses
type: Class
subclass of: Viruses
editor preferred term: ssRNA negative-strand viruses
imported from: NCBITaxon

Thogotovirus
type: Class
subclass of: organism
subclass of: Orthomyxoviridae
editor preferred term: Thogotovirus
imported from: NCBITaxon

Suina
type: Class
subclass of: Cetartiodactyla
editor preferred term: Suina
imported from: NCBITaxon

Haplorrhini
type: Class
subclass of: Primates
editor preferred term: Haplorrhini
imported from: NCBITaxon

Caniformia
type: Class
subclass of: Carnivora
editor preferred term: Caniformia
imported from: NCBITaxon

Murinae
type: Class
subclass of: Muridae
editor preferred term: Murinae
imported from: NCBITaxon

Mammalia
type: Class
subclass of: Amniota
editor preferred term: Mammalia
imported from: NCBITaxon

Dinosauria
type: Class
subclass of: Archosauria
editor preferred term: Dinosauria
imported from: NCBITaxon

Saurischia
type: Class
subclass of: Dinosauria
editor preferred term: Saurischia
imported from: NCBITaxon

Theropoda
type: Class
subclass of: Saurischia
editor preferred term: Theropoda
imported from: NCBITaxon

Coelurosauria
type: Class
subclass of: Theropoda
editor preferred term: Coelurosauria
imported from: NCBITaxon

Eumetazoa
type: Class
subclass of: Metazoa
editor preferred term: Eumetazoa
imported from: NCBITaxon

Chordata
type: Class
subclass of: Deuterostomia
editor preferred term: Chordata
imported from: NCBITaxon

Vertebrata
type: Class
subclass of: Craniata
editor preferred term: Vertebrata
imported from: NCBITaxon

Gnathostomata
type: Class
subclass of: Vertebrata
editor preferred term: Gnathostomata
imported from: NCBITaxon

Sarcopterygii
type: Class
subclass of: Euteleostomi
editor preferred term: Sarcopterygii
imported from: NCBITaxon

Sauropsida
type: Class
subclass of: Amniota
editor preferred term: Sauropsida
imported from: NCBITaxon

Archosauria
type: Class
subclass of: Sauria
editor preferred term: Archosauria
imported from: NCBITaxon

Aves
type: Class
subclass of: organism
subclass of: Coelurosauria
editor preferred term: Aves
imported from: NCBITaxon

Craniata
type: Class
subclass of: Chordata
editor preferred term: Craniata
imported from: NCBITaxon

Cetartiodactyla
type: Class
subclass of: Laurasiatheria
editor preferred term: Cetartiodactyla
imported from: NCBITaxon

Eutheria
type: Class
subclass of: Theria
editor preferred term: Eutheria
imported from: NCBITaxon

Primates
type: Class
subclass of: Euarchontoglires
editor preferred term: Primates
imported from: NCBITaxon

Catarrhini
type: Class
subclass of: Simiiformes
editor preferred term: Catarrhini
imported from: NCBITaxon

Hominidae
type: Class
subclass of: Hominoidea
editor preferred term: Hominidae
imported from: NCBITaxon

Homo
type: Class
subclass of: Homo/Pan/Gorilla group
editor preferred term: Homo
imported from: NCBITaxon

Homo sapiens
type: Class
subclass of: organism
subclass of: Homo
editor preferred term: Homo sapiens
imported from: NCBITaxon

Mustelidae
type: Class
subclass of: Caniformia
editor preferred term: Mustelidae
imported from: NCBITaxon

Mustela
type: Class
subclass of: Mustelinae
editor preferred term: Mustela
imported from: NCBITaxon

Mustela putorius
type: Class
subclass of: Mustela
editor preferred term: Mustela putorius
imported from: NCBITaxon

Mustela putorius furo
type: Class
subclass of: organism
subclass of: Mustela putorius
editor preferred term: Mustela putorius furo
imported from: NCBITaxon

Suidae
type: Class
subclass of: Suina
editor preferred term: Suidae
imported from: NCBITaxon

Sus
type: Class
subclass of: Suidae
editor preferred term: Sus
imported from: NCBITaxon

Sus scrofa
type: Class
subclass of: organism
subclass of: Sus
editor preferred term: Sus scrofa
imported from: NCBITaxon

Rodentia
type: Class
subclass of: Glires
editor preferred term: Rodentia
imported from: NCBITaxon

age
type: Class
subclass of: time
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
editor preferred term: age
imported from: PATO

biological sex
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
editor preferred term: biological sex
imported from: PATO

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
editor preferred term: morphology
imported from: PATO

trophic quality
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's disposition to synthesize a particular organic compound required for its growth.
editor preferred term: trophic quality
imported from: PATO

size
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
editor preferred term: size
imported from: PATO

length
type: Class
subclass of: 1-D extent
subclass of: quality
editor preferred term: length
definition: A 1-D extent quality which is equal to the distance between two points.
imported from: PATO

mass
type: Class
subclass of: physical quality
subclass of: quality
editor preferred term: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: PATO

weight
type: Class
subclass of: force
definition: A physical quality inhering in a bearer that has mass near a gravitational body.
editor preferred term: weight
imported from: PATO

time
type: Class
subclass of: physical quality
definition: A quality in which events occur in sequence.
editor preferred term: time
imported from: PATO

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

female
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
editor preferred term: female
imported from: PATO

male
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
editor preferred term: male
imported from: PATO

auxotrophic
type: Class
subclass of: trophic quality
definition: A nutritional quality inhering in a bearer by virtue of the bearer's inability to synthesize a particular organic compound required for its growth.
editor preferred term: auxotrophic
imported from: PATO

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
editor preferred term: physical quality
imported from: PATO

force
type: Class
subclass of: physical quality
definition: A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.
editor preferred term: force
imported from: PATO

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

dead
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
editor preferred term: dead
imported from: PATO

1-D extent
type: Class
subclass of: size
editor preferred term: 1-D extent
definition: A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
imported from: PATO

phenotypic sex
type: Class
subclass of: biological sex
editor preferred term: phenotypic sex
imported from: PATO

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

transmission process
type: Class
label: Suggested label: pathogen transmission process
subclass of: processual_entity
definition: Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species.
definition: A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
imported from: Transmission Ontology: http://purl.org/obo/owl/TRANS
editor preferred term: transmission process
imported from: TRANS

Suggested label: indirect pathogen transmission process
type: Class
label: indirect
subclass of: transmission process
definition: Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles.
editor preferred term: indirect
imported from: TRANS

contact
type: Class
subclass of: transmission process
definition: Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen.
editor preferred term: contact
imported from: TRANS

droplet spread
type: Class
subclass of: transmission process
definition: Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking.
editor preferred term: droplet spread
imported from: TRANS

airborne
type: Class
subclass of: transmission process
definition: Airborne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host while suspended in the air as dust.
editor preferred term: airborne
imported from: TRANS

vehicle-borne
type: Class
subclass of: transmission process
definition: Vehicle-borne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by inanimate intermediary vehicle objects.
editor preferred term: vehicle-borne
imported from: TRANS

vehicle-borne ingestion
type: Class
subclass of: vehicle-borne
definition: Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products.
editor preferred term: vehicle-borne ingestion
imported from: TRANS

blood
type: Class
subclass of: anatomical entity
imported from: UBERON

adipose tissue
type: Class
subclass of: material_entity
definition: Dense irregular connective tissue, which predominantly consists of adipocytes. Fat is stored in adipose tissue.
editor preferred term: adipose tissue
imported from: UBERON

tarsometatarsus
type: Class
subclass of: material_entity
definition: The tarsometatarsus is a bone that is found in the lower leg of certain tetrapods, namely birds. It is formed from the fusion of several bones found in other types of animals, and homologous to the mammalian tarsal (ankle) and metatarsal (foot) bones. Despite this, the tarsometatarsus of birds is often referred to as just the tarsus or metatarsus.
editor preferred term: tarsometatarsus
imported from: UBERON

length unit
type: Class
subclass of: measurement unit label
editor preferred term: length unit
imported from: UO

mass unit
type: Class
subclass of: measurement unit label
editor preferred term: mass unit
imported from: UO

time unit
type: Class
subclass of: measurement unit label
editor preferred term: time unit
imported from: UO

entity
type: Class
equivalent class: Class
  union of: continuant
  union of: occurrent
subclass of: Thing

continuant
type: Class
equivalent class: Class
  union of: dependent_continuant
  union of: independent_continuant
  union of: spatial_region
subclass of: entity
disjoint with: occurrent
comment: Definition: An entity [bfo: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.
comment: Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
comment: Synonyms: endurant

dependent_continuant
type: Class
equivalent class: Class
  union of: generically_dependent_continuant
  union of: specifically_dependent_continuant
subclass of: continuant
disjoint with: independent_continuant
disjoint with: spatial_region
comment: Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.

disposition
type: Class
subclass of: realizable_entity
disjoint with: function
disjoint with: role
comment: Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
comment: Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity.

fiat_object_part
type: Class
subclass of: material_entity
disjoint with: object
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
comment: Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso
comment: Synonyms: fiat substance part

function
type: Class
subclass of: realizable_entity
disjoint with: role
comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
comment: Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law

generically_dependent_continuant
type: Class
subclass of: dependent_continuant
disjoint with: specifically_dependent_continuant
comment: Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
comment: Examples: a certain PDF file that exists in different and in several hard drives

independent_continuant
type: Class
equivalent class: Class
  union of: material_entity
  union of: object_boundary
  union of: site
subclass of: continuant
disjoint with: spatial_region
comment: Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
comment: Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
comment: Synonyms: substantial entity

material_entity
type: Class
equivalent class: Class
  union of: fiat_object_part
  union of: object
  union of: object_aggregate
subclass of: independent_continuant
disjoint with: object_boundary
disjoint with: site
comment: Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
comment: Examples: collection of random bacteria, a chair, dorsal surface of the body

object
type: Class
subclass of: material_entity
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
comment: Examples: an organism, a heart, a chair, a lung, an apple
comment: Synonyms: substance

object_aggregate
type: Class
subclass of: material_entity
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
comment: Synonyms: substance aggregate

object_boundary
type: Class
subclass of: independent_continuant
disjoint with: site
comment: Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
comment: Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
comment: Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
comment: Synonyms: substance boundary

one_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: three_dimensional_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with one dimension.
comment: Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space

quality
type: Class
subclass of: specifically_dependent_continuant
disjoint with: realizable_entity
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
comment: Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee

realizable_entity
type: Class
subclass of: specifically_dependent_continuant
comment: Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap: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.
comment: Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity

role
type: Class
subclass of: realizable_entity
comment: Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
comment: Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university

site
type: Class
subclass of: independent_continuant
comment: Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
comment: Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
comment: Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.

spatial_region
type: Class
equivalent class: Class
  union of: one_dimensional_region
  union of: three_dimensional_region
  union of: two_dimensional_region
  union of: zero_dimensional_region
subclass of: continuant
comment: Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
comment: Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
comment: Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
comment: Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
comment: Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe

specifically_dependent_continuant
type: Class
equivalent class: Class
  union of: quality
  union of: realizable_entity
subclass of: dependent_continuant
comment: Definition: A continuant [snap: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.
comment: Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
comment: Synonyms: property, trope, mode

three_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with three dimensions.
comment: Examples: a cube-shaped part of space, a sphere-shaped part of space

two_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with two dimensions.
comment: Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space

zero_dimensional_region
type: Class
subclass of: spatial_region
comment: Definition: A spatial region [snap:SpatialRegion] with no dimensions.
comment: Examples: a point

connected_spatiotemporal_region
type: Class
equivalent class: Class
  union of: spatiotemporal_instant
  union of: spatiotemporal_interval
subclass of: spatiotemporal_region
disjoint with: scattered_spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].
comment: Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus

connected_temporal_region
type: Class
equivalent class: Class
  union of: temporal_instant
  union of: temporal_interval
subclass of: temporal_region
disjoint with: scattered_temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
comment: Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis

fiat_process_part
type: Class
subclass of: processual_entity
disjoint with: process
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life

occurrent
type: Class
equivalent class: Class
  union of: processual_entity
  union of: spatiotemporal_region
  union of: temporal_region
subclass of: entity
comment: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
comment: Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
comment: Synonyms: perdurant

process
type: Class
subclass of: processual_entity
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: the life of an organism, the process of sleeping, the process of cell-division

process_aggregate
type: Class
subclass of: processual_entity
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
comment: Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together

process_boundary
type: Class
subclass of: processual_entity
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
comment: Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery

processual_context
type: Class
subclass of: processual_entity
comment: Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
comment: Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
comment: Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.

processual_entity
type: Class
equivalent class: Class
  union of: fiat_process_part
  union of: process
  union of: process_aggregate
  union of: process_boundary
  union of: processual_context
subclass of: occurrent
disjoint with: spatiotemporal_region
disjoint with: temporal_region
comment: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
comment: Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird

scattered_spatiotemporal_region
type: Class
subclass of: spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
comment: Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair

scattered_temporal_region
type: Class
subclass of: temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
comment: Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair

spatiotemporal_instant
type: Class
subclass of: connected_spatiotemporal_region
disjoint with: spatiotemporal_interval
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
comment: Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process

spatiotemporal_interval
type: Class
subclass of: connected_spatiotemporal_region
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
comment: Examples: the spatiotemporal region occupied by a process or by a fiat processual part

spatiotemporal_region
type: Class
equivalent class: Class
  union of: connected_spatiotemporal_region
  union of: scattered_spatiotemporal_region
subclass of: occurrent
disjoint with: temporal_region
comment: Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.
comment: Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.
comment: Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.
comment: Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
comment: Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis

temporal_instant
type: Class
subclass of: connected_temporal_region
disjoint with: temporal_interval
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
comment: Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death

temporal_interval
type: Class
subclass of: connected_temporal_region
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
comment: Examples: any continuous temporal duration during which a process occurs

temporal_region
type: Class
equivalent class: Class
  union of: connected_temporal_region
  union of: scattered_temporal_region
subclass of: occurrent
comment: Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
comment: Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
comment: Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
comment: Definition: An occurrent [span:Occurrent] that is part of time.
comment: Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death

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

failed exploratory term
type: Thing
type: obsolescence reason specification
type: NamedIndividual
definition editor: Person:Alan Ruttenberg
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job

metadata complete
type: Thing
type: curation status specification
type: NamedIndividual
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
type: curation status specification
label: placeholder
definition: This isn't a class that OBI will keep - it's a placeholder for edits that are underway. The class name should start with an underscore
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
definition: Class has undergone final review, is ready for use, and will be included in the next OBI release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor.

core
type: NamedIndividual
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by OBI to identify main classes.
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot

placeholder removed
type: NamedIndividual
type: obsolescence reason specification

terms merged
type: NamedIndividual
type: obsolescence reason specification
editor note: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

other
type: NamedIndividual
type: obsolescence reason specification
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.

defined class
type: NamedIndividual
type: denotator type
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
definition editor: Alan Ruttenberg
definition source: group:OBI