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
term 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
term 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
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
has curation status: pending final vetting

has obsolescence reason
type: AnnotationProperty
term editor: PERSON:Alan Ruttenberg
term 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

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.

BrightonFormula
type: AnnotationProperty
example of usage: AngEdGenLoc - angioedema, localized or generalized
definition: An annotation property reflecting the string used by Brighton in their ABC tool to encode the term
example of usage: SuddOnset = sudden onset

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.

axiom id
type: AnnotationProperty

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.

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.

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.

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

has_specified_input
type: AnnotationProperty
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
editor preferred 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.
term editor: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
type: ObjectProperty
sub property of: has participant
domain: planned process

expand expression to
type: AnnotationProperty
term 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.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
editor preferred term: expand expression to

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>
term 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.
term editor: GROUP:OBI
definition source: OBI_0000277
editor preferred term: in branch

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

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

antisymmetric property
type: AnnotationProperty
term 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

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.

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

has_specified_output
type: AnnotationProperty
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term 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.
term editor: PERSON: Alan Ruttenberg
imported from: obi.owl
type: ObjectProperty
sub property of: has participant
domain: planned process
inverse of: is_specified_output_of

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

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

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>
term editor: PERSON:Daniel Schober
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred term: editor preferred term
has curation status: ready for release

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

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
term 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

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

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

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

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

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.

has component
type: ObjectProperty
sub property of: has part

is part of
type: ObjectProperty
type: TransitiveProperty
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
alternative term: part of
alternative term: part_of
domain: entity
range: entity
inverse of: has part
sub property of: is located in

domain of part of
type: Axiom
annotated target: entity
annotated source: is part of
axiom id: BFO_0010001
annotated property: domain

has part
type: ObjectProperty
type: TransitiveProperty
alternative term: has_part

inheres in
type: ObjectProperty
type: FunctionalProperty
alternative term: inheres_in
range: independent continuant
domain: dependent continuant
inverse of: is bearer of
sub property of: s depends on

is bearer of
type: ObjectProperty
alternative term: bearer of
alternative term: bearer_of
domain: independent continuant
range: dependent continuant

is realized by
type: ObjectProperty
alternative term: realized by
alternative term: realized_by

realizes
type: ObjectProperty
domain: process
range: realizable entity
inverse of: is realized by

participates in
type: ObjectProperty
alternative term: participates_in

has participant
type: ObjectProperty
alternative term: has_participant
range: continuant
domain: process
inverse of: participates in
property chain axiom: realizes
property chain axiom: inheres in

is concretization of
type: ObjectProperty
alternative term: concretization of
alternative term: concretization_of
range: specifically dependent continuant
domain: generically dependent continuant

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
inverse of: is concretization of

is immediately preceded by
type: ObjectProperty
type: FunctionalProperty
alternative term: immediately preceded by
alternative term: immediately_preceded_by
sub property of: is preceded by

immediately precedes
type: ObjectProperty
type: FunctionalProperty
alternative term: immediately_precedes
domain: process
range: process
inverse of: is immediately preceded by
sub property of: precedes

is preceded by
type: ObjectProperty
type: TransitiveProperty
alternative term: preceded by
alternative term: preceded_by

precedes
type: ObjectProperty
type: TransitiveProperty
range: process
domain: process
inverse of: is preceded by

is course of
type: ObjectProperty
alternative term: course of
alternative term: course_of
sub property of: has participant

has course
type: ObjectProperty
alternative term: has_course
domain: continuant
range: process
sub property of: participates in
inverse of: is course of

occurs in
type: ObjectProperty
alternative term: occurs_in
range: independent continuant
domain: process
inverse of: has site of
property chain axiom: is part of

has site of
type: ObjectProperty
alternative term: has_site_of

begins to exist during
type: ObjectProperty
alternative term: begins_to_exist_during
domain: continuant
range: process
sub property of: participates in

ceases to exist during
type: ObjectProperty
alternative term: ceases_to_exist_during
domain: continuant
range: process
sub property of: participates in

s depends on
type: ObjectProperty
alternative term: s_depends_on
range: independent continuant
domain: specifically dependent continuant

has granular part
type: ObjectProperty
alternative term: has_granular_part
sub property of: has part

has granular process part
type: ObjectProperty
alternative term: has_granular_process_part
sub property of: has part

is granular part of
type: ObjectProperty
alternative term: granular part of
alternative term: granular_part_of
range: material entity
domain: material entity
sub property of: is part of
inverse of: has granular part

is granular part of process
type: ObjectProperty
alternative term: granular part of process
alternative term: granular_part_of_process
domain: process
range: process
sub property of: is part of
inverse of: has granular process part

is aggregate of
type: ObjectProperty
alternative term: aggregate of
alternative term: aggregate_of
sub property of: is part of

is fiat part of
type: ObjectProperty
alternative term: fiat part of
alternative term: fiat_part_of
sub property of: is part of

has participant beginning to exist
type: ObjectProperty
alternative term: has_participant_beginning_to_exist
sub property of: has participant
inverse of: begins to exist during

has participant ceasing to exist
type: ObjectProperty
alternative term: has_participant_ceasing_to_exist
sub property of: has participant
inverse of: ceases to exist during

is function of
type: ObjectProperty
alternative term: function of
alternative term: function_of
domain: function
sub property of: inheres in

is quality of
type: ObjectProperty
alternative term: quality of
alternative term: quality_of
domain: quality
sub property of: inheres in

is role of
type: ObjectProperty
alternative term: role of
alternative term: role_of
domain: role
sub property of: inheres in

is located in
type: ObjectProperty
alternative term: located in
alternative term: located_in

is located at
type: ObjectProperty
alternative term: located at
alternative term: located_at

g depends on
type: ObjectProperty
alternative term: g_depends_on
range: independent continuant
domain: generically dependent continuant

has function
type: ObjectProperty
alternative term: has_function

has quality
type: ObjectProperty
label: has_quality
alternative term: has_quality
sub property of: is bearer of
imported from: obi.owl

has role
type: ObjectProperty
alternative term: has_role

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

obsolete_specifically denotes
type: ObjectProperty
editor note: 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
term editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
definition: c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
has obsolescence reason: failed exploratory term
has curation status: pending final vetting
sub property of: ObsoleteProperty

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.
term 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
term editor: PERSON: Jonathan Rees
term 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
term editor: person:Alan Ruttenberg
sub property of: is about

obsolete_materially denotes
type: ObjectProperty
editor note: see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
has obsolescence reason: failed exploratory term
sub property of: ObsoleteProperty

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
term 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
range: quality
domain: measurement datum
sub property of: is about

obsolete_describes
type: ObjectProperty
has obsolescence reason: failed exploratory term
sub property of: ObsoleteProperty

obsolete_represents
type: ObjectProperty
has obsolescence reason: failed exploratory term
sub property of: ObsoleteProperty

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
sub property of: has part
domain: cartesian spatial coordinate datum
range: length unit

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

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
term 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
term editor: Person:Alan Ruttenberg
term 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
term editor: Person:Alan Ruttenberg
term 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
term editor: Alan Ruttenberg
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
sub property of: has part
has curation status: metadata incomplete
range: time measurement datum
domain: time stamped measurement datum

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

is_specified_output_of
type: ObjectProperty
term 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.
term editor: Alan Ruttenberg
sub property of: participates in
range: planned process
imported from: obi.owl

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

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

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

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

diagnosis guideline
type: Class
subclass of: directive information entity
definition: A directive information entity that specifies how to establish a diagnosis based on clinical findings

disorder resulting from an AEFI process
type: Class
equivalent class: Class
  intersection of: disorder resulting from an adverse event process
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: adverse event following immunization process
subclass of: disorder resulting from an adverse event process
comment: MC, 20110120: AR mentioned that the use of is_specified_output is not appropriate, as this would indicate that the adverse event process is a planned process - specified output are things that are specified in the plan to realize a process. Adverse events are not planned process but processual entities, and therefore this should be updated. AR mentioned that BFO will include an appropriate relation.
comment: MC, 20110120: This class should have a different label for OBO Foundry unique label. "adverse event following immunization" is a term in use by the clinician community, however in the context if the Foundry it may be confusing to associate the word "event" which seem to refer to a process with the hierarchical position under continuant. Proposed OBO Foundry label: disorder resulting from an AEFI
comment: MC, 20110126: class renamed from "adverse event following immunization continuant" following AR suggestion

Brighton case definition
type: Class
subclass of: diagnosis guideline
definition: A diagnosis guideline specifying how to establish a diagnosis of adverse event with an associated degree of certainty, as developed by the Brighton Collaboration, http://www.brightoncollaboration.org/
comment: MC, 20110126: this should be linked to the different adverse events reported. AR suggests using a new relation to appear in BFO2, maybe "ascription"

Brighton assessment of generalized convulsive seizure as an adverse event following immunization
type: Class
equivalent class: Class
  one of: Level 1 of certainty of generalized convulsive seizure as an adverse event following immunization
  one of: not a case of generalized convulsive seizure
  one of: Reported generalized convulsive seizure with insufficient evidence to meet the case definition
  one of: Level 2 of certainty of generalized convulsive seizure as an adverse event following immunization
  one of: Level 3 of certainty of generalized convulsive seizure as an adverse event following immunization
subclass of: Brighton assessment
subclass of: Restriction
  on property: is about
  some values from: adverse event
definition source: a categorical measurement datum whose instances are used to classify adverse events according to whether or not they have some likelihood of being a seizure and if so, to what degree
definition source: PMID:14741144#Generalized convulsive seizure as an adverse event following immunization: case definition and guidelines for data collection, analysis, and presentation.

disorder resulting from an adverse event process
type: Class
equivalent class: Class
  intersection of: disorder
  intersection of: Restriction
    on property: begins to exist during
    some values from: adverse event process
comment: MC, 20110120: AR mentioned that the use of is_specified_output is not appropriate, as this would indicate that the adverse event process is a planned process - specified output are things that are specified in the plan to realize a process. Adverse events are not planned process but processual entities, and therefore this should be updated. AR mentioned that BFO will include an appropriate relation.
comment: MC, 20110120: This class was initially labeled "adverse event continuant". After discussion with AR, and due to the fact that the word "event" implicitely refers to a process, we renamed this class.

adverse event rash
type: Class
equivalent class: Class
  intersection of: disorder resulting from an adverse event process
  intersection of: rash
comment: MC, 20110120: This class should have a different label for OBO Foundry unique label. "adverse event rash" is a term in use by the clinician community, however in the context if the Foundry it may be confusing to associate the word "event" which seem to refer to a process with the hierarchical position under continuant. Proposed OBO Foundry label: rash resulting from an adverse event

AEFI rash
type: Class
equivalent class: Class
  intersection of: disorder resulting from an AEFI process
  intersection of: rash
comment: MC, 20110120: This class should have a different label for OBO Foundry unique label. "AEFI_rash" is a term in use by the clinician community, however in the context if the Foundry it may be confusing to associate the word "event" which seem to refer to a process with the hierarchical position under continuant. Proposed OBO Foundry label: rash resulting from an AEFI process

rash
type: Class
subclass of: disorder
definition: A rash is a change of the skin which affects its color, appearance or texture.
definition source: WEB: http://en.wikipedia.org/wiki/Rash

adverse event
type: Class
equivalent class: Class
  union of: disorder resulting from an adverse event process
  union of: adverse event process
definition: An adverse event is an undesirable, unfavorable and unintended medical occurrence presenting in a predetermined time frame following administration of a compound or usage of a device
comment: I initialy made adverse event a defined class: is_a sign and preceded by administration. However, by doing so, and as the range of preceded by is processual entities, I was implicitely making adverse event a subclass of processual entity, therfore making adverse event rash (a continuant) inconsistent.
definition source: ICH Topic E 2 A Clinical Safety Data Management: Definitions and Standards for Expedited Reporting

adverse event following immunization
type: Class
equivalent class: Class
  union of: disorder resulting from an AEFI process
  union of: adverse event following immunization process
subclass of: adverse event
definition: An adverse event is an undesirable, unfavorable and unintended medical occurrence presenting in a predetermined time frame following administration of a vaccine
definition source: Adapted from ICH Topic E 2 A Clinical Safety Data Management: Definitions and Standards for Expedited Reporting

_manifestations
type: Class
subclass of: process
comment: temporary placeholder - to be removed This class just helps me group some terms during development of the structure

Idiopathic thrombocytopenic purpura
type: Class
subclass of: _manifestations
definition: Idiopathic thrombocytopenic purpura (ITP) is the condition of having a low platelet count (thrombocytopenia) of no known cause (idiopathic).v
definition source: http://en.wikipedia.org/wiki/Idiopathic_thrombocytopenic_purpura

encephalitis
type: Class
subclass of: _manifestations
subclass of: Restriction
  on property: stimulates
  some values from: inflammatory response
subclass of: Restriction
  on property: unfolds_in
  some values from: brain
definition: Encephalitis is an inflammation of the brain. It may be caused by a number of different factors. One of the most common causes is direct infection of the brain by a virus or bacterium. Inflammation can also occur as a complication of some other disorder, such as mumps (see mumps entry) or herpes simplex (see herpes infections entry).
definition source: http://www.faqs.org/health/Sick-V2/Encephalitis-Definition.html

motor manifestation
type: Class
subclass of: _manifestations
definition: A _manifestation involving the motor system

adverse event process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: is preceded by
    some values from: Class
      union of: adding a material entity into a target
      union of: administering substance in vivo
definition: An adverse event process is a processual entity occurring in a pre determined time frame following administration of a compound or usage of a device
comment: I included the usage of a device into the definition of adverse event as I am aiming at being inclusive, and cover cases such as those described by MAUDE - Manufacturer and User Facility Device Experience. See for example http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfMAUDE/detail.cfm?mdrfoi__id=1942591 - a patient get fitted with bioprosthetic heart valves and dies within the following 4 months.
comment: Note that this definition of adverse event doesn't imply any type of causality between the sign observed and the coumpond administration/device utilization. For our purposes, we consider any type of sign presenting within a specific time frame after the coumpound administration/device utilization to be an adverse event.

adverse event following immunization process
type: Class
equivalent class: Class
  intersection of: adverse event process
  intersection of: Restriction
    on property: is preceded by
    some values from: vaccination
subclass of: adverse event process

generalized convulsive seizure according to Brighton criteria
type: Class
subclass of: process
subclass of: Restriction
  on property: has part
  some values from: motor manifestation
subclass of: Class
  intersection of: Restriction
    on property: regulates
    some values from: behavior
  intersection of: Restriction
    on property: unfolds_in
    some values from: nervous system

AEFI generalized convulsive seizure according to Brighton guideline
type: Class
equivalent class: Class
  intersection of: adverse event
  intersection of: Restriction
    on property: is preceded by
    some values from: vaccination
  intersection of: Restriction
    on property:
      inverse of: is about
    some values from: Class
      one of: Level 1 of certainty of generalized convulsive seizure as an adverse event following immunization
      one of: Level 2 of certainty of generalized convulsive seizure as an adverse event following immunization
      one of: Level 3 of certainty of generalized convulsive seizure as an adverse event following immunization

seizure level 1 of certainty according to the Brighton criteria
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: witnessed sudden loss of consciousness
  intersection of: Restriction
    on property: has part
    some values from: Class
      union of: generalized atonic motor manifestation
      union of: generalized clonic motor manifestation
      union of: generalized tonic motor manifestation
      union of: generalized tonic-clonic motor manifestation
subclass of: generalized convulsive seizure according to Brighton criteria
comment: MC, 20110126: this needs to be linked to the Brighton guideline defined under directive information entity
definition: witnessed sudden loss of consciousness AND generalized, tonic, clonic, tonic–clonic, or atonic motor manifestations. (atonic In the absence of: hypotonic hyporesponsive episode (as deﬁned by the Brighton Collaboration), syncope, and myoclonic jerks.

seizure level 2 of certainty according to the Brighton criteria
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: history of unconsciousness
  intersection of: Restriction
    on property: has part
    some values from: Class
      union of: generalized atonic motor manifestation
      union of: generalized clonic motor manifestation
      union of: generalized tonic motor manifestation
      union of: generalized tonic-clonic motor manifestation
subclass of: generalized convulsive seizure according to Brighton criteria
comment: MC, 20110126: this needs to be linked to the Brighton guideline defined under directive information entity
definition: history of unconsciousness AND generalized, tonic, clonic, tonic–clonic, or atonic motor manifestations. (atonic In the absence of: hypotonic hyporesponsive episode (as deﬁned by the Brighton Collaboration), syncope, and myoclonic jerks.

seizure level 3 of certainty according to the Brighton criteria
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: generalized motor manifestation
  intersection of: Restriction
    on property: has part
    some values from: history of unconsciousness
subclass of: generalized convulsive seizure according to Brighton criteria
comment: MC, 20110126: this needs to be linked to the Brighton guideline defined under directive information entity
definition: history of unconsciousness AND other generalized motor manifestations.

atonic motor manifestation
type: Class
subclass of: motor manifestation
definition: A sudden loss of tone in postural muscle, often preceded by a myoclonic jerk and precipitated by hyperventilation
definition source: Brighton Collaboration, http://www.brightoncollaboration.org/

generalized atonic motor manifestation
type: Class
equivalent class: Class
  intersection of: atonic motor manifestation
  intersection of: generalized motor manifestation
subclass of: atonic motor manifestation

clonic motor manifestation
type: Class
subclass of: motor manifestation
definition source: Brighton Collaboration, http://www.brightoncollaboration.org/
definition: Sudden, brief (100ms) involuntary contractions of the same muscle groups, regularly repetitive at a frequency of about two to three contractions per second.

generalized motor manifestation
type: Class
equivalent class: Class
  intersection of: motor manifestation
  intersection of: Restriction
    on property: unfolds_in
    all values from: bilateral site
definition source: Brighton Collaboration, http://www.brightoncollaboration.org/
definition: bilateral motor manifestation, more than minimal muscle involvement

generalized clonic motor manifestation
type: Class
equivalent class: Class
  intersection of: clonic motor manifestation
  intersection of: generalized motor manifestation

generalized tonic motor manifestation
type: Class
equivalent class: Class
  intersection of: generalized motor manifestation
  intersection of: tonic motor manifestation

generalized tonic-clonic motor manifestation
type: Class
equivalent class: Class
  intersection of: generalized motor manifestation
  intersection of: tonic motor manifestation

hypotonic-hyporesponsive episode
type: Class
subclass of: _manifestations
alternative term: HHE
definition: HHE is characterized by sudde onset of reduced muscle tone, hyporesponsiveness (i.e., less responsive than usual to verbal or other sensorial stimuli) and change of skin color (pallor or cyanosis)

bilateral
type: Class
subclass of: quality
definition source: http://www.thefreedictionary.com/bilateral
definition: Affecting or undertaken by two sides equally; binding on both parties

diagnosing generalized convulsive seizure according to Brighton guidelines
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: is concretization of
    all values from: Brighton case definition of generalized convulsive seizure as an adverse event following immunization
subclass of: performing a diagnosis according to a Brighton case definition
subclass of: Restriction
  on property: has_specified_output
  some values from: Brighton assessment of generalized convulsive seizure as an adverse event following immunization
definition: performing a diagnosis specified by the Brighton case definition for convulsive seizure as an adverse event following immunization

Brighton case definition of generalized convulsive seizure as an adverse event following immunization
type: Class
subclass of: Brighton case definition
subclass of: Restriction
  on property: concretizes
  some values from: Restriction
    on property: is realized by
    all values from: diagnosing generalized convulsive seizure according to Brighton guidelines
definition source: PMID:14741144#Generalized convulsive seizure as an adverse event following immunization: case definition and guidelines for data collection, analysis, and presentation.
definition: A Brighton case definition of generalized convulsive seizure as an adverse event following immunization

shaking
type: Class
subclass of: motor manifestation
alternative term: quivering
definition: repetitive, cyclical movements of the body or a body part; usually involuntary, but can also manifest in response to an attempt at movement
alternative term: shivering
alternative term: trembling
alternative term: tremor

bilateral shaking
type: Class
equivalent class: Class
  intersection of: shaking
  intersection of: Restriction
    on property: unfolds_in
    all values from: bilateral site
subclass of: shaking
definition: A shaking process which unfolds in both sides of an organism

syncope
type: Class
subclass of: motor manifestation
comment: MC, 20110126: The Brighton guideline on which this is based needs to be checked. Email correspondance with Brighton: [MC] One thing is unclear to me: Level 1 of diagnostic certainty is defined as "witnessed sudden loss of consciousness AND generalized, tonic, clonic, tonicâclonic, or atonic motor manifestations." A footnote adds: atonic in the absence of: hypotonic hyporesponsive episode (as deï¬ned by the Brighton Collaboration), syncope, and myoclonic jerks. If we define syncope as being a loss of consciousness, how can I have a witnessed sudden loss of consciousness and a generalized atonic motor manifestation in the absence of syncope? [Brighton] Thank you for your question. You are right, that there is an overlap between the clinical presentation of an atonic seizure and a Syncope. This is also true for HHE. This is the very reasonf or the footnote to alert the user of the definition to this differential diagnosis. If you are working on a database and only have the clinical criteria vailable, you may have some false positives for the atonic seizure cases, unless you obtain additional information, e.g. that the Syncope was vasovagal or orthostatic, or arrhythmic, etc.
definition source: http://en.wikipedia.org/wiki/Syncope_%28medicine%29
definition: loss of consciousness, fainting

myoclonic jerk
type: Class
subclass of: motor manifestation
definition: A myoclonic jerk is the brief, involuntary twitching of a muscle or group of muscles. It may be caused either by a sudden muscle contraction, or a sudden lapse of contraction. This happens when a person is on the verge of falling asleep, and suddenly have a sensation or feeling that they are free falling through the air. Contractions are called positive myoclonus; relaxations are called negative myoclonus. When falling asleep, it is common for people to experience a type of myoclonic jerk known as a hypnic jerk. Hiccups are also a kind of myoclonic jerk specifically affecting the diaphragm.
definition source: http://house.wikia.com/wiki/Myoclonic_jerk

tonic motor manifestation
type: Class
label: tonic-clonic motor manifestation
subclass of: motor manifestation
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: tonic motor manifestation
    intersection of: Restriction
      on property: precedes
      all values from: clonic motor manifestation
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: clonic motor manifestation
    intersection of: Restriction
      on property: is preceded by
      all values from: tonic motor manifestation
definition: A sequence consisting of a tonic followed by a clonic phase
definition: A sustained increase in muscle contraction lasting a few seconds to minutes

loss of consciousness
type: Class
subclass of: motor manifestation
definition: i.e., unreactive to verbal and painful stimuli

history of unconsciousness
type: Class
subclass of: loss of consciousness
definition source: Brighton Collaboration, http://www.brightoncollaboration.org/
comment: MC, 20110126: AR suggest that "history of consciousness is not a process. definition reads "the sudden loss of consciousness was not observed, but the patient was found unconscious", so maybe updating the label would be better : "unwitnessed loss of consciousness with history of unconsciousness" would help
definition: the sudden loss of consciousness was not observed, but the patient was found unconscious

witnessed sudden loss of consciousness
type: Class
subclass of: history of unconsciousness
subclass of: Restriction
  on property: realizes
  some values from: witness role
definition source: Brighton Collaboration, http://www.brightoncollaboration.org/

bilateral site
type: Class
subclass of: site
subclass of: Restriction
  on property: has quality
  some values from: bilateral

witness role
type: Class
subclass of: role
definition: A role inhering in a person that is realized when the bearer sees an event and reports what happened
definition source: adapted from http://golovchenko.org/cgi-bin/wnsearch?q=witness

AEFI encephalitis
type: Class
equivalent class: Class
  intersection of: encephalitis
  intersection of: Restriction
    on property: is preceded by
    some values from: vaccination
subclass of: encephalitis

AEFI Idiopathic thrombocytopenic purpura
type: Class
equivalent class: Class
  intersection of: Idiopathic thrombocytopenic purpura
  intersection of: Restriction
    on property: is preceded by
    some values from: vaccination
subclass of: Idiopathic thrombocytopenic purpura

AEFI: hypotonic-hyporesponsive episode
type: Class
equivalent class: Class
  intersection of: hypotonic-hyporesponsive episode
  intersection of: Restriction
    on property: is preceded by
    some values from: vaccination
subclass of: hypotonic-hyporesponsive episode

adverse side effect
type: Class
subclass of: adverse event
definition: side effect is an adverse event of a type that has been determined by a review board to be causally related to the intervention.
comment: while in some cases the particular may not be actually caused by the intervention, it is an adverse side effect nonetheless.

device malfunction
type: Class
subclass of: process
subclass of: Restriction
  on property: has_specified_input
  some values from: device
definition: A process in which the device doesn't perform as expected
editor preferred term: device malfunction

adverse event report
type: Class
subclass of: report
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: adverse event
    union of: device malfunction
subclass of: Restriction
  on property: is_specified_output_of
  some values from: adverse event reporting process
definition: A report as submitted in an adverse event reporting system
editor note: MC, 20110719: not all adverse event report are about adverse event. See for example cases in MAUDE database that are about potential adverse events such as device malfunctions.
editor preferred term: adverse event report

reporting process
type: Class
subclass of: process
subclass of: Restriction
  on property: has_specified_output
  some values from: report
definition: The process of creating documentation about something and adding it to a system allowing further analysis of the reported entity

sudden onset
type: Class
subclass of: BrightonTerms
definition: The term sudden onsets refers to an event that occurred unexpectedly and without warning leading to a marked change in a subjects previously stable condition
definition source: Anaphylaxis: Case definition and guidelines for data collection, analysis, and presentation of immunization safety data. Vaccine 25 (2007) 5675–5684
BrightonFormula: SuddOnset

rapid progression
type: Class
subclass of: BrightonTerms
definition: The term rapid progression is a conventional clinical term. An exact timeframe sould not be offered since it would have to refer to a wide range of signs and symptoms without a scientific evidence base. Using an arbitrarily restrictive setpoint might bias future data collection unnecessarily.
definition source: Anaphylaxis: Case definition and guidelines for data collection, analysis, and presentation of immunization safety data. Vaccine 25 (2007) 5675–5684
BrightonFormula: RapidProgr

anaphylaxis
type: Class
subclass of: BrightonDiagnosis

generalized urticaria
type: Class
subclass of: BrightonTerms
alternative term: hives
BrightonFormula: UrticariaGen

generalized erythema
type: Class
subclass of: BrightonTerms
BrightonFormula: ErythemaGen

angioedema
type: Class
subclass of: BrightonTerms
curator note: localized or generalized
BrightonFormula: AngEdGenLoc

generalized pruritus
type: Class
subclass of: BrightonTerms
BrightonFormula: PruritusGen

skin rash
type: Class
subclass of: BrightonTerms
BrightonFormula: SkinRash

measured hypotension
type: Class
subclass of: BrightonTerms
BrightonFormula: HypotensMeas

tachycardia
type: Class
subclass of: uncompensated shock sign
BrightonFormula: TacchyCard

capillary refill time > 3s
type: Class
subclass of: uncompensated shock sign
BrightonFormula: CapRefillOver3

reduced central pulse volume
type: Class
subclass of: uncompensated shock sign
BrightonFormula: PulseVolRed

decreased level of consciousness or loss of consciousness
type: Class
subclass of: uncompensated shock sign
curator note: should be a union class
BrightonFormula: ConscDecr

bilateral wheeze
type: Class
subclass of: BrightonTerms
alternative term: bronchospasm
BrightonFormula: WheezeBilat

stridor
type: Class
subclass of: BrightonTerms
BrightonFormula: Stridor
definition: a harsh or vibrating noise when breathing caused by obstruction of the windpipe or larynx.

upper airway swelling
type: Class
subclass of: BrightonTerms
curator note: lip, tongue, throat, uvula or larynx
BrightonFormula: SwellUpAirways

tachypnoea
type: Class
subclass of: respiratory distress sign
disjoint with: cyanosis
BrightonFormula: TachyPnea

increased use of accessory respiratory muscles
type: Class
subclass of: respiratory distress sign
disjoint with: cyanosis
BrightonFormula: RespMuscAccIncr
curator note: sternocleidomastoid, intercostals, etc

recession
type: Class
subclass of: respiratory distress sign
disjoint with: cyanosis
BrightonFormula: Recess

cyanosis
type: Class
subclass of: respiratory distress sign
disjoint with: grunting
BrightonFormula: Cyanosis

grunting
type: Class
subclass of: respiratory distress sign
BrightonFormula: Grunting

respiratory distress
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has component
    on class: respiratory distress sign
    min qualified cardinality: 2
  intersection of: Restriction
    on property: has component
    on class: tachypnoea
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: increased use of accessory respiratory muscles
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: recession
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: cyanosis
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: grunting
    max qualified cardinality: 1
subclass of: _BrightonMidLevelTerms
definition: respiratory distress—2 or more of the following: • tachypnoea • increased use of accessory respiratory muscles (sternocleidomastoid, intercostals, etc.) • recession • cyanosis • grunting

respiratory distress sign
type: Class
subclass of: BrightonTerms
curator note: a helper class which allows us to define a qualified cardinality restriction for respiratory distress such as used in the case definition of anaphylaxis.Respiratory distress is defined as having at least 2 respiratory distress signs

infected abscess
type: Class
subclass of: disorder
definition: A localized collection of pus in a cavity formed by the disintegration of tissue, usually caused by microorganisms that invade the tissues.
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf

sterile abscess
type: Class
subclass of: disorder
definition: An abscess whose contents are not caused by pyogenic bacteria.
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf

cellulitis
type: Class
subclass of: inflammatory response
definition: A diffuse inflammatory process within solid tissues, characterized by edema, redness, pain, and interference with function, usually caused by infection with streptococci, staphylococci, or similar organisms.
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf

nodule
type: Class
subclass of: disorder
definition: A firm, small mass of tissue at the injection site with discrete or well demarcated borders in the absence of abscess formation, erythema and warmth.
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf

lymphadenitis
type: Class
subclass of: inflammatory response
definition: Inflammation of one or more lymph nodes, usually caused by a primary focus of infection elsewhere in the body.
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf

erythema
type: Class
subclass of: rash
definition: Abnormal redness of the skin.
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf

induration
type: Class
subclass of: disorder
definition source: PHAC user guide, http://www.phac-aspc.gc.ca/im/pdf/AEFI-ug-gu-eng.pdf
definition: Palpable thickening, firmness or hardening of soft tissue that is assessed by a health care provider

performing a diagnosis according to a Brighton case definition
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: is concretization of
    some values from: Brighton case definition
subclass of: performing a diagnosis

Brighton assessment
type: Class
subclass of: categorical measurement datum
definition: The assessment performed upon review of an adverse event report according to the Brighton case definitions

adverse event reporting process
type: Class
subclass of: reporting process
subclass of: Restriction
  on property: has_specified_output
  some values from: adverse event report
definition: The process of creating documentation about an adverse event and adding it to a system allowing further analysis of the event

clinical diagnosis of uncompensated shock
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has component
    on class: uncompensated shock sign
    min qualified cardinality: 2
  intersection of: Restriction
    on property: has component
    on class: tachycardia
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: capillary refill time > 3s
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: reduced central pulse volume
    max qualified cardinality: 1
  intersection of: Restriction
    on property: has component
    on class: decreased level of consciousness or loss of consciousness
    max qualified cardinality: 1
subclass of: _BrightonMidLevelTerms
definition: combination of at least 3 of the following: - tachycardia - capillary refill time > 3s - reduced central pulse volume - decreased level of consciousness or loss of consciousness

uncompensated shock sign
type: Class
subclass of: BrightonTerms
definition: a helper class which allows us to define a qualified cardinality restriction for uncompensated shock such as used in the case definition of anaphylaxis. Clinical diagnosis of uncompensated shock is defined as having at least 3 uncompensated shock signs

entity
type: Class
subclass of: Thing
editor preferred term: entity

continuant
type: Class
subclass of: entity
disjoint with: occurrent
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
example of usage: a heart
example of usage: a person
example of usage: a symphony orchestra
editor preferred term: continuant
alternative term: endurant
example of usage: the color of a tomato
example of usage: the disposition of blood to coagulate
example of usage: the lawn and atmosphere in front of our building
example of usage: the mass of a cloud

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
example of usage: a surgical operation as processual context for a nosocomical infection
editor preferred term: occurrent
alternative term: perdurant
example of usage: the life of an organism
example of usage: the most interesting part of Van Gogh's life
example of usage: the spatiotemporal context occupied by a process of cellular meiosis
example of usage: the spatiotemporal region occupied by the development of a cancer tumor

independent continuant
type: Class
subclass of: continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a person
example of usage: a symphony orchestra
example of usage: an organism
editor preferred term: independent continuant
alternative term: substantial entity
example of usage: the bottom right portion of a human torso
example of usage: the lawn and atmosphere in front of our building

dependent continuant
type: Class
subclass of: continuant
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
editor preferred term: dependent continuant

spatial region
type: Class
subclass of: continuant
definition: A continuant that is neither bearer of quality entities nor inheres in any other entities.
editor note: 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.
editor note: 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].
editor note: 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.
example of usage: parts of the sum total of all space in the universe
editor preferred term: spatial region
example of usage: the sum total of all space in the universe

process
type: Class
subclass of: occurrent
definition: A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
editor preferred term: process
example of usage: the life of an organism
example of usage: the process of cell-division
example of usage: the process of sleeping

temporal region
type: Class
subclass of: occurrent
editor note: 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].
editor note: 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.
definition: An occurrent that is part of time.
editor note: 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].
editor preferred term: temporal region
example of usage: the duration of a surgical procedure
example of usage: the moment of death
example of usage: the time it takes to run a marathon

two dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with two dimensions.
example of usage: the surface of a cube-shaped part of space
example of usage: the surface of a rectilinear planar figure-shaped part of space
example of usage: the surface of a sphere-shaped part of space
editor preferred term: two dimensional region

disposition
type: Class
subclass of: realizable entity
definition: A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object has the disposition D to (transform, initiate a process) R under conditions C.
editor preferred term: disposition
example of usage: the disposition of a patient with a weakened immune system to contract disease
example of usage: the disposition of a vase to brake if dropped
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
example of usage: the disposition of vegetables to decay when not refrigerated

realizable entity
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
editor note: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
editor preferred term: realizable entity
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
example of usage: the function of the reproductive organs
example of usage: the role of being a doctor

zero dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with no dimensions.
example of usage: a point
editor preferred term: zero dimensional region

quality
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
editor preferred term: quality
example of usage: the ambient temperature of air
example of usage: the circumference of a waist
example of usage: the color of a tomato
example of usage: the mass of a piece of gold
example of usage: the shape of a nose
example of usage: the weight of a chimpanzee

specifically dependent continuant
type: Class
subclass of: dependent continuant
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
alternative term: mode
alternative term: property
editor preferred term: specifically dependent continuant
example of usage: the color of a tomato
example of usage: the disposition of fish to decay
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
example of usage: the liquidity of blood
example of usage: the mass of a cloud
example of usage: the role of being a doctor
example of usage: the smell of mozzarella
alternative term: trope

temporal instant
type: Class
subclass of: connected temporal region
definition: A connected temporal region comprising a single moment of time.
example of usage: right now
editor preferred term: temporal instant
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death

connected temporal region
type: Class
subclass of: temporal region
definition: A temporal region every point of which is mediately or immediately connected with every other point of which.
editor preferred term: connected temporal region
example of usage: the 1970s years
example of usage: the time from the beginning to the end of a heart attack
example of usage: the time taken up by cellular meiosis

role
type: Class
subclass of: realizable entity
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor preferred term: role
example of usage: the role of a biological grandfather as legal guardian in the context of a system of laws
example of usage: the role of a chemical compound in an experiment
example of usage: the role of a patient relative as defined by a hospital administrative form
example of usage: the role of a person as a surgeon
example of usage: the role of a student in a university
example of usage: the role of a woman as a legal mother in the context of system of laws
example of usage: the role of ingested matter in digestion

object boundary
type: Class
subclass of: independent continuant
definition: An independent continuant that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object entities that exist at exactly the point where the object is separated off from the rest of the existing entities in the world.
editor note: 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.
editor preferred term: object boundary
alternative term: substance boundary
example of usage: the outer surface of a cell or cell wall
example of usage: the surface of the earth
example of usage: the surface of the interior of the stomach
example of usage: the surface of the skin

one dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with one dimension.
example of usage: an edge of a cube-shaped part of space
editor preferred term: one dimensional region
example of usage: the part of space that is a line stretching from one end of absolute space to the other

three dimensional region
type: Class
subclass of: spatial region
definition: A spatial region with three dimensions.
example of usage: a cube-shaped part of space
example of usage: a sphere-shaped part of space
editor preferred term: three dimensional region

site
type: Class
subclass of: independent continuant
definition: An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.
editor note: 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 sites) 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).
example of usage: Maria's nostril or her intestines for a variety of bacteria
example of usage: a particular room in a particular hospital
editor preferred term: site

generically dependent continuant
type: Class
subclass of: dependent continuant
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
example of usage: a certain PDF file that exists in different and in several hard drives
editor preferred term: generically dependent continuant

scattered temporal region
type: Class
subclass of: temporal region
definition: A temporal region every point of which is not mediately or immediately connected with every other point of which.
editor preferred term: scattered temporal region
example of usage: the time occupied by the individual games of the World Cup
example of usage: the time occupied by the individual liaisons in a romantic affair

function
type: Class
subclass of: disposition
definition: A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
editor preferred term: function
example of usage: the digestive function of the stomach to nutriate the body
example of usage: the function of a birth canal to enable transport
example of usage: the function of a computer program to compute mathematical equations
example of usage: the function of a hammer to drive in nails
example of usage: the function of a judge in a court of law
example of usage: the function of an automobile to provide transportation
example of usage: the function of reproduction in the transmission of genetic material
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.

process boundary
type: Class
subclass of: occurrent
definition: A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
example of usage: birth
example of usage: death
editor preferred term: process boundary
example of usage: the detaching of a finger in an industrial accident
example of usage: the final separation of two cells at the end of cell-division
example of usage: the forming of a synapse
example of usage: the incision at the beginning of a surgery
example of usage: the onset of REM sleep

temporal interval
type: Class
subclass of: connected temporal region
definition: A connected temporal region lasting for more than a single moment of time.
example of usage: any continuous temporal duration during which a process occurs
editor preferred term: temporal interval

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: Examples: collection of random bacteria, a chair, dorsal surface of the body
editor note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
editor preferred term: material entity

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.owl

conditional specification
type: Class
subclass of: directive information entity
definition source: OBI branch derived
definition source: OBI_0000349
term 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: datum 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.
term editor: PERSON: Alan Ruttenberg
term 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
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
term editor: person:Chris Stoeckert
has curation status: uncurated

action specification
type: Class
subclass of: directive information entity
term 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

obsolete_artifact
type: Class
subclass of: ObsoleteClass
has obsolescence reason: failed exploratory term

datum label
type: Class
subclass of: information content entity
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
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
term editor: GROUP: IAO
editor preferred term: datum label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
has curation status: metadata incomplete

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
editor preferred term: software
has curation status: metadata complete

obsolete2_digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000261
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
definition: A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
definition source: group:OBI
editor preferred term: obsolete_digital entity
term editor: person:Chris Stoeckert
has obsolescence reason: failed exploratory term

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
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
has curation status: metadata complete

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
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
term 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.
term 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

obsolete_material_entity
type: Class
subclass of: ObsoleteClass
has obsolescence reason: placeholder removed

obsolete2_binary digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000244
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
definition: A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
example of usage: MS Word document, ZIP file, DICOM file, JPEG file
editor preferred term: binary digital entity
editor note: digital_entity
definition source: group:OBI
term editor: person:Chris Stoeckert
has obsolescence reason: failed exploratory term

obsolete_unit of measure
type: Class
subclass of: ObsoleteClass
term editor: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: The length of a ruler.
definition: a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
has obsolescence reason: failed exploratory term

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
term editor: person:Alan Ruttenberg
term 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
alternative term: data
editor preferred 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
term 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.
term 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
term 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
term 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
has curation status: 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.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
has curation status: metadata incomplete

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

obsolete_study interpretation
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
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.
definition source: OBI_0000005
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
alternative term: conclusion
definition: A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
term editor: Lawrence Hunter
term editor: PERSON: Jennifer Fostel
editor note: The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
editor preferred term: obsolete_study interpretation
has obsolescence reason: failed exploratory term
has curation status: pending final vetting

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
term editor: person:Allyson Lister
term 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
term editor: PERSON: Lawrence Hunter
editor preferred term: graph
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
has curation status: pending final vetting

obsolete2_text based digital entity
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000132
definition source: group:OBI
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
definition: A text based digital entity is a digital entity that is encoded so that it only contains text characters.
example of usage: XML file, C++ source code file
editor note: digital_entity
term editor: person:Chris Stoeckert
editor preferred term: text based digital entity
has obsolescence reason: failed exploratory term

rule
type: Class
subclass of: conditional specification
editor note: MSI
definition source: OBI_0500021
definition source: PRS
term 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
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: example to be eventually removed

obsolete2_report figure
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000027
definition: A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
editor note: I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
editor note: Replaced by defined version of figure
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
editor preferred term: report figure
has obsolescence reason: failed exploratory term
has curation status: uncurated

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.
term editor: Philippe Rocca-Serra
term 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: A software interpreter is a software application that executes some specified input software.
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
term editor: person:Alan Ruttenberg
term 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: 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
term 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
term editor: person:Allyson Lister
term 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
term 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

obsolete_report element
type: Class
subclass of: ObsoleteClass
editor note: 2009-03-16: needs some more work (clarify relations).
editor note: 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
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 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000001
term editor: PERSON: Melanie Courtot
editor note: Replaced by textual entity and figure
definition: A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
definition source: GROUP:OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Allyson Lister
editor note: There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
editor preferred term: report element
has obsolescence reason: failed exploratory term
has curation status: metadata complete

obsolete2_binary executable
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000222
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'
definition: Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
editor preferred term: binary executable
definition source: group:OBI
term editor: person:Jennifer Fostel
has obsolescence reason: failed exploratory term

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
term editor: person:Alan Ruttenberg
term editor: person:Chris Stoeckert
editor preferred term: source code module
has curation status: uncurated

obsolete_report table
type: Class
subclass of: ObsoleteClass
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
definition source: OBI_0000265
definition: A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
definition source: group:OBI
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
editor preferred term: report table
has curation status: example to be eventually removed
has obsolescence reason: failed exploratory term

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
term editor: PERSON: Alan Ruttenberg
term 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
term editor: person:Allyson Lister
term 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
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
has curation status: ready for release

data about an ontology part
type: Class
subclass of: data item
term 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: action specification
subclass of: Restriction
  on property: has part
  some values from: objective 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.
term 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

obsolete2_digital document
type: Class
subclass of: ObsoleteClass
definition source: OBI_0000195
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
definition: A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
editor preferred term: digital document
definition source: group:OBI
term editor: person:Jennifer Fostel
has obsolescence reason: failed exploratory term

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
term editor: person:Chris Stoeckert
has curation status: metadata complete

obsolete_identifier
type: Class
subclass of: ObsoleteClass
editor note: _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
has curation status: organizational term
has obsolescence reason: placeholder removed

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.
term 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.
term 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.
term 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

obsolete_digital quality
type: Class
subclass of: ObsoleteClass
editor note: Need to rework digital entity. Digital quality was suggested by Barry.
editor note: 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
has obsolescence reason: failed exploratory term

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.
term 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: is bearer of
    some values from: Restriction
      on property: concretizes
      some values from: information content entity
subclass of: material entity
definition: An information bearer is a material_entity in which a concretization of an information content entity inheres.
term 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
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term 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
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term 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.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term 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

obsolete_survival curve
type: Class
subclass of: ObsoleteClass
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
editor preferred term: obsolete_survival curve
has obsolescence reason: failed exploratory term
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.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term 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
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Joanne Luciano
term 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: is bearer of
    some values from: Restriction
      on property: concretizes
      some values from: photograph
subclass of: material information bearer
definition: A photographic print is a material entity upon which a photograph generically depends.
term editor: PERSON:Alan Ruttenberg
term 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: 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
term editor: PERSON: Alan Ruttenberg
term 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.
term 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
term 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: written name
definition: A textual entity intended to identify a particular author
example of usage: L. Hunter
term 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
term 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.
term 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
term 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
term 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
term 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
term 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.
term 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
term 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
term 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
term 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
term 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: is part of
  some values from: document
example of usage: An abstract, introduction, method or results section.
term 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.
term 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)
term 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
term 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
term 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
term 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
term 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
term 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
term 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.
term editor: PERSON: Lawrence Hunter
editor preferred term: author contributions section
has curation status: metadata complete

acknowledgements section
type: Class
subclass of: document part
term 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.
term 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
term 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).
term 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).
term 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
term 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
term 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
term 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: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero dimensional region
    intersection of: Restriction
      on property: is part of
      some values from: one dimensional region
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
term 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: is 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
term 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: is part of
      some values from: three dimensional region
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z 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
term 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
term 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.
term 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
term 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.
term 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
term 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

email address
type: Class
subclass of: information content entity
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
editor preferred term: email address
has curation status: metadata incomplete

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.
term editor: PERSON: Alan Ruttenberg
term 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
term editor: Person:Alan Ruttenberg
has curation status: metadata complete

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: document
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
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
term 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
term editor: PERSON:Chris Stoeckert
term 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 registry
subclass of: Restriction
  on property: has participant
  some values from: CRID symbol
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.
term editor: Person:Alan Ruttenberg
term editor: Person:Bjoern Peters
term 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_output
  some values from: CRID symbol
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
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
term editor: PERSON:Alan Ruttenberg
has curation status: metadata complete

obsolete_establishing a CRID registry
type: Class
subclass of: ObsoleteClass
definition: a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
editor note: MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
has obsolescence reason: failed exploratory term

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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term 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 participant
  some values from: CRID registry
subclass of: Restriction
  on property: has_specified_input
  some values from: CRID symbol
definition: A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term 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.
term editor: Alan Ruttenberg
alternative term: experimental time series
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete

written name
type: Class
subclass of: textual entity
example of usage: "Bill Clinton"
example of usage: "The Eiffel Tower"
example of usage: "United States of America"
definition: A textual entity that denotes a particular in reality.
term editor: PERSON: Bill Hogan
curator note: The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
editor preferred term: written name
has curation status: pending final vetting

software method
type: Class
subclass of: software
definition: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software module
type: Class
subclass of: software
definition: A software module is software composed of a collection of software methods.
term editor: PERSON: Melanei Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software library
type: Class
subclass of: software
definition: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software application
type: Class
subclass of: software
definition: A software application is software that can be directly executed by some processing unit.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

software script
type: Class
subclass of: software
definition: A software script is software whose instructions can be executed using a software interpreter.
term editor: PERSON: Melanie Courtot
term editor: PERSON: Michel Dumontier
definition source: http://code.google.com/p/information-artifact-ontology/issues/detail
has curation status: metadata incomplete

planned process
type: Class
subclass of: process
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

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

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

adding a material entity into a target
type: Class
subclass of: material combination
editor preferred term: adding a material entity into a target
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
imported from: obi.owl

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

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

categorical measurement datum
type: Class
subclass of: measurement datum
imported from: obi.owl

device
type: Class
subclass of: material entity
imported from: obi.owl

performing a diagnosis
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: clinical finding
imported from: obi.owl

anatomical entity
type: Class
subclass of: material entity
definition: An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
editor preferred term: anatomical entity
imported from: obi.owl

data transformation
type: Class
subclass of: planned process
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

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

clinical finding
type: Class
subclass of: data item
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

etiological process
type: Class
subclass of: process
subclass of: Restriction
  on property:
    inverse of: begins to exist during
  some values from: disorder
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
term editor: Albert Goldfain
definition: A process in an organism that leads to a subsequent disorder.

length
type: Class
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.owl

mass
type: Class
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.owl

length unit
type: Class
subclass of: measurement unit label
editor preferred term: length unit
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred term: mass unit
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred term: time unit
imported from: uo.owl

vaccination
type: Class
subclass of: administering substance in vivo
editor preferred term: vaccination
definition: Vaccination is: an 'administering substance in vivo' that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intend to invoke a protective immune response.
imported from: VO.owl

_BrightonMidLevelTerms
type: Class
subclass of: entity

fever
type: Class
subclass of: process
definition: A rise in body temperature above the normal, often as a response to infection.
editor preferred term: fever
imported from: GO

inflammatory response
type: Class
subclass of: process
definition: The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
editor preferred term: inflammatory response
imported from: GO

behavior
type: Class
subclass of: process
definition: The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
editor preferred term: behavior
imported from: GO

peripheral nervous system
type: Class
subclass of: anatomical entity
subclass of: Restriction
  on property: is part of
  some values from: nervous system
has definition: Nervous structures including ganglia outside of the central nervous system. Divided into somatic nervous system and autonomic nervous system [FB:gg, OMD:peripheral+nervous+system, Wikipedia:Peripheral_nervous_system, ZFIN:curator] comment: This class was created automatically from a combination of ontologies
imported from: UBERON

brain
type: Class
subclass of: anatomical entity
subclass of: Restriction
  on property: is part of
  some values from: nervous system
definition: def: "The supra-esophageal ganglion of the central nervous system, composed of three primitive ganglia known as protocerebrum, deutocerebrum and tritocerebrum. In the context of Drosophila refers to the preoral ganglionic mass of the central nervous system containing the ventral ganglia. // Organ component of neuraxis that has as its parts gray matter and white matter that surround the cerebral ventricular system; Examples: There is only one brain. // Organ that is a component of the central nervous system and is responsible for the coordination and control of bodily activities and the interpretation of information from the senses. It appears when the neural tube segregates in forebrain, midbrain, and hindbrain at NF stage 22. The general pattern of the brain has been mainly established at NF stage 28. Yolky material is consumed and the fibre tracts and later the commissures develop. In general all of its parts are well developed at NF stage 53 and later development consists mainly of growth and some further cytological differentiation. In the period of metamorphosis only topographical changes take place." [FB:gg, ISBN:0815318960, ISBN:3110148986, OMD:brain, Wikipedia:Brain] comment: This class was created automatically from a combination of ontologies
imported from: UBERON

nervous system
type: Class
subclass of: anatomical entity
has db xref: UBERON:0001016
alternative term: UBERON:FBbt_00005093-FMA_7157-MA_0000016-MIAA_0000026-WBbt_0005735-XAO_0000177-ZFA_0000396
editor note: MC, 20100112: I am using the UBERON term as this one is non human specific, compared to FMA.
definition: a network of specialized cells that communicate information about an organism's surroundings and itself[Wikipedia].
imported from: UBERON

Level 1 of certainty of generalized convulsive seizure as an adverse event following immunization
type: NamedIndividual
type: Brighton assessment of generalized convulsive seizure as an adverse event following immunization

Level 2 of certainty of generalized convulsive seizure as an adverse event following immunization
type: NamedIndividual
type: Brighton assessment of generalized convulsive seizure as an adverse event following immunization

Level 3 of certainty of generalized convulsive seizure as an adverse event following immunization
type: NamedIndividual
type: Brighton assessment of generalized convulsive seizure as an adverse event following immunization

Reported generalized convulsive seizure with insufficient evidence to meet the case definition
type: NamedIndividual
type: Brighton assessment of generalized convulsive seizure as an adverse event following immunization

not a case of generalized convulsive seizure
type: NamedIndividual
type: Brighton assessment of generalized convulsive seizure as an adverse event following immunization

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

failed exploratory term
type: Thing
type: obsolescence reason specification
type: NamedIndividual
term 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
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 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 term 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 the ontology to identify main classes.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot

placeholder removed
type: Thing
type: obsolescence reason specification
type: NamedIndividual

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
deprecated: true
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
term 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.
term editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
term 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.
term 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
term 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.
term editor: Alan Ruttenberg
definition source: group:OBI

core-classes.owl
Source: Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations"
Source: Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO"
publisher: Institute for Formal Ontology and Medical Information Science (IFOMIS)
Source: Barry Smith: "Basic Tools of Formal Ontology"
Contributor: Pierre Grenon
Source: Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE"
Source: Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain"
Source: Barry Smith: "Beyond Concepts: Ontology as Reality Representation"
Source: Barry Smith: "Against Fantology"
Source: Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization"