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

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

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

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

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

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

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

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

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.

inheres in
type: AnnotationProperty
editor note: This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant.
editor note: This relation belongs in BFO/RO, and will be in BFO 2
domain: specifically_dependent_continuant
type: ObjectProperty
inverse of: bearer of
range: independent_continuant

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.

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

definition
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition 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.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
editor preferred term: has_specified_input
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition editor: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
domain: planned process
type: ObjectProperty
sub property of: has_participant

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

obsolete_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>
editor note: Replaced by IAO_0000412
editor preferred term: obsolete_imported from
has obsolescence reason: other

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

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

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

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

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
definition 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.
definition editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting

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

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

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

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

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

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

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

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

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

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

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

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

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

conforms to
type: ObjectProperty
domain: information content entity
range: directive information entity

is descriptor of
type: ObjectProperty
domain: data item
sub property of: is about
range: specifically_dependent_continuant

has output
type: ObjectProperty
domain: process
sub property of: has_participant

has input
type: ObjectProperty
domain: process
sub property of: has_participant
range: Thing

has attribute
type: ObjectProperty
range: data item
inverse of: is attribute of

is attribute of
type: ObjectProperty
domain: data item

is variant of
type: ObjectProperty
type: SymmetricProperty

should execute with input
type: ObjectProperty
range: data item
domain: algorithm

should execute with output
type: ObjectProperty
range: data item
domain: algorithm

is execution output of
type: ObjectProperty
domain: data item
range: algorithm
inverse of: should execute with output

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

agent_in
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000022
sub property of: participates_in

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

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

derived_into
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000016
has OBO namespace: relationship

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

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

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

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

has_part
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000003

has_participant
type: ObjectProperty
comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has alternative id: OBO_REL:0000019
has OBO namespace: relationship
inverse of: participates_in
has definition: P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

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

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

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

located_in
type: ObjectProperty
type: TransitiveProperty
comment: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
has OBO namespace: relationship
has alternative id: OBO_REL:0000008
inverse of: location_of
has definition: Definition
  label: C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

location_of
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000009
has OBO namespace: relationship

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

participates_in
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000020

preceded_by
type: ObjectProperty
type: TransitiveProperty
comment: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
has alternative id: OBO_REL:0000017
has OBO namespace: relationship
inverse of: precedes
has definition: P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
  type: Definition
  has db xref: PMID:15892874
    type: DbXref
    has URI: http://purl.org/obo/owl/PMID#PMID_15892874

precedes
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000018
has OBO namespace: relationship

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

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

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

transformed_into
type: ObjectProperty
comment: Obsoleted
has OBO namespace: relationship
has alternative id: OBO_REL:0000014
sub property of: ObsoleteProperty

is output of
type: ObjectProperty
inverse of: has output
sub property of: participates_in

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

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

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

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

has uncertainty value
type: DatatypeProperty
type: FunctionalProperty
domain: information content entity
sub property of: has value
range: float

has value
type: DatatypeProperty
domain: data item
range: anyType

histidine count
type: Class
subclass of: amino acid count

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

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

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

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

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

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

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

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

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

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

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

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

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
definition editor: person:Chris Stoeckert
has obsolescence reason: failed exploratory term

obsolete_unit of measure
type: Class
subclass of: ObsoleteClass
definition 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
definition editor: person:Alan Ruttenberg
definition editor: person:Chris Stoeckert
editor preferred term: programming language
has curation status: metadata complete

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

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

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

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

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

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

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

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

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
definition editor: PERSON: Alan Ruttenberg
definition 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
definition editor: Lawrence Hunter
definition 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
definition editor: person:Allyson Lister
definition editor: person:Chris Stoeckert
has curation status: example to be eventually removed

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

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
definition 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
definition editor: PRS
definition: a rule is an executable which guides, defines, restricts actions
example of usage: example to be added
editor preferred term: rule
has curation status: uncurated

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

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
definition editor: person:Alan Ruttenberg
definition 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.
has alternative id: BODO:Algorithm
definition source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
definition editor: Philippe Rocca-Serra
definition editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: metadata complete

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

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

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

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

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
definition 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
definition editor: PERSON: Alan Ruttenberg
definition 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
definition 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
definition editor: person:Alan Ruttenberg
definition 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
definition editor: person:Alan Ruttenberg
definition 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: metadata incomplete

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

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

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

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has_part
  some values from: 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.
definition editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
editor preferred term: plan specification
has curation status: metadata complete

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
definition editor: person:Jennifer Fostel
has obsolescence reason: failed exploratory term

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

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.
definition editor: GROUP: IAO
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
editor preferred term: version number
has curation status: uncurated

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

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

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

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.
definition editor: Person:Alan Ruttenberg
editor preferred term: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete

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

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

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

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

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.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition 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.
definition editor: PERSON:Chris Stoeckert
definition editor: PERSON:James Malone
definition editor: PERSON:Melanie Courtot
definition source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: dendrogram
has curation status: ready for release

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
example of usage: PMID:12345, 12345 in a database column which has header "pubmedID"

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

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

looking up a CRID
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
has curation status: metadata complete

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

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

planned process
type: Class
subclass of: process
subclass of: processual_entity
imported from: http://purl.obolibrary.org/obo/obi.owl
definition: A planned process is the realization of a plan borne by an agent that initiates this process in order to bring about the objective(s) specified as part of the plan specification.
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor preferred term: planned process

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).
imported from: http://purl.obolibrary.org/obo/obi.owl
definition: An investigation is a process with the objective to generate an information entity by planning protocol applications included in an overall study design, carrying them out and documenting the results. In addition, an investigation can include a sub process of interpreting the data to draw conclusions.
editor preferred term: investigation

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

NMR instrument
type: Class
subclass of: device

device
type: Class
subclass of: material_entity

study design
type: Class
subclass of: plan specification
definition: A study design is a plan comprising of protocols and/or data transformations that are executed as part of an investigation. The objective of the study design is to produce results (information). The study design specifies how the different data produced in the execution of the investigation are related, how they are interpreted, and what are the desired results.
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.
imported from: http://purl.obolibrary.org/obo/obi.owl
editor preferred term: study design

molecular entity
type: Class
subclass of: chemical entity
has alternative id: CHEBI:23367

atom
type: Class
subclass of: chemical entity
has alternative id: CHEBI:33250

polyatomic entity
type: Class
subclass of: molecular entity
has alternative id: CHEBI:36357

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

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

1-D extent
type: Class
subclass of: dimensional extent quality
description: A one dimensional extent is a dimensional extent in only one dimension, e.g. a length.

length unit
type: Class
subclass of: measurement unit label
imported from: http://purl.org/obo/owl/UO
editor preferred term: length unit
editor preferred term: length unit label

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

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

chemical graph
type: Class
subclass of: structural descriptor
description: A chemical graph is a structural descriptor in which the connectivity and constitution of the chemical entity are described in terms of a mathematical graph, usually with atoms as vertices and bonds as edges, but other variants exist.

parameter data item
type: Class
subclass of: data item
definition: A parameter data item is a data item that plays the role of a parameter to a software method.

numeric data item
type: Class
subclass of: data item
subclass of: Restriction
  on property: conforms to
  some values from: numeric data format specification
subclass of: Restriction
  on property: has value
  some values from: Datatype
    union of: decimal
    union of: float
    union of: integer
    union of: long
disjoint with: textual data item
definition: A numeric data item is a data item which has a value which is numeric.

textual data item
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value
  some values from: string
subclass of: Restriction
  on property: conforms to
  some values from: textual data format specification
definition: A textual data item is a data item which has a value that has at least some non-numeric characters included in it.

numeric parameter
type: Class
equivalent class: Class
  intersection of: parameter data item
  intersection of: numeric data item
subclass of: parameter data item
subclass of: numeric data item

textual parameter
type: Class
equivalent class: Class
  intersection of: parameter data item
  intersection of: textual data item
subclass of: parameter data item
subclass of: textual data item

numeric data format specification
type: Class
subclass of: data format specification
definition: A numeric data format specification is a data format specification for data items which are numeric, that is, they contain only numeric values.

textual data format specification
type: Class
subclass of: data format specification
definition: A textual data format specification is a specification of the format of data items which are textual, that is, they consist of character data.

numeric chemical descriptor
type: Class
equivalent class: Class
  intersection of: numeric data item
  intersection of: chemical descriptor
subclass of: chemical descriptor

textual chemical descriptor
type: Class
equivalent class: Class
  intersection of: textual data item
  intersection of: chemical descriptor
subclass of: chemical descriptor

chemical substance descriptor
type: Class
equivalent class: Class
  intersection of: chemical descriptor
  intersection of: Restriction
    on property: is about
    some values from: chemical substance
subclass of: chemical descriptor

The Chemistry Development Kit Library
type: Class
subclass of: software library

org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
type: Class
equivalent class: Class
  intersection of: software module to calculate a molecular descriptor
  intersection of: Restriction
    on property: conforms to
    some values from: Atom Counting algorithm
type: NamedIndividual
part_of: CDK_000001

chemical entity
type: Class
subclass of: material_entity
has alternative id: CHEBI:24431
description: A chemical entity is any molecular entity or chemical substance.

molar refractivity
type: Class
subclass of: charge delocalization descriptor
description: Molar refractviity is a measure of the total polarizability of a mole of a substance and is dependent on the temperature, the index of refraction, and the pressure.

atomic polarizability sum
type: Class
subclass of: charge delocalization descriptor
description: atomic polarizability sum is the sum of the atomic polarizabilities (including implicit hydrogens).

partial positive surface area
type: Class
subclass of: surface area descriptor
description: sum of surface area on positive parts of molecule
short name: PPSA-1

PPSA-2
type: Class
subclass of: surface area descriptor
short name: PPSA-2
description: partial positive surface area * total positive charge on the molecule

RS stereochemical descriptor
type: Class
subclass of: stereochemical descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: chiral
subclass of: Restriction
  on property: conforms to
  some values from: RS stereochemistry specification

R stereochemical descriptor
type: Class
subclass of: RS stereochemical descriptor
disjoint with: S stereochemical descriptor

canonical SMILES descriptor
type: Class
subclass of: SMILES descriptor
description: A canonical SMILES descriptor is a SMILES descriptor that is produced using a canonicalization algorithm which results in one special generic SMILES among all valid possibilities.

charge weighted partial positive surface area
type: Class
subclass of: surface area descriptor
description: charge weighted partial positive surface area
short name: PPSA-3

atomic order
type: Class
subclass of: positional descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: has value
  some values from: int
description: Atomic order is an atomic descriptor that specifies the ordinal position of an atom.

partial negative surface area
type: Class
subclass of: surface area descriptor
short name: PNSA-1
description: sum of surface area on negative parts of molecule

chirality
type: Class
subclass of: molecular entity quality
description: Chirality is a molecular entity quality which inheres in a molecular entity by virtue of the existence of another molecular entity which is the mirror image of the first one, yet non-superposable on it.

molecular entity information format specification
type: Class
subclass of: data format specification
description: A molecular entity information format specification is an information content entity which specifies a format in which information about a molecular entity should be encoded.

PNSA-2
type: Class
subclass of: surface area descriptor
short name: PNSA-2
description: partial negative surface area * total negative charge on the molecule

energetic descriptor
type: Class
subclass of: chemical descriptor
description: An energetic descriptor is a chemical descriptor which captures information about some aspect of the energetic behaviour of a chemical entity.

information about a chemical entity
type: Class
equivalent class: Restriction
  on property: is about
  some values from: chemical entity
subclass of: information content entity

SMILES descriptor
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: conforms to
  some values from: SMILES format specification
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A SMILES descriptor is a structure descriptor that denotes a molecular structure as a graph.

SMARTS descriptor
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: conforms to
  some values from: SMARTS format specification
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A SMARTS descriptor is a molecular structure descriptor that conforms to the SMARTS specification.

SMILES format specification
type: Class
subclass of: atomic connectivity molecular structure encoding format specification
description: The simplified molecular input line entry specification (SMILES) is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules (source:wikipedia).

SMARTS format specification
type: Class
subclass of: atomic connectivity molecular structure encoding format specification
description: Smiles ARbitrary Target Specification (SMARTS) is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing (source:Wikipedia)

molecular structure encoding format specification
type: Class
subclass of: molecular entity information format specification
description: A molecular structure encoding format specification is a molecular entity format specification which specifies a format in which a molecular structure information entity may be encoded.

molecular stereochemistry format specification
type: Class
subclass of: molecular structure encoding format specification
description: A molecular stereochemistry format specification is a molecular structure format specification that specifies how to encode the stereochemical aspects of a molecular structure.

RS stereochemistry specification
type: Class
subclass of: specification of stereochemistry by configuration

physical descriptor
type: Class
subclass of: chemical descriptor
description: A physical descriptor is a chemical descriptor which describes some physical property (quality or disposition) of a chemical entity.

DL stereochemistry specification
type: Class
subclass of: specification of stereochemistry by configuration

stereochemical descriptor
type: Class
subclass of: chemical descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: chirality
description: A stereochemical descriptor is a chemical descriptor which describes some aspect of the three dimensional structure of a chemical entity.

specification of stereochemistry by configuration
type: Class
subclass of: molecular stereochemistry format specification
description: A specification of stereochemistry by configuration specifies a format in which the stereochemistry of a molecule should be encoded with reference to the configuration of attachments around the stereogenic centre.

specification of stereochemistry by optical activity
type: Class
subclass of: molecular stereochemistry format specification
description: A specification of stereochemistry by optical activity specifies a format by which the stereochemistry of a molecule should be encoded by reference to the observable optical activity of a chiral molecule.

+/- stereochemistry specification
type: Class
subclass of: specification of stereochemistry by optical activity

molecular entity quality
type: Class
subclass of: chemical quality
subclass of: Restriction
  on property:
    inverse of: bearer of
  some values from: molecular entity
description: A molecular entity quality is a quality which inheres in a molecular entity.

isomeric SMILES descriptor
type: Class
subclass of: SMILES descriptor
description: an isomeric SMILES descriptor is a SMILES descriptor that written with isotopic and chiral specifications.

molecular structure
type: Class
subclass of: molecular entity quality
description: Molecular structure is a molecular entity quality that inheres in a molecule by virtue of its shape - the way in which the atoms which constitute the molecule are bonded together and the shape which they therefore form.

S stereochemical descriptor
type: Class
subclass of: RS stereochemical descriptor

atomic connectivity molecular structure encoding format specification
type: Class
subclass of: molecular structure encoding format specification
description: An atomic connectivity molecular structure encoding format specification is a molecular structure encoding format specification which specifies a format in which the connectivity of atoms within a molecule may be specified.

molecular composition format specification
type: Class
subclass of: molecular entity information format specification
description: A molecular composition format specification is a molecular entity information format specification which specifies a format in which a molecular composition may be encoded.

IUPAC chemical formula
type: Class
subclass of: molecular composition format specification

InChI format specification
type: Class
subclass of: atomic connectivity molecular structure encoding format specification
description: The IUPAC International Chemical Identifier (InChI) is a textual identifier for chemical substances, designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web. Developed by IUPAC and NIST during 2000-2005, the format and algorithms are non-proprietary and the software is freely available under the open source LGPL license (though the term "InChI" is a trademark of IUPAC). [source: Wikipedia, http://en.wikipedia.org/wiki/International_Chemical_Identifier]

molecular entity name format specification
type: Class
subclass of: molecular entity information format specification
description: A molecular entity name format specification is a molecular entity information format specification which specifies a format in which a molecular entity name may be encoded.

Preferred IUPAC Name for Organic Compounds
type: Class
subclass of: molecular entity name format specification
comment: http://www.iupac.org/web/ins/2001-043-1-800

positional descriptor
type: Class
subclass of: chemical descriptor
description: A positional descriptor is a chemical descriptor which describes some aspect of the position, or location of a chemical entity, or of the relative parts of a chemical entity with respct to one another.

molecular formula
type: Class
subclass of: constitutional descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: molecular composition
description: A molecular formula is a structure descriptor which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecule of that compound.

molecular entity name
type: Class
subclass of: identifying descriptor
subclass of: Restriction
  on property: conforms to
  some values from: molecular entity name format specification
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: An information entity about a molecular entity which serves to name that molecular entity.

preferred name
type: Class
subclass of: molecular entity name
description: A preferred name is a molecular entity name which is preferred, or recommended, for usage in textual annotations referring to that molecular entity.

Preferred IUPAC Name for Inorganic Compounds
type: Class
subclass of: molecular entity name format specification
comment: http://www.iupac.org/web/ins/2006-038-1-800

zagreb index
type: Class
subclass of: count descriptor
description: The sum of the squared atom degrees of all heavy atoms.

+/- stereochemical descriptor
type: Class
subclass of: stereochemical descriptor
subclass of: Restriction
  on property: conforms to
  some values from: +/- stereochemistry specification
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: is descriptor of
  some values from: chiral

+ stereochemical descriptor
type: Class
subclass of: +/- stereochemical descriptor
disjoint with: - stereochemical descriptor

- stereochemical descriptor
type: Class
subclass of: +/- stereochemical descriptor

DL stereochemical descriptor
type: Class
subclass of: stereochemical descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: chiral
subclass of: Restriction
  on property: is about
  some values from: molecular entity

D stereochemical descriptor
type: Class
subclass of: DL stereochemical descriptor
disjoint with: L stereochemical descriptor

L stereochemical descriptor
type: Class
subclass of: DL stereochemical descriptor

molecular composition
type: Class
subclass of: molecular entity quality
description: Molecular composition is a molecular entity quality that inheres in a molecule by virtue of the atoms which constitute the molecule.

chemical connectivity table
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A chemical connectivity table is a structure descriptor which consists of a connection table representing bonds between atoms in a molecular entity.

aromaticity descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: aromaticity
description: An aromaticity descriptor is a chemical descriptor which indicates the aromaticity of a molecular entity.

file
type: Class
subclass of: document

MOLfile
type: Class
subclass of: information about a chemical entity
subclass of: file
description: A MOLfile is a file which contains a MOLfile encoding of a chemical structure representation. It is the concretization of a MOLfile descriptor.

InChIKey
type: Class
subclass of: identifying descriptor
subclass of: Restriction
  on property: is about
  some values from: polyatomic entity

dimensional extent descriptor
type: Class
subclass of: geometric descriptor
description: A dimensional extent descriptor is a physical property descriptor which describes some measurable length, area or volume aspect of a chemical entity.

identifying descriptor
type: Class
subclass of: chemical descriptor
description: An identifying descriptor is a chemical descriptor which provides an identifier for the chemical entity it is about, which in most cases should aim to be unique and easy to use as an unambiguous reference for the chemical entity.

bond order descriptor
type: Class
subclass of: geometric descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical bond
description: A bond order descriptor is a descriptor associated with a bond in a chemical entity which indicates the order of the bond (single, double or triple).

chemical bond
type: Class
subclass of: chemical entity

QSAR descriptor
type: Class
subclass of: chemical descriptor
has alternative id: BODO:Descriptor
comment: NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.
description: A Quantitative Structure Activity Relationship (QSAR) descriptor is a chemical descriptor which gives a numeric, quantitative value which is believed to be associated with some aspect of the chemical or biological activity of the chemical entity.

molecular entity descriptor
type: Class
equivalent class: Class
  intersection of: chemical descriptor
  intersection of: Restriction
    on property: is about
    some values from: molecular entity
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: conforms to
  some values from: molecular entity information format specification
description: a molecular entity descriptor is a chemical descriptor that provides information about a molecular entity.

information about a polyatomic entity
type: Class
equivalent class: Class
  intersection of: information about a chemical entity
  intersection of: Restriction
    on property: is about
    some values from: polyatomic entity
subclass of: information about a chemical entity
comment: An information entity which is about a polyatomic molecular entity.

cyclicity
type: Class
subclass of: molecular entity quality
description: cyclicity is a quality that inheres in a molecular entity by virtue of the presence of cycles in the connection of the atoms within the molecular entity.

functional group descriptor
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A functional group descriptor is a structural descriptor which describes specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.

polarity
type: Class
subclass of: molecular entity quality
description: Polarity is a quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole.

polar
type: Class
subclass of: polarity
disjoint with: nonpolar
description: Polar polarity is a quality that inheres in a molecular entity when the molecular entity is polar, i.e. does possess an electric dipole.

nonpolar
type: Class
subclass of: polarity
description: Nonpolar polarity is a quality which inheres in a molecular entity when the molecular entity does not possess an electrical dipole.

cyclic
type: Class
subclass of: cyclicity
disjoint with: acyclic
description: Cyclic cyclicity inheres in a molecule when the atoms of the molecule do contain at least one cycle in the atom-atom connection paths (through bonds).

acyclic
type: Class
subclass of: cyclicity
description: Acyclic cyclicity inheres in a molecule when the atoms within the molecule do not contain at least one cycle in the atom-atom connection paths (through the bonds).

chiral
type: Class
subclass of: chirality
disjoint with: achiral

achiral
type: Class
subclass of: chirality

aromatic
type: Class
subclass of: aromaticity
disjoint with: non-aromatic
description: Aromatic aromaticity is a quality that inheres in a molecular entity when it possesses at least one ring that is aromatic.

non-aromatic
type: Class
subclass of: aromaticity
description: Non aromatic aromaticity is a quality that inheres in a molecular entity by virtue of the molecule possessing no rings that are aromatic.

neutron count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: is descriptor of
  some values from: molecular composition
description: The (integer) number of neutrons in the atoms nucleus.

proton count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: is descriptor of
  some values from: molecular composition
description: The (integer) number of protons in the atoms nucleus.

cis-trans stereochemical descriptor
type: Class
subclass of: stereochemical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical bond
subclass of: Restriction
  on property: conforms to
  some values from: cis-trans stereochemistry specification
comment: Descriptors which show the relationship between two ligands attached to separate atoms that are connected by a double bond or are contained in a ring. The two ligands are said to be located cis to each other if they lie on the same side of a plane. If they are on opposite sides, their relative position is described as trans. The appropriate reference plane of a double bond is perpendicular to that of the relevant s-bonds and passes through the double bond.[source:IUPAC Gold Book - http://goldbook.iupac.org/C01092.html]

cis stereochemical descriptor
type: Class
subclass of: cis-trans stereochemical descriptor

trans stereochemical descriptor
type: Class
subclass of: cis-trans stereochemical descriptor

mass descriptor
type: Class
subclass of: physical descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: mass
subclass of: Restriction
  on property: is about
  some values from: molecular entity

atomic mass descriptor
type: Class
subclass of: mass descriptor
subclass of: Restriction
  on property: is about
  some values from: atom

structural descriptor
type: Class
subclass of: chemical descriptor
description: A structural descriptor is a chemical descriptor which is about some aspect of the molecular structure (composition) of a chemical entity.

chemical quality
type: Class
subclass of: quality
description: A chemical quality is a quality that inheres in a molecular entity or aggregate molecular substance.

electronic descriptor
type: Class
subclass of: chemical descriptor

molecular mass descriptor
type: Class
subclass of: mass descriptor
subclass of: Restriction
  on property: is about
  some values from: polyatomic entity

polarizability
type: Class
subclass of: chemical disposition
description: The ease of distortion of the electron cloud of a molecular entity by an electric field [source: IUPAC Gold Book - http://goldbook.iupac.org/P04711.html]

atomic degree
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: The integer number of non-H substituents of an atom.

hybridization
type: Class
subclass of: molecular entity quality
description: The quality of an atom that reflects the combination of its atomic orbitals to create bonding orbitals.

topological descriptor
type: Class
subclass of: chemical descriptor
description: A topological descriptor is a chemical descriptor which pertains to spatial properties of a geometric object that are preserved under continuous deformations of objects, for example, deformations that involve stretching.

geometric descriptor
type: Class
subclass of: chemical descriptor
description: A geometric descriptor is a descriptor that concerns information about size, shape, and relative position.

charge delocalization descriptor
type: Class
subclass of: electronic descriptor

hybridization descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: is descriptor of
  some values from: hybridization
description: A hybridization descriptor is a chemical descriptor that is about the hybridization of atomic orbitals in a molecular entity.

atomic valence
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: Atomic valence is an atomic descriptor that specifies the maximum number of univalent atoms (originally hydrogen or chlorine atoms) which may combine with an atom of the element under consideration, or with a fragment, or for which an atom of this element can be substituted [source: IUPAC Gold Book - http://goldbook.iupac.org/V06588.html]

atomic hardness descriptor
type: Class
subclass of: charge delocalization descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: An atomic hardness descriptor is an atomic descriptor that estimates the difference between the ionization potential and the electron affinity of a given atom.

valency
type: Class
subclass of: molecular entity quality
description: Valency is an atomic quality of the number of chemical bonds formed by the atom.

atomic softness descriptor
type: Class
subclass of: charge delocalization descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: An atomic softness descriptor is an atomic descriptor which is about the charge delocalizing ability of a given atom.

MOLfile format specification
type: Class
subclass of: atomic connectivity molecular structure encoding format specification
description: The MOLfile atomic connectivity molecular structure encoding format specification may be found described at http://en.wikipedia.org/wiki/Chemical_table_file#Molfiles. It is composed primarily of a connection table (atoms and bonds); hydrogen may be implicit or explicit.

chemical substance quality
type: Class
subclass of: chemical quality
subclass of: Restriction
  on property:
    inverse of: bearer of
  some values from: chemical substance
description: A chemical substance quality is a quality that inheres in an aggregate molecular substance, such as a portion of solid or liquid matter.

crystal structure
type: Class
subclass of: chemical substance quality
description: A crystal structure is a chemical substance quality which inheres in a crystalline solid or liquid crystal substance by virtue of the way the molecules are ordered within the crystal.

software module to calculate a chemical descriptor
type: Class
subclass of: software module
subclass of: Restriction
  on property: should execute with output
  some values from: chemical descriptor
subclass of: Restriction
  on property: conforms to
  some values from: algorithm to calculate a chemical descriptor
description: A software module to calculate a chemical descriptor is software module that implements an algorithm which calculates a descriptor value for a chemical entity.

molecular QSAR descriptor
type: Class
subclass of: QSAR descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A molecular QSAR descriptor is a OSAR descriptor which gives a quantitative value to some aspect of a molecular entity.

cycle basis
type: Class
subclass of: structural descriptor
description: The cycle basis of a molecular structure is the smallest set of cycles (closed paths) formed in the graph representation of the structure, from which all other cycles can be computed.

systematic name
type: Class
subclass of: molecular entity name
description: A systematic name is a molecular entity name which is formulated systematically from the structure of the molecular entity.

IUPAC name
type: Class
subclass of: systematic name
description: An IUPAC name is a systematic name which is formulated according to the rules and recommendations for chemical nomenclature set out by the International Union of Pure and Applied Chemistry (IUPAC).

atomic quality
type: Class
subclass of: molecular entity quality
subclass of: Restriction
  on property:
    inverse of: bearer of
  some values from: atom
description: An atomic quality is a molecular entity quality which inheres in an atom.

trivial name
type: Class
subclass of: molecular entity name
description: A trivial name is a molecular entity name that is in common public use and may not be related to the structure of the molecular entity.

fused cycles
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: The fused cycles in a molecular structure are those cycles from the cycle basis which share at least one bond.

CML format specification
type: Class
subclass of: atomic connectivity molecular structure encoding format specification
description: A CML (Chemical Markup Language) file is an XML-based representation of the atomic connectivity of a molecular entity.

atomic QSAR descriptor
type: Class
subclass of: QSAR descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: An atomic QSAR descriptor is a QSAR descriptor which gives a quantitative value to some aspect of an atom which is part of a molecular entity.

InChI descriptor
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: conforms to
  some values from: InChI format specification
description: An InChI descriptor is a structure descriptor which conforms to the InChI format specification.

MOLfile descriptor
type: Class
subclass of: structural descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: conforms to
  some values from: MOLfile format specification
description: A MOLfile descriptor is a structure descriptor which conforms to the MOLfile format specification.

aromaticity
type: Class
subclass of: molecular entity quality
description: Aromaticity is a molecular entity quality that inheres in a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals that exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.

atomic connectivity index
type: Class
subclass of: geometric descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: An atomic connectivity index is an atomic descriptor that is a measure of atomic connectivity, which can take various forms (e.g. zero-order, or first-order).

Wiener path number
type: Class
subclass of: topological descriptor
description: Half the sum of all the distance matrix entries, topological index of atom-atom distances.

formal charge descriptor
type: Class
subclass of: charge descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: The formal charge gives the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity. The formal charge of any atom in a molecule can be calculated by the following equation: FC = number of valence electrons of the atom in isolation (atom in ground state) - number of non-bonding electrons on this atom in the molecule - half the total number of electrons shared in covalent bonds with other atoms in the molecule. [source:wikipedia]

partial charge descriptor
type: Class
subclass of: charge descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
description: A partial charge descriptor gives the charge with an absolute value of less than one elementary charge unit (that is, smaller than the charge of the electron). [source:wikipedia]

charge
type: Class
subclass of: molecular entity quality
description: Charge is a quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons.

electronegativity
type: Class
subclass of: chemical disposition
description: Electronegativity is an atomic quality that describes its power to attract electrons to itself [source:IUPAC Gold Book - http://goldbook.iupac.org/E01990.html]

electronegativity descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: atom
subclass of: Restriction
  on property: is descriptor of
  some values from: electronegativity
description: An electronegativity descriptor is a chemical descriptor that is about the electronegativity quality of an atom.

chemical descriptor
type: Class
subclass of: data item
subclass of: Restriction
  on property: is descriptor of
  some values from: Class
    union of: chemical quality
    union of: chemical disposition
subclass of: Restriction
  on property: is descriptor of
  some values from: specifically_dependent_continuant
subclass of: Restriction
  on property: is about
  some values from: chemical entity
description: A chemical descriptor is a data item (quantity or value) about a chemical entity that conforms to a specification for how it is calculated, measured or recorded.

radius
type: Class
subclass of: 1-D extent
description: A 1-D extent quality inhering in a bearer by virtue of the bearer's dimension of extension to the circumference of a circle or sphere.

atomic radius
type: Class
subclass of: radius
comment: Atomic radius is the 1D extent of the electron cloud surrounding the atom.

ionic radius
type: Class
subclass of: radius

van der Waal's radius
type: Class
subclass of: atomic radius

covalent radius
type: Class
subclass of: atomic radius

bond multiplicity
type: Class
subclass of: molecular entity quality
description: Bond multiplicity is the extent to which participating electrons are localized in the bonding orbitals.

bond multiplicity descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: bond multiplicity
subclass of: Restriction
  on property: is about
  some values from: chemical bond
description: A bond multiplicity descriptor is a chemical descriptor that in primitive cases is defined as half of the difference between the number of bonding and antibonding electrons in a particular system, but may also be defined with relation to the strength of a single bond.

charge descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: charge
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A charge descriptor is a chemical descriptor which indicates the charge of a chemical entity.

bond length descriptor
type: Class
subclass of: dimensional extent descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: length
subclass of: Restriction
  on property: is about
  some values from: chemical bond
description: A bond length descriptor is a dimensional extent descriptor which gives the measured or predicted (idealised) length of an atom to atom bond within a chemical entity.

sp hybridized
type: Class
subclass of: hybridization
description: The quality of an atom in which the 2s orbital mixes with only one of the three p-orbitals resulting in two sp orbitals and two remaining unchanged p orbitals. spsp overlap between two atoms form a s bond and two additional p bonds formed by pp overlap.

sp2 hybridized
type: Class
subclass of: hybridization

sp3 hybridized
type: Class
subclass of: hybridization

constitutional descriptor
type: Class
subclass of: chemical descriptor

Wiener polarity number descriptor
type: Class
subclass of: topological descriptor
description: Half the sum of all the distance matrix entries with a value of 3

software execution
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_participant
  some values from: software application
comment: software execution is a process in which the instruction set that comprises the software program is executed on a machine.

software implementation
type: Class
subclass of: software

PubChem compound identifier (CID)
type: Class
subclass of: identifying descriptor

PubChem substance identifier (SID)
type: Class
subclass of: identifying descriptor

Pipeline Pilot library
type: Class
subclass of: software library
definition: http://accelrys.com/products/pipeline-pilot/

algorithm to calculate a chemical descriptor
type: Class
subclass of: algorithm
subclass of: Restriction
  on property: should execute with output
  some values from: chemical descriptor

topological surface area descriptor
type: Class
subclass of: surface area descriptor

parameterized software execution
type: Class
subclass of: software execution
subclass of: Restriction
  on property: has output
  some values from: data item
subclass of: Restriction
  on property: has input
  some values from: parameter data item

generic SMILES descriptor
type: Class
subclass of: SMILES descriptor
description: a generic SMILES descriptor is a SMILES descriptor that denotes only the labeled molecular graph (i.e. atoms and bonds, but no chiral or isotopic information).

isomeric SMILES format specification
type: Class
subclass of: SMILES format specification

canonical SMILES format specification
type: Class
subclass of: isomeric SMILES format specification

topological polar surface area descriptor
type: Class
subclass of: topological surface area descriptor

charge weighted partial negative surface area
type: Class
subclass of: surface area descriptor
short name: PNSA-3
description: charge weighted partial negative surface area

DPSA-1
type: Class
subclass of: surface area descriptor
short name: DPSA-1
description: difference of PPSA-1 and PNSA-1

DPSA-2
type: Class
subclass of: surface area descriptor
description: difference of FPSA-2 and PNSA-2
short name: DPSA-2

DPSA-3
type: Class
subclass of: surface area descriptor
short name: DPSA-3
description: difference of PPSA-3 and PNSA-3

FPSA-1
type: Class
subclass of: surface area descriptor
description: PPSA-1 / total molecular surface area
short name: FPSA-1

FPSA-2
type: Class
subclass of: surface area descriptor
short name: FPSA-2
description: PPSA-2 / total molecular surface area

FPSA-3
type: Class
subclass of: surface area descriptor
short name: FPSA-3
description: PPSA-3 / total molecular surface area

FNSA-1
type: Class
subclass of: surface area descriptor
description: PNSA-1 / total molecular surface area
short name: FNSA-1

FNSA-2
type: Class
subclass of: surface area descriptor
short name: FNSA-2
description: PNSA-2 / total molecular surface area

FNSA-3
type: Class
subclass of: surface area descriptor
short name: FNSA-3
description: PNSA-3 / total molecular surface area

WPSA-1
type: Class
subclass of: surface area descriptor
description: PPSA-1 * total molecular surface area / 1000
short name: WPSA-1

WPSA-2
type: Class
subclass of: surface area descriptor
short name: WPSA-2
description: PPSA-2 * total molecular surface area /1000

WPSA-3
type: Class
subclass of: surface area descriptor
description: PPSA-3 * total molecular surface area /1000
short name: WPSA-3

WNSA-1
type: Class
subclass of: surface area descriptor
description: PNSA-1 * total molecular surface area /1000
short name: WNSA-1

WNSA-2
type: Class
subclass of: surface area descriptor
short name: WNSA-2
description: PNSA-2 * total molecular surface area /1000

WNSA-3
type: Class
subclass of: surface area descriptor
short name: WNSA-3
description: PNSA-3 * total molecular surface area /1000

relative positive charge
type: Class
subclass of: surface area descriptor
description: most positive charge / total positive charge
short name: RPCG

relative negative charge
type: Class
subclass of: surface area descriptor
description: most negative charge / total negative charge
short name: RNCG

relative positive charge surface area
type: Class
subclass of: surface area descriptor
short name: RPCS
description: most positive surface area * RPCG

relative negative charge surface area
type: Class
subclass of: surface area descriptor
description: most negative surface area * RNCG
short name: RNCS

THSA
type: Class
subclass of: surface area descriptor
description: sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2
short name: THSA

TPSA
type: Class
subclass of: surface area descriptor
description: sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2
short name: TPSA

RHSA
type: Class
subclass of: surface area descriptor
short name: RHSA
description: THSA / total molecular surface area

RPSA
type: Class
subclass of: surface area descriptor
description: TPSA / total molecular surface area
short name: RPSA

collection of 3D coordinates
type: Class
subclass of: structural descriptor

collection of 3D atomic coordinates
type: Class
subclass of: collection of 3D coordinates
subclass of: Restriction
  on property: has_proper_part
  some values from: three dimensional cartesian spatial coordinate datum

molecular polarizability
type: Class
subclass of: charge delocalization descriptor
description: Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens)
short name: BPol

fragment complexity descriptor
type: Class
subclass of: complexity descriptor
description: defined as @cdk.cite{Nilakantan06}
short name: FragmentComplexity

vertex adjacency matrix descriptor
type: Class
subclass of: geometric descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity

Petitjean Topological Shape Index
type: Class
subclass of: Petitjean Shape Index
description: A measure of the anisotropy in a molecule (as per Petitjean et al)

Petitjean Geometric Shape Index
type: Class
subclass of: Petitjean Shape Index
description: A measure of the anisotropy in a molecule (as per Bath et al)

Petitjean number
type: Class
subclass of: topological descriptor
short name: petitjeanNumber
description: the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph. The distance is obtained from the distance matrix as the count of edges between the two vertices. If r i is the largest matrix entry in row i of the distance matrix D, then the radius is defined as the smallest of the r i . The graph diameter D is defined as the largest vertex eccentricity in the graph. Petitjean Number is the value of ( diameter - radius ) diameter .

Petitjean Shape Index
type: Class
subclass of: topological descriptor
description: A measure of the anisotropy in a molecule
short name: petitjeanShapeIndex

XLogP descriptor
type: Class
subclass of: logP descriptor
description: A LogP descriptor based on the atom-type method described in Wang, R., Fu, Y., and Lai, L.. A New Atom-Additive Method for Calculating Partition Coefficients, Journal of Chemical Information and Computer Sciences. vol. 37. 1997, pp. 615-621.
short name: XLogP

MLogP descriptor
type: Class
subclass of: logP descriptor
description: A LogP descriptor based on a simple equation using the number of carbons and hetero atoms.
short name: MannholdLogP

maximal ratio of length to breadth descriptor
type: Class
subclass of: ratio of length to breath descriptor

ratio of length to breath descriptor
type: Class
subclass of: geometric descriptor

minimal ratio of length to breadth descriptor
type: Class
subclass of: ratio of length to breath descriptor

ionization potential descriptor
type: Class
subclass of: charge delocalization descriptor

eccentric connectivity index descriptor
type: Class
subclass of: topological descriptor
short name: EccentricConnectivityIndex

equilibrium constant
type: Class
subclass of: electronic descriptor

acid dissociation constant
type: Class
subclass of: equilibrium constant
description: the acid dissociation constant, Ka, is quantitative measure of the strength of an acid in solution. It is the equilibrium constant for a chemical reaction known as dissociation in the context of acid-base reactions.
short name: Ka

pKa
type: Class
subclass of: equilibrium constant
description: the logarithmic measure of the acid dissociation constant (Ka)
short name: pKa

cycle
type: Class
subclass of: substructure
description: A cycle is a part of a molecular entity that is cyclic, that is, consists of a chain of atoms where each is reachable by a bond connected to another atom, and the first atom is reachable from itself.

substructure
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: has_proper_part
  some values from: atom
description: A substructure is a contiguous part of a molecule composed of at least two atoms and a bond.

molecular weight calculated by pipeline pilot
type: Class
subclass of: molecular weight descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction
definition: A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool.

absolute SMILES descriptor
type: Class
subclass of: isomeric SMILES descriptor
description: An absolute SMILES descriptor is an isomeric SMILES descriptor that is produced using a canonicalization algorithm.

tautomer count
type: Class
subclass of: count descriptor
description: a count descriptor that denotes the number of tautomers.

stereocenter count
type: Class
subclass of: count descriptor

atom stereocenter count
type: Class
subclass of: stereocenter count
disjoint with: bond stereocenter count

defined atom stereocenter count
type: Class
subclass of: atom stereocenter count

formation energy descriptor
type: Class
subclass of: energetic descriptor
description: A formation energy descriptor is an energetic descriptor which gives the value for the energy of formation of a chemical entity.

solvation energy descriptor
type: Class
subclass of: energetic descriptor
description: A solvation energy descriptor is a chemical descriptor which gives the value for the energy of dissolving a particular chemical entity in a solvent.

count descriptor
type: Class
subclass of: constitutional descriptor
description: A count descriptor is a chemical descriptor which is calculated by counting the number of features of a certain kind which are present in the chemical entity.

dissociation energy descriptor
type: Class
subclass of: energetic descriptor
description: A dissociation energy descriptor is an energetic descriptor which gives a value for the dissociation energy for a chemical entity.

dimensional extent quality
type: Class
subclass of: quality
description: A dimensional extent quality is a quality that inheres in a molecular entity by virtue of a measurement of length, area or volume in a one, two or three dimensional extent.

undefined atom stereocenter count
type: Class
subclass of: atom stereocenter count

bond stereocenter count
type: Class
subclass of: stereocenter count

defined bond stereocenter count
type: Class
subclass of: bond stereocenter count

undefined bond stereocenter count
type: Class
subclass of: bond stereocenter count

molecular weight descriptor
type: Class
subclass of: mass descriptor
description: The mass of a molecule calculated using the average mass of each element weighted for its natural isotopic abundance. E.g., Carbon has two natural isotopes 12 and 13 with relative abundances of 98.9% and 1.1% to yield an average mass of 12.011 g/mol

exact mass descriptor
type: Class
subclass of: mass descriptor
description: an exact mass descriptor corresponds to the mass of the most intense molecule/ion peak in an MS spec, and when calculated denotes the mass of an ion or a molecule containing most likely isotopic composition for a single random molecule.

monoisotopic mass descriptor
type: Class
subclass of: mass descriptor
description: The mass of a molecule calculated using the mass of the most abundant isotope of each element. E.g., Carbon has a monoisotopic mass of 12.000 g/mol.

complexity descriptor
type: Class
subclass of: structural descriptor
description: A complexity descriptor denotes the how complicated a structure is, seen from both the point of view of the elements contained and its structural features .

cis-trans stereochemistry specification
type: Class
subclass of: specification of stereochemistry by configuration

Ghose/Crippen ALogP calculation algorithm
type: Class
subclass of: algorithm to calculate a molecular descriptor
definition: Fragment Method used for the calculation of ALogP as defined by Ghose and Crippen. Ghose, A.K., Viswanadhan V.N., and Wendoloski, J.J., Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragment Methods: An Analysis of AlogP and CLogP Methods. J. Phys. Chem. A, 1998, 102, 3762-3772.

volume
type: Class
subclass of: 3-D extent

pi-system size
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
description: The integer number of atoms in a pi-orbital system.
short name: LargestPiSystem

bond dissociation Gibbs energy descriptor
type: Class
subclass of: dissociation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical bond
subclass of: Restriction
  on property: is descriptor of
  some values from: disposition to dissociate
description: Bond dissociation Gibbs energy descriptor captures the Gibbs energy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.

solvation Gibbs energy descriptor
type: Class
subclass of: solvation energy descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: solubility
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: The molecular entity solvation Gibbs energy descriptor reflects the Gibbs energy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.

bond charge density descriptor
type: Class
subclass of: charge density descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical bond

3-D extent
type: Class
subclass of: dimensional extent quality
description: A three dimensional extent is a dimensional extent in three dimensions, e.g. a volume.

refractive index
type: Class
subclass of: chemical disposition
description: The refractive index of a chemical substance is a measure of the manner in which light waves are bent when they enter the medium of the chemical substance.

surface area descriptor
type: Class
subclass of: dimensional extent descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: surface area
description: A surface area descriptor is a descriptor which describes a measure or calculation of the surface area of a chemical entity.

composition
type: Class
subclass of: molecular entity quality
comment: From PATO.

charge density descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: charge density
description: A charge density descriptor is a chemical entity descriptor which indicates the distribution of the electric charge over the volume of the chemical entity.

aromatic atom count
type: Class
subclass of: atom count
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
description: A descriptor that provides the integer count of aromatic atoms in a given molecular entity.

bond count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A descriptor that specifies the integer count of bonds in a given molecular entity.

PubChem conformer identifier
type: Class
subclass of: identifying descriptor

disposition to dissociate
type: Class
subclass of: chemical disposition
description: The disposition to dissociate is the disposition of an ionic compound (complexes, or salts) to separate or split into smaller particles, ions, or radicals, usually in a reversible manner.

charge density
type: Class
subclass of: molecular entity quality
description: The linear, surface, or volume charge density is the amount of electric charge in a line, surface, or volume respectively. [source: Wikipedia, http://en.wikipedia.org/wiki/Charge_density]

bond aromaticity descriptor
type: Class
subclass of: aromaticity descriptor
subclass of: Restriction
  on property: has value
  some values from: boolean
subclass of: Restriction
  on property: is descriptor of
  some values from: aromaticity
description: A bond aromaticity descriptor is an aromaticity descriptor associated with a bond within a chemical entity which indicates whether that bond belongs to an aromatic system.

meltability
type: Class
subclass of: chemical disposition
has synonym: fusibility
description: The meltability of a chemical substance is a quality which inheres in the chemical substance by virtue of the ease with which the substance can be changed from a solid to a liquid state especially by the application of heat.

formation Gibbs energy descriptor
type: Class
subclass of: formation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: disposition to form
description: The formation Gibbs energy descriptor captures the Gibbs energy associated with the formation of a molecular entity, relative to the standard state of constituent atoms. This can be measured, calculated in vacuo, or calculated with respect to a specific solvent, at a particular temperature and pressure. When calculated, the formation Gibbs energy value depends on the molecular conformation.

size of largest aliphatic chain
type: Class
subclass of: size of largest chain
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: The largest aliphatic chain size descriptor is a count descriptor that gives the integer length (number of atoms) in the largest unbranched chain of atoms that does not contain aromatic atoms, within a given molecular entity.

formation enthalpy descriptor
type: Class
subclass of: formation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: disposition to form
description: Molecular entity formation enthaply descriptor captures the enthalpy associated with the formation of the molecular entity in question, relative to the standard state of constituent atoms. This could be measured or calculated in vacuo or in a specific Solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.

volume descriptor
type: Class
subclass of: dimensional extent descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: volume
description: A volume descriptor is a descriptor which describes a measure or calculation of the volume of a chemical entity.

aromatic bond count
type: Class
subclass of: bond count
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A descriptor that provides the integer count of aromatic bonds in a given molecular entity.

hydrogen bond donor count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A descriptor that reflects the integer number of hydrogen bond donors in a given molecular entity, as determined by a given method. In highly simplified terms, this is usually the count of all negatively or partially negatively charged heteroatoms (e.g. alcohol oxygen) that have covalently attached to them partially positively charged hydrogen atoms that are capable of participating in a hydrogen bond.

hydrogen bond acceptor count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A descriptor that reflects the integer number of hydrogen bond acceptors in a given molecular entity, as determined by a given method. In highly simplified terms, this is usually the count of all negatively or partially negatively charged heteroatoms (e.g. alcohol oxygen) capable of accepting a hydrogen bond.

size of largest chain
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
description: The largest chain size descriptor is a count descriptor that gives the integer length (number of atoms) in the largest chain in a molecular entity.

surface area
type: Class
subclass of: 2-D extent

relative permittivity
type: Class
subclass of: chemical disposition
description: Relative permittivity is a chemical substance quality that reflects the ability of a medium composed of molecules of a given type to transmit an electric field.

solvation entropy descriptor
type: Class
subclass of: solvation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: solubility
description: The molecular entity solvation entropy descriptor reflects the entropy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.

solvation enthalpy descriptor
type: Class
subclass of: solvation energy descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: solubility
description: The molecular entity solvation enthalpy descriptor reflects the enthalpy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.

logP descriptor
type: Class
subclass of: physical descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: solubility
subclass of: Restriction
  on property: is about
  some values from: chemical substance
description: The logarithm of octanol-water partition coefficient, which is the ratio of the molecules dissolved in octanol to those dissolved in pure un-ionized water upon mixture equilibration. This can be measured or predicted. The value is dimensionless. May depend on molecular conformation when computed.

bond dissociation enthalpy descriptor
type: Class
subclass of: dissociation energy descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: disposition to dissociate
subclass of: Restriction
  on property: is about
  some values from: chemical bond
description: Bond dissociation enthalpy descriptor captures the enthalpy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.

refractive index descriptor
type: Class
subclass of: physical descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: refractive index
subclass of: Restriction
  on property: is about
  some values from: chemical substance
description: Chemical substance refractive index descriptor is a unitless descriptor that specifies the ratio of the speed of light in vacuum to that in a given chemical substance. [IUPAC: http://goldbook.iupac.org/R05240.html]

rotatable bond count
type: Class
subclass of: bond count
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: has value
  some values from: int
description: a bond count that denotes the integer number of rotors in the molecule, generally single bonds torsion around which produces non-identical geometric molecular configurations.
short name: RotatableBondsCount

vaporizability
type: Class
subclass of: chemical disposition
description: The vaporizability of a chemical substance is a quality which inheres in the chemical substance by virtue of the ease with which the substance can be changed into a gaseous state.

melting point descriptor
type: Class
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
subclass of: Restriction
  on property: is descriptor of
  some values from: meltability
comment: Melting point descriptor specifies the temperature at which a chemical substance undergoes the transition from solid to liquid state under standard conditions.

boiling point descriptor
type: Class
subclass of: physical descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
subclass of: Restriction
  on property: is descriptor of
  some values from: vaporizability
comment: The boiling point descriptor indicates the temperature at which a chemical substance undergoes a state transition from liquid to gas, at standard conditions.

solubility
type: Class
subclass of: chemical disposition

disposition to form
type: Class
subclass of: chemical disposition
description: The disposition to form is the disposition of an ionic compound (complexes, or salts) to form from the smaller particles, ions, or radicals from which it is constituted.

formation entropy descriptor
type: Class
subclass of: formation energy descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: disposition to form
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: Molecular entity formaiton entropy descriptor captures the entropy associated with the formation of the molecular entity in question, relative to the standard state of constituent atoms. This could be measured or calculated in vacuo or in a specific Solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.

relative permittivity descriptor
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical substance
subclass of: Restriction
  on property: is descriptor of
  some values from: relative permittivity
description: The relative permittivity descriptor specifies the ratio of the electric field strength in vacuum to that in a given medium. It was formerly called the dielectric constant. [IUPAC Gold Book: http://goldbook.iupac.org/R05273.html ]

2-D extent
type: Class
subclass of: dimensional extent quality
description: A two dimensional extent is a dimensional extent in two dimensions, e.g. an area.

atom count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A descriptor that specifies the integer count of atoms in a given molecular entity.

atomic charge density descriptor
type: Class
subclass of: charge density descriptor
subclass of: Restriction
  on property: is about
  some values from: atom

bond dissociation entropy descriptor
type: Class
subclass of: dissociation energy descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: disposition to dissociate
subclass of: Restriction
  on property: is about
  some values from: chemical bond
description: Bond dissociation entropy descriptor captures the entropy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.

chemical substance
type: Class
subclass of: chemical entity
comment: Chemical substance constitutes matter of constant composition, that may contain a collection of molecular entities. [IUPAC: http://goldbook.iupac.org/C01039.html]

effective rotor count
type: Class
subclass of: count descriptor
description: A count descriptor that takes into account flexibility of rings and rotatable bonds.

total formal charge descriptor
type: Class
subclass of: charge descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A charge descriptor that gives the total charge for a molecule

conformer volume descriptor
type: Class
subclass of: volume descriptor

amino acid count
type: Class
subclass of: count descriptor
description: a count of the number of amino acid residues.

alanine count
type: Class
subclass of: amino acid count

arginine count
type: Class
subclass of: amino acid count

asparagine count
type: Class
subclass of: amino acid count

aspartate count
type: Class
subclass of: amino acid count

cysteine count
type: Class
subclass of: amino acid count

phenylalanine count
type: Class
subclass of: amino acid count

glutamate count
type: Class
subclass of: amino acid count

glutamine count
type: Class
subclass of: amino acid count

glycine count
type: Class
subclass of: amino acid count

covalent unit count
type: Class
subclass of: count descriptor
description: The number of covalent units (molecule / ion) in a chemical structure

isoleucine count
type: Class
subclass of: amino acid count

proline count
type: Class
subclass of: amino acid count

leucine count
type: Class
subclass of: amino acid count

lysine count
type: Class
subclass of: amino acid count

methionine count
type: Class
subclass of: amino acid count

serine count
type: Class
subclass of: amino acid count

threonine count
type: Class
subclass of: amino acid count

tyrosine count
type: Class
subclass of: amino acid count

valine count
type: Class
subclass of: amino acid count

tryptophan count
type: Class
subclass of: amino acid count

Highest Occupied Molecular Orbital Energy
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is about
  some values from: chemical entity
subclass of: Restriction
  on property: is descriptor of
  some values from: chemical quality
description: A descriptor that the energy of the highest occupied 'molecular' orbital of the chemical entity.

Lowest Unoccupied Molecular Orbital Energy
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: chemical quality
subclass of: Restriction
  on property: is about
  some values from: chemical entity
description: A descriptor that the energy of the lowest unoccupied 'molecular' orbital of the chemical entity.

acidic group count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is about
  some values from: molecular entity
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
description: A descriptor that specifies the integer count of acidic groups in a given molecular entity.

basic group count
type: Class
subclass of: count descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: composition
subclass of: Restriction
  on property: has value
  some values from: int
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: A descriptor that specifies the integer count of basic groups in a given molecular entity.

ALogP descriptor
type: Class
subclass of: logP descriptor
short name: ALogP
description: The ALogP descriptor described by Ghose and Crippen in 1986 and 1987.

hybridization descriptor (VSEPR)
type: Class
subclass of: hybridization descriptor

inductive atomic hardness
type: Class
subclass of: electronic descriptor

TPSA (fragments)
type: Class
subclass of: topological polar surface area descriptor

VABC volume descriptor
type: Class
subclass of: volume descriptor

heavy atom count
type: Class
subclass of: atom count
description: The sum of all non-hydrogen atoms

isotope atom count
type: Class
subclass of: atom count
description: The sum of all atoms enriched with respect to a particular atom isotope

PubMed Identifier
type: Class
subclass of: identifying descriptor

GenBank Protein Identifier
type: Class
subclass of: identifying descriptor

GenBank Nucleotide Identifier
type: Class
subclass of: identifying descriptor

ALogP calculated by Pipeline Pilot
type: Class
subclass of: ALogP descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

Ertl polar surface area calculation algorithm
type: Class
subclass of: algorithm to calculate a molecular descriptor
definition: Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties, Ertl, P., Rohde, B., Selzer, P., J. Med. Chem. 2000, 43, 3714-3717.

polar surface area descriptor
type: Class
subclass of: surface area descriptor

polar surface area descriptor calculated by Pipeline Pilot
type: Class
subclass of: polar surface area descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

hydrogen bond acceptor count calculated by pipeline pilot
type: Class
subclass of: hydrogen bond acceptor count
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

hydrogen bond donor count calculated by pipeline pilot
type: Class
subclass of: hydrogen bond donor count
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

rotatable bond count calculated by pipeline pilot
type: Class
subclass of: rotatable bond count
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

rule of five violations descriptor
type: Class
subclass of: physical descriptor
definition: Number of properties defined in Lipinski’s Rule of 5 (RO5) that the compound fails. Conditions which violate the RO5 are: Molecular weight>=500 AlogP>=5 HBD>=5 HBA>=10

Lipinski rule of five violation calculation algorithm
type: Class
subclass of: algorithm to calculate a molecular descriptor
definition: Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25.

rule of five violations calculated by pipeline pilot
type: Class
subclass of: rule of five violations descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

rule of three passes descriptor
type: Class
subclass of: physical descriptor
definition: Rule of 3 passes. It is suggested that compounds that pass all these criteria are more likely to be hits in fragment screening. molecular weight <=300, number of hydrogen bond donors <=3, number of hydrogen bond acceptors <=3 AlogP <=3. RTB <=3 PSA<=60

rule of three passes calculation algorithm
type: Class
subclass of: algorithm to calculate a molecular descriptor
definition: A ‘Rule of Three’ for fragment-based lead discovery? Miles Congreve, Robin Carr, Chris Murray and Harren Jhoti. Drug Discovery Today, 2003,8(19), 876-877

rule of three passes calculated by pipeline pilot
type: Class
subclass of: rule of three passes descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

medchem friendly descriptor
type: Class
subclass of: physical descriptor
definition: MedChem Friendly These are functional groups that may not be desirable from a medicinal chemistry perspective. For example reactive groups will be flagged as “N” (not MedChem Friendly). Molecules which do not contain any of these groups will be flagged as “Y” (MedChem Friendly). The groups are defined by the following list of SMARTS: [N+]([O-])=O [C;!R](-[C;!R]=O)=[C;!R] C(-N)=S P O-N=C OS(=O)=O O1-CC-O-C-1 C(-N)=C [C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2] OC1OCC(O)C1 C=N-C(-O) [N;H]-[C;H]-[N;H] [C;!R]=[C;!R]-N-[C;D1&H3,D2&H2,D3&H1,D4] [S;!R]-[C;!R]-[O;!R] [O;D2]-[C;!H0](([F,Br,I,Cl])([F,Br,I,Cl])([!F,!Br,!I,!Cl])) CC([O;!R])([O;!R]) C1-C-O1 C(=O)-S-C(=S) [S;H] SC#N

medchem friendly descriptor calculated by pipeline pilot
type: Class
subclass of: medchem friendly descriptor
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_participant
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction

ACD/Labs PhysChem software library
type: Class
subclass of: software library
definition: http://www.acdlabs.com/resources/knowledgebase/app_notes/physchem/

logP calculated by ACD/Labs PhysChem software
type: Class
subclass of: logP descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01

logD descriptor
type: Class
subclass of: physical descriptor
definition: octanol-water distribution coefficient calculated at a given pH.

logD calculated at pH 7.4 by ACD/Labs PhysChem software
type: Class
subclass of: logD descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
definition: ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4

most acidic pKa calculated by ACD/Labs PhysChem software library
type: Class
subclass of: pKa
subclass of: Restriction
  on property: is output of
  some values from: Class
    intersection of: software execution
    intersection of: Restriction
      on property: has_agent
      some values from: Class
        intersection of: software module to calculate a chemical descriptor
        intersection of: Restriction
definition: Most acidic pKa of the molecule

most basic pKa calculated by ACD/Labs PhysChem software library
type: Class
subclass of: pKa
definition: Most basic pKa of the molecule

molecular species at pH 7.4 descriptor
type: Class
subclass of: physical descriptor
definition: Molecular Species is a description of the predominant form of the molecule at pH7.4.

molecular species at pH 7.4 calculated by ACD/Labs PhysChem software
type: Class
subclass of: molecular species at pH 7.4 descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
definition: These are defined according to the definitions: Acid(A) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa<8.5 Bas (B) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa>8.5 Neutral (N) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa<8.5 Zwitterion (ZW) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa>8.5

ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: ACD/Labs PhysChem software library

Pipeline Pilot Server Version 8.5.0
type: Class
subclass of: Pipeline Pilot library

software module
type: Class
subclass of: software implementation
subclass of: Restriction
  on property: has_part
  some values from: software method
comment: Is this equivalent to IAO 'source code module' (IAO_0000096) on the same level as 'software'? From the textual definition in IAO it seems fairly close. (JH)
description: A software module is a collection of software methods.

software method
type: Class
subclass of: software implementation
subclass of: Restriction
  on property: should execute with output
  some values from: software message data item
subclass of: Restriction
  on property: should execute with output
  some values from: parameter data item
subclass of: Restriction
  on property: should execute with input
  some values from: parameter data item
description: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is a programming language implementation of a plan specification which is capable of realizing some objective specification when part of a software application.

software library
type: Class
subclass of: software application
subclass of: Restriction
  on property: has_part
  some values from: Class
    union of: software module
    union of: software method
description: A software library is a collection of programming language mplementations (e.g. modules, methods) capable of realizing some objective specification when linked to a application software.

software application
type: Class
subclass of: software implementation
description: A software application is a programming language implementation of a plan specification capable of realizing some objective specification.

logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: logD descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01.

hydrogen bond acceptor count calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: hydrogen bond acceptor count
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Hydrogen bond acceptor count that has been calculated by ACD/Labs PhysChem software library version 12.01.

hydrogen bond donor count calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: hydrogen bond donor count
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Hydrogen bond donor count that has been calculated by ACD/Labs PhysChem software library version 12.01.

Boiling point at 760 mmHg pressure calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: boiling point descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: The boiling point of a substance at 760 mmHg pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.

number of freely rotating bonds calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: rotatable bond count
description: Number of freely rotating bonds that has been calculated by ACD/Labs PhysChem software library version 12.01.

polar surface area calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: polar surface area descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.

molecular weight of the corresponding free base
type: Class
subclass of: molecular weight descriptor
description: The molecular weight for the free base chemical structure matching this chemical structure.

molar refractivity calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: molar refractivity
description: Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01.

index of refraction calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: refractive index descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Index of refraction that has been calculated by ACD/Labs PhysChem software library version 12.01.

polarizability calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: polarizability
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Polarizability that has been calculated by ACD/Labs PhysChem software library version 12.01.

execution of ACD/Labs PhysChem software library version 12.01
type: Class
equivalent class: Class
  intersection of: software execution
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: software module to calculate a chemical descriptor
      intersection of: Restriction
        on property: part_of
        some values from: Pipeline Pilot library
description: A parameterized software execution of ACD/Labs PhysChem software library version 12.01. This refers to a particular run of the software.

execution of Pipeline Pilot
type: Class
equivalent class: Class
  intersection of: software execution
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: software module to calculate a chemical descriptor
      intersection of: Restriction
        on property: part_of
        some values from: ACD/Labs PhysChem software library version 12.01
description: A parameterized software execution of Pipeline Pilot. This refers to a particular run of the software.

GGA Indigo
type: Class
subclass of: software library
definition: http://ggasoftware.com/opensource/indigo

execution of GGA Indigo
type: Class
equivalent class: Class
  intersection of: software execution
  intersection of: Restriction
    on property: has_participant
    some values from: Class
      intersection of: software module to calculate a chemical descriptor
      intersection of: Restriction
        on property: part_of
        some values from: GGA Indigo
description: A parameterized software execution of GGA Indigo. This refers to a particular run of the software.

molar volume calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: molar volume descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01.

density calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: density descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Density that has been calculated by ACD/Labs PhysChem software library version 12.01.

flash point calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: flash point descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Flash point that has been calculated by ACD/Labs PhysChem software library version 12.01.

enthalpy of vaporization calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: enthalpy of vaporization descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Enthalpy of vaporization that has been calculated by ACD/Labs PhysChem software library version 12.01.

vapour pressure calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: vapour pressure descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Vapour pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.

organic carbon adsorption coefficient at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: organic carbon adsorption descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Organic carbon adsorption coefficient at pH 5.5 that has been calculated by ACD/Labs PhysChem software library version 12.01.

organic carbon adsorption coefficient at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: organic carbon adsorption descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Organic carbon adsorption coefficient at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.

bioconcentration factor at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: bioconcentration factor descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.

bioconcentration factor at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: bioconcentration factor descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.

number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: rule of five violations descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Number of rule of five violations for a chemical structure that has been calculated by ACD/Labs PhysChem software library version 12.01.

surface tension calculated by ACD/Labs PhysChem software library version 12.01
type: Class
subclass of: surface tension descriptor
subclass of: Restriction
  on property: is output of
  some values from: execution of ACD/Labs PhysChem software library version 12.01
description: Surface tension, in dyne per centimetre, that has been calculated by ACD/Labs PhysChem software library version 12.01.

neutral charge
type: Class
subclass of: charge
description: Neutral charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing the same amount of electrons overall as protons, thus having an overall neutral charge.

positive charge
type: Class
subclass of: charge
description: Positive charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing more protons overall than electrons, thus having an overall positive charge.

negative charge
type: Class
subclass of: charge
description: Negative charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing more electrons overall than protons, thus having an overall negative charge.

chemical disposition
type: Class
subclass of: disposition
description: A chemical disposition is a disposition which inheres in a chemical entity.

ChemSpider identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by ChemSpider.

DrugBank identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by DrugBank.

ChEBI identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by ChEBI.

HMDB identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by Human Metabolome Database.

KEGG identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by KEGG.

Wikipedia identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by Wikipedia.

Reactome identifier
type: Class
subclass of: identifying descriptor
description: Database identifier used by Reactome.

ChEMBL identifier
type: Class
subclass of: identifying descriptor
description: Identifier used by the ChEMBL database for compounds, assays, target, etc.

organic carbon adsorption descriptor
type: Class
subclass of: physical descriptor
description: A descriptor of the ratio of the amount of a given chemical substance adsorbed per unit weight of organic carbon in soil or sediment to the concentration of the chemical substance in solution at equilibrium.
definition editor: Colin Batchelor

bioconcentration factor descriptor
type: Class
subclass of: physical descriptor
definition editor: Colin Batchelor
description: A descriptor of the ratio of the concentration of a chemical substance in an organism immersed in water to that in the surrounding water at equilibrium.

molar volume descriptor
type: Class
subclass of: physical descriptor
definition editor: Colin Batchelor
description: A descriptor of the volume occupied by one mole of the given substance at a given temperature and pressure.

density descriptor
type: Class
subclass of: physical descriptor
definition editor: Colin Batchelor
description: A descriptor of the density of a given substance at a given temperature and pressure.

flash point descriptor
type: Class
subclass of: physical descriptor
description: A descriptor of the flash point of a substance at a given pressure. The flash point is the minimum temperature at which a mixture of the substance with air can be ignited, within its explosive range.
definition editor: Colin Batchelor

enthalpy of vaporization descriptor
type: Class
subclass of: physical descriptor
description: A descriptor of the energy taken in by a chemical substance on vaporization at a given temperature and pressure.
definition editor: Colin Batchelor

vapour pressure descriptor
type: Class
subclass of: physical descriptor
description: A descriptor of the pressure exerted by the vapour phase of a chemical substance on its condensed phase at a given temperature and pressure.
definition editor: Colin Batchelor

surface tension descriptor
type: Class
subclass of: physical descriptor
definition editor: Colin Batchelor
description: A descriptor of the disposition of a portion of liquid to resist a force.

validation algorithm
type: Class
subclass of: algorithm
definition editor: Colin Batchelor
description: An algorithm that specifies how to determine whether data meets given criteria for correctness.

standardization algorithm
type: Class
subclass of: algorithm
definition editor: Colin Batchelor
description: An algorithm that specifies how to transform data such that the resulting data meets given criteria for correctness.

structural validation algorithm
type: Class
subclass of: validation algorithm
subclass of: Restriction
  on property: should execute with input
  some values from: structural descriptor
definition editor: Colin Batchelor
description: A validation algorithm that specifies how to determine whether a structural descriptor meets given criteria for correctness.

structural standardization algorithm
type: Class
subclass of: standardization algorithm
subclass of: Restriction
  on property: should execute with input
  some values from: structural descriptor
description: A standardization algorithm that specifies how to transform a structural descriptor such that it meets given criteria for correctness.
definition editor: Colin Batchelor

structural validation warning
type: Class
subclass of: warning message
subclass of: Restriction
  on property: is execution output of
  some values from: structural validation algorithm
description: A warning message that indicates that a structural descriptor does not meet some criterion for correctness.
definition editor: Colin Batchelor

structural validation error
type: Class
subclass of: error message
subclass of: Restriction
  on property: is execution output of
  some values from: structural standardization algorithm
definition editor: Colin Batchelor
description: An error message that indicates that a structural descriptor cannot be parsed.

structural standardization
type: Class
subclass of: Class
  intersection of: software execution
  intersection of: Restriction
    on property: has_participant
    some values from: structural standardization algorithm
description: An execution of code which implements a structural standardization algorithm.
definition editor: Colin Batchelor

structural validation
type: Class
subclass of: Class
  intersection of: software execution
  intersection of: Restriction
    on property: has_participant
    some values from: structural validation algorithm
description: An execution of code which implements a structural validation algorithm.
definition editor: Colin Batchelor

algorithm to calculate a molecular descriptor
type: Class
equivalent class: Class
  intersection of: algorithm to calculate a chemical descriptor
  intersection of: Restriction
    on property: should execute with output
    some values from: molecular entity descriptor

software module to calculate a molecular descriptor
type: Class
equivalent class: Class
  intersection of: software module to calculate a chemical descriptor
  intersection of: Restriction
    on property: should execute with output
    some values from: molecular entity descriptor
subclass of: Restriction
  on property: conforms to
  some values from: algorithm to calculate a molecular descriptor
description: A software module to calculate a molecular descriptor is software module that implements an algorithm which calculates a descriptor value for a molecular entity.

software message data item
type: Class
subclass of: data item
definition: A software message data item is a data item that plays the role of a message generated by a software implementation, for example, an error, warning or success message.

warning message
type: Class
subclass of: software message data item

error message
type: Class
subclass of: software message data item

success message
type: Class
subclass of: software message data item

ChEBI name
type: Class
subclass of: preferred name
definition: A ChEBI name is a preferred name annotated by the ChEBI database. The ChEBI name has the additional feature that it is unique within the ChEBI dataset.

Atom Counting algorithm
type: Class
equivalent class: Class
  intersection of: algorithm to calculate a molecular descriptor
  intersection of: Restriction
    on property: should execute with output
    some values from: atom count

Bond Polarizabilities
type: Class
subclass of: electronic descriptor
subclass of: Restriction
  on property: is descriptor of
  some values from: chemical quality
subclass of: Restriction
  on property: is about
  some values from: molecular entity
description: Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).

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

continuant
type: Class
equivalent class: Class
  union of: dependent_continuant
  union of: independent_continuant
  union of: spatial_region
subclass of: entity
disjoint with: occurrent
comment: Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
comment: Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
comment: Synonyms: endurant

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

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

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

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

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

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

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

object
type: Class
subclass of: material_entity
disjoint with: object_aggregate
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
comment: Examples: an organism, a heart, a chair, a lung, an apple
comment: Synonyms: substance

object_aggregate
type: Class
subclass of: material_entity
disjoint with: object_boundary
disjoint with: site
comment: Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
comment: Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
comment: Synonyms: substance aggregate

object_boundary
type: Class
subclass of: independent_continuant
disjoint with: site
comment: Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
comment: Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
comment: Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
comment: Synonyms: substance boundary

one_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: three_dimensional_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with one dimension.
comment: Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space

quality
type: Class
subclass of: specifically_dependent_continuant
disjoint with: realizable_entity
comment: Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
comment: Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee

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

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

site
type: Class
subclass of: independent_continuant
comment: Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
comment: Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
comment: Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.

spatial_region
type: Class
equivalent class: Class
  union of: one_dimensional_region
  union of: three_dimensional_region
  union of: two_dimensional_region
  union of: zero_dimensional_region
subclass of: continuant
comment: Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
comment: Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
comment: Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
comment: Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
comment: Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe

specifically_dependent_continuant
type: Class
equivalent class: Class
  union of: quality
  union of: realizable_entity
subclass of: dependent_continuant
comment: Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
comment: Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
comment: Synonyms: property, trope, mode

three_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: two_dimensional_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with three dimensions.
comment: Examples: a cube-shaped part of space, a sphere-shaped part of space

two_dimensional_region
type: Class
subclass of: spatial_region
disjoint with: zero_dimensional_region
comment: Definition: A spatial region [snap:SpatialRegion] with two dimensions.
comment: Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space

zero_dimensional_region
type: Class
subclass of: spatial_region
comment: Definition: A spatial region [snap:SpatialRegion] with no dimensions.
comment: Examples: a point

connected_spatiotemporal_region
type: Class
equivalent class: Class
  union of: spatiotemporal_instant
  union of: spatiotemporal_interval
subclass of: spatiotemporal_region
disjoint with: scattered_spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].
comment: Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus

connected_temporal_region
type: Class
equivalent class: Class
  union of: temporal_instant
  union of: temporal_interval
subclass of: temporal_region
disjoint with: scattered_temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
comment: Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis

fiat_process_part
type: Class
subclass of: processual_entity
disjoint with: process
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life

occurrent
type: Class
equivalent class: Class
  union of: processual_entity
  union of: spatiotemporal_region
  union of: temporal_region
subclass of: entity
comment: Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
comment: Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
comment: Synonyms: perdurant

process
type: Class
subclass of: processual_entity
disjoint with: process_aggregate
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
comment: Examples: the life of an organism, the process of sleeping, the process of cell-division

process_aggregate
type: Class
subclass of: processual_entity
disjoint with: process_boundary
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
comment: Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together

process_boundary
type: Class
subclass of: processual_entity
disjoint with: processual_context
comment: Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
comment: Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery

processual_context
type: Class
subclass of: processual_entity
comment: Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
comment: Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
comment: Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.

processual_entity
type: Class
equivalent class: Class
  union of: fiat_process_part
  union of: process
  union of: process_aggregate
  union of: process_boundary
  union of: processual_context
subclass of: occurrent
disjoint with: spatiotemporal_region
disjoint with: temporal_region
comment: Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
comment: Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird

scattered_spatiotemporal_region
type: Class
subclass of: spatiotemporal_region
comment: Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
comment: Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair

scattered_temporal_region
type: Class
subclass of: temporal_region
comment: Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
comment: Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair

spatiotemporal_instant
type: Class
subclass of: connected_spatiotemporal_region
disjoint with: spatiotemporal_interval
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
comment: Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process

spatiotemporal_interval
type: Class
subclass of: connected_spatiotemporal_region
comment: Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
comment: Examples: the spatiotemporal region occupied by a process or by a fiat processual part

spatiotemporal_region
type: Class
equivalent class: Class
  union of: connected_spatiotemporal_region
  union of: scattered_spatiotemporal_region
subclass of: occurrent
disjoint with: temporal_region
comment: Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.
comment: Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.
comment: Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.
comment: Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
comment: Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis

temporal_instant
type: Class
subclass of: connected_temporal_region
disjoint with: temporal_interval
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
comment: Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death

temporal_interval
type: Class
subclass of: connected_temporal_region
comment: Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
comment: Examples: any continuous temporal duration during which a process occurs

temporal_region
type: Class
equivalent class: Class
  union of: connected_temporal_region
  union of: scattered_temporal_region
subclass of: occurrent
comment: Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
comment: Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
comment: Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
comment: Definition: An occurrent [span:Occurrent] that is part of time.
comment: Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death

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

failed exploratory term
type: Thing
type: obsolescence reason specification
type: NamedIndividual
definition editor: Person:Alan Ruttenberg
definition: The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job

metadata complete
type: Thing
type: curation status specification
type: NamedIndividual
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
type: curation status specification
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 definition editor.

core
type: NamedIndividual
type: Subset
definition: Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
definition editor: PERSON: Alan Ruttenberg
definition 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
editor note: This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
editor note: We expect to be able to mine these new reasons and add instances as required.

universal
type: NamedIndividual
type: denotator type
definition source: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
definition editor: Alan Ruttenberg
editor note: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.

defined class
type: NamedIndividual
type: denotator type
editor note: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
definition editor: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
definition editor: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
definition editor: Alan Ruttenberg
editor note: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
definition editor: Alan Ruttenberg
definition source: group:OBI