Semanticscience Integrated Ontology (SIO)
type: Ontology
default language: en
contributor: Contributors are those that engage in discussions in the context of SIO (in alphabetical order): sivaram arabandi christopher baker joachim baran jerven bolleman matthew brush alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong elisa kendall tatsuya kushida luke mccarthy jim mccusker jose miguel cruz-toledo chris mungall robert hoehndorf simon jupp jin-dong kim dana klassen thomas luetteke james malone chris mungall david osumi-sutherland tazro ohta nuria queralt stephen reed alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales
creator: Michel Dumontier
creator: http://orcid.org/0000-0003-4727-9435
description: The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology
issued: 2010-03-29
license: http://creativecommons.org/licenses/by/4.0/
rights: free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/].
cites as authority: http://www.jbiomedsem.com/content/5/1/14
preferred namespace prefix: sio
preferred namespace uri: http://semanticscience.org/resource/
comment: general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in'
version info: 1.51
subset: sio-subset-core.owl
subset: sio-subset-relations.owl
subset: sio-subset-nlp.owl
subset: sio-subset-sadi.owl
subset: sio-subset-ovopub.owl
subset: sio-subset-emotion.owl
subset: sio-subset-process.owl
subset: sio-subset-ice.owl
subset: sio-subset-math.owl
subset: sio-subset-capability.owl
subset: sio-subset-chemical.owl
subset: sio-subset-behaviour.owl
subset: sio-subset-geometry.owl
subset: sio-subset-equivs.owl
subset: sio-subset-labels.owl
version IRI: sio-release.owl
modified: 2021-02-19

is related to
type: ObjectProperty
type: SymmetricProperty
domain: Thing
range: Thing
description: A is related to B iff there is some relation between A and B.
comment: 'is related to' is the top level relation in SIO
subset: core
subset: relations+

has attribute
type: ObjectProperty
sub property of: is related to
inverse of: is attribute of
description: has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.
subset: core

is attribute of
type: ObjectProperty
sub property of: is related to
description: is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.

denotes
type: ObjectProperty
sub property of: represents
inverse of: is denoted by
description: denotes is a relation between an entity and what it is a sign or indication of, or what specifically means.
example: the symbol '%' denotes a proportion in relation to a whole.

has part
type: ObjectProperty
type: TransitiveProperty
type: ReflexiveProperty
sub property of: is location of
inverse of: is part of
description: has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part.
example: a collection of cars has as a car as a part;a car has an engine as a part; a car has a piston as a part;

is time boundary of
type: ObjectProperty
sub property of: is boundary of
inverse of: has time boundary
domain: time instant

has proper part
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
sub property of: has part
inverse of: is proper part of
description: has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part.
example: a car has an engine as a proper part; a car has a piston as a proper part;

has boundary
type: ObjectProperty
sub property of: has proper part
inverse of: is boundary of
description: has boundary is a mereological relation between a whole and boundary located at its periphery.
example: the surface of an apple is a 2D boundary of the apple.

has member
type: ObjectProperty
type: IrreflexiveProperty
sub property of: has attribute
inverse of: is member of
description: has member is a mereological relation between a collection and an item.
example: a collection of cars has as a car as a member
subset: core

is denoted by
type: ObjectProperty
sub property of: is represented by

is located in
type: ObjectProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to
inverse of: is location of
description: A is located in B iff the spatial region occupied by A is part of the spatial region occupied by B. [T][R]
equivalent to: OBO_REL:located_in
example: A parasite in the interior of a person's intestine is located in their intestinal lumen.
subset: core

is participant in
type: ObjectProperty
sub property of: is spatiotemporally related to
inverse of: has participant
range: process
description: is participant in is a relation that describes the participation of the subject in the (processual) object.
example: a car is a participant in a car race; glucose is a participant in glycolysis

is agent in
type: ObjectProperty
sub property of: is participant in
inverse of: has agent
description: is agent in is a relation between an entity and a process, where the entity is present throughout the process, no permanent material change occurs, and is a causal participant in the process.
example: hexokinase is an agent in the conversion of glucose to glucose-6-phosphate
subset: sadi

is provider of
type: ObjectProperty
sub property of: is source of
inverse of: has provider
description: is provider of is a relation between a source and the entity it makes available.

has provider
type: ObjectProperty
sub property of: has source
description: is provided by is a relation between an entity and the entity that provides it.
equivalent to: dc:source

is part of
type: ObjectProperty
type: TransitiveProperty
type: ReflexiveProperty
sub property of: is located in
description: is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole.
equivalent to: OBO_REL:part_of
subset: core

is proper part of
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
sub property of: is part of
description: is proper part of is an asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.
equivalent to: OBO_REL:proper_part_of
subset: core

is member of
type: ObjectProperty
sub property of: is attribute of
description: is member of is a mereological relation between a item and a collection.

is boundary of
type: ObjectProperty
sub property of: is proper part of
description: is boundary of is a mereological relation between a boundary located at the periphery of a whole.

is contained in
type: ObjectProperty
type: TransitiveProperty
sub property of: is located in
inverse of: contains
description: A is contained in B iff the spatial region occupied by A is part of the spatial region occupied by B and A is not part of B. [T]
equivalent to: OBO_REL:contained_in
subset: core

has participant
type: ObjectProperty
sub property of: is spatiotemporally related to
domain: process
description: has participant is a relation that describes the participation of the object in the (processual) subject.
equivalent to: OBO_REL:has_participant
subset: core

has agent
type: ObjectProperty
sub property of: has participant
description: has agent is a relation between a process and an entity, where the entity is present throughout the process and is a causal participant in the process.
equivalent to: OBO_REL:has_agent
subset: core
subset: sadi

is location of
type: ObjectProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to
description: A is location of B iff the spatial region occupied by A has the spatial region occupied by B as a part. [T][R]
subset: nlp+

contains
type: ObjectProperty
type: TransitiveProperty
sub property of: is location of
description: A contains B iff the spatial region occupied by A has the spatial region occupied by B as a part, and B is not part of A. [T]

is connected to
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to
description: A is connected to B iff there exists a fiat, material or temporal path between A and B. [S][T]
alternative: interacts with
subset: core
subset: nlp

is adjacent to
type: ObjectProperty
type: SymmetricProperty
sub property of: is spatiotemporally related to
description: A is adjacent to B iff there is a small, but non-zero distance between A and B
equivalent to: OBO_REL:adjacent_to
subset: core
subset: nlp

is represented by
type: ObjectProperty
sub property of: is referred to by
inverse of: represents
description: is represented by: a relation between an entity and some symbol.

is supported by
type: ObjectProperty
sub property of: has evidence
inverse of: is supporting evidence for
description: is supported by is a relation between a proposition and something that supports the truth of the assertion.

is disputed by
type: ObjectProperty
sub property of: has evidence
inverse of: is disputing evidence for
description: has disputing evidence is a relation between a proposition and something that disputes (does not directly support) the truth of the assertion.

is supporting evidence for
type: ObjectProperty
sub property of: is evidence for

is disputing evidence for
type: ObjectProperty
sub property of: is evidence for

represents
type: ObjectProperty
sub property of: refers to
description: a represents b when a serves as a sign, symbol or model of b.
subset: core

is positionally after
type: ObjectProperty
type: TransitiveProperty
sub property of: is connected to
inverse of: is positionally before
description: is positionally after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity.

is referred to by
type: ObjectProperty
sub property of: is related to
inverse of: refers to
description: A is referred to by B iff B is an informational entity that makes reference to A.

has concretization
type: ObjectProperty
sub property of: is generically related with
inverse of: is concretization of
description: A has concretization B iff A is an informational entity and B is the a quality of some material entity.

is concretization of
type: ObjectProperty
sub property of: is generically related with
description: A is concretization of B iff A is a quality of a material entity and B is an informational entity.

is measurement value of
type: ObjectProperty
sub property of: is attribute of
inverse of: has measurement value
domain: measurement value
description: is measurement value of is a relation between a value and the entity that it is a measurement of.

has measurement value
type: ObjectProperty
sub property of: has attribute
range: measurement value
description: has measurement value is a relation between a quality/realizable and a measurement value.
subset: core

has quality
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has property
inverse of: is quality of
range: quality
description: has quality is a relation between an entity and the quality that it bears.

is quality of
type: ObjectProperty
sub property of: is property of
domain: quality
description: is quality of is a relation between a quality and the entity that it is a property of.

is source of
type: ObjectProperty
sub property of: is attribute of
inverse of: has source
description: is source of is a relation between a source of information about some entity.

has unit
type: ObjectProperty
type: FunctionalProperty
sub property of: has attribute
inverse of: is unit of
range: unit of measurement
description: has unit is a relation between a quantity and the unit it is a multiple of.
subset: core

is unit of
type: ObjectProperty
sub property of: is attribute of
domain: unit of measurement
description: is unit of is a relation between a unit and a quantity that it is a multiple of.

has property
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has attribute
inverse of: is property of
description: has property is a relation between an entity and the quality, capability or role that it and it alone bears.
example: michel's hair has the quality of being brown in colour.

is property of
type: ObjectProperty
type: FunctionalProperty
sub property of: is attribute of
description: is property of is a relation betweena quality, capability or role and the entity that it and it alone bears.

has function
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has disposition
inverse of: is function of
range: function
description: has function is the relation between an entity and a function that is ascribed to it.

is function of
type: ObjectProperty
type: FunctionalProperty
sub property of: is disposition of
domain: function
description: is function of is a relation between a function and an entity that it is a property of.

is role of
type: ObjectProperty
type: FunctionalProperty
sub property of: is realizable property of
inverse of: has role
domain: role
description: is role of is a relation between a role and the entity that it is a property of.

has role
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has realizable property
range: role
description: has role is a relation between an entity and a role that it bears.

has output
type: ObjectProperty
sub property of: has participant
inverse of: is output of
description: has output is a relation between an process and an entity, where the entity is present at the end of the process.
subset: core
subset: sadi

has input
type: ObjectProperty
sub property of: has participant
inverse of: is input in
description: has input is a relation between a process and an entity, where the entity is present at the beginning of the process.
subset: core
subset: sadi

is input in
type: ObjectProperty
sub property of: is participant in
description: is input in is a relation between an entity and a process, where the entity is present at the beginning of the process.
example: glucose and ATP are inputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
subset: sadi

is output of
type: ObjectProperty
sub property of: is participant in
description: is output of is a relation between an entity and a process, where the entity is present at the end of the process.
example: glucose-6-phosphate and ADP are outputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
subset: sadi

is implementation of
type: ObjectProperty
sub property of: is attribute of
inverse of: has implementation
description: is implementation of is a relation between an information entity and a specification that it conforms to.

has implementation
type: ObjectProperty
sub property of: has attribute
description: has implementation is a relation between a specification and an implementation that conforms to it.

has disposition
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has capability
inverse of: is disposition of
range: disposition
description: has disposition is the relation between an entity and a disposition that it bears.

is disposition of
type: ObjectProperty
type: FunctionalProperty
sub property of: is capability of
domain: disposition
description: is disposition of is a relation between a disposition and the entity that it is a property of.

is positionally before
type: ObjectProperty
type: TransitiveProperty
sub property of: is connected to
description: is positionally before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity.

is directly after
type: ObjectProperty
type: FunctionalProperty
sub property of: is positionally after
sub property of: is directly connected to
inverse of: is directly before
description: is directly after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity, and the entities are adjacent to one another.

is directly before
type: ObjectProperty
type: FunctionalProperty
sub property of: is positionally before
sub property of: is directly connected to
description: is directly before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity, and the entities are adjacent to one another.

is causally related with
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to
description: A transitive, symmetric, temporal relation in which one entity is causally related with another non-identical entity.
subset: core

is derived from
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related from
inverse of: derives into
description: A transitive temporal relation in which one entity was materially formed from another non-identical entity.
equivalent to: OBO_REL:derives_from
subset: core

derives into
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related to
domain: object
range: object
description: a derives to b if and only if a or some part thereof is consumed in the formation of b.

immediately derives into
type: ObjectProperty
sub property of: derives into
inverse of: is immediately derived from
description: a immediately derives into b if and only if a or some significant part thereof is consumed in the formation of b and there are no identifiable intermediate entities between a and b.

is immediately derived from
type: ObjectProperty
sub property of: is derived from
description: A non-transitive temporal relation in which one entity is immediately derived from a non-identical entity such that there are no intermediate entities between them.

precedes
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related from
inverse of: is preceded by
description: A transitive, temporal relation in which one process precedes (has occured earlier than) another process.
subset: core

is preceded by
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related to
equivalent to: OBO_REL:preceded_by

immediately precedes
type: ObjectProperty
sub property of: precedes
inverse of: is immediately preceded by
description: A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes.

is immediately preceded by
type: ObjectProperty
sub property of: is preceded by
description: A non-transitive temporal relation in which one process is immediately preceded by another process, such that there is no interval of time between the two processes.

is referenced by
type: ObjectProperty
sub property of: is referred to by
inverse of: references
description: is reference for is a relation between a document that provides information about an entity.

has source
type: ObjectProperty
sub property of: has attribute
description: has source is a relation between an entity and another entity from which it stems from.

is annotation of
type: ObjectProperty
sub property of: is attribute of
inverse of: has annotation
domain: language entity
description: is annotation of is a relation between some textual entity and the entity that it annotates.

has annotation
type: ObjectProperty
sub property of: has attribute
range: language entity
description: has annotation is a relation between an entity and some textual anntotation.
example: document x is annotated with the keywords 'ontology','semantic web'
alternative: is annotated with
alternative: was annotated with

is variant of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is comparable to
description: is variant of: a relationship indicating that two entities are different (by some measure), but either achieve the same objectives in different ways or are permutations of one another (temporal, logical or otherwise)
subset: core

has direct part
type: ObjectProperty
sub property of: has proper part
inverse of: is direct part of
description: has direct part is a relation to specify a part at a particular level of granularity
example: a car has an engine as a direct part

is prior version of
type: ObjectProperty
sub property of: is derived from
sub property of: is version of
inverse of: is subsequent version of
description: A is prior version of B iff A is a variant of B and B derives from A.

cites
type: ObjectProperty
sub property of: references
inverse of: is cited by
description: cites is a relation to refer to by way of example, authority or proof.

is cited by
type: ObjectProperty
sub property of: is referenced by
description: is cited by is a relation from an object that is referred to by way of example, authority or proof.

is similar to
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of
description: is similar to is a relation between two entities that share one or more features.

is subsequent version of
type: ObjectProperty
sub property of: is version of
description: A is subsequent version of B iff A is a variant of B and A derives from B.

is covalently connected to (transitive)
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is connected to
domain: atom
range: atom

has target
type: ObjectProperty
sub property of: has input
inverse of: is target in
description: has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process.

is target in
type: ObjectProperty
sub property of: is input in
description: is target in is a relation between an entity and a process, where the entity is present at the beginning of the process and undergoes a change or transformation in the process.
example: glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.

is weakly interacting with (transitive)
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is connected to
domain: Class
  union of: molecule
  union of: Restriction
    on property: is part of
    some values from: molecule
range: Class
  union of: molecule
  union of: Restriction
    on property: is part of
    some values from: molecule
description: is weakly interacting with is a symmetric relation between two molecular entities (or any part thereof) that are interacting through some weak force (van der waals, hydrogen bonds, electrostatic interactions)

is causally related to
type: ObjectProperty
sub property of: is causally related with
inverse of: is causally related from
description: a is causally related to b iff there is a causal chain of events from a to b

is direct part of
type: ObjectProperty
sub property of: is proper part of
description: is direct part of is a relation between a specific part (at some level of granularity) and its whole.
subset: core

is product of
type: ObjectProperty
sub property of: is output of
inverse of: has product
description: is product of is a relation between an entity and a process, where the entity is present at the end of the process as a result of a transformation in the process target.
example: glucose-6-phosphate is the product of the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
subset: sadi

has product
type: ObjectProperty
sub property of: has output
description: has product is a relation between an process and an entity, where a new entity exists at the end of the process.
subset: sadi

is component part of
type: ObjectProperty
sub property of: is direct part of
inverse of: has component part
description: is component part of is a relation between a component and a whole, where the component is instrinsic to the whole, and loss of the part would change the kind that the whole is.
subset: core

is spatiotemporally related to
type: ObjectProperty
type: SymmetricProperty
sub property of: is related to
description: A is spatiotemporally related to B iff A is in the spatial or temporal vicinity of B
subset: core

is surrounded by
type: ObjectProperty
sub property of: is contained in
inverse of: surrounds
description: A 'is surrounded by' B iff the A 'is contained by' B and A 'is adjacent to' B or A 'is directly connected to' B.

surrounds
type: ObjectProperty
sub property of: contains
description: A 'surrounds' B iff the A 'contains' B and A 'is adjacent to' B or A 'is directly connected to' B.

overlaps with
type: ObjectProperty
type: SymmetricProperty
type: ReflexiveProperty
sub property of: is spatiotemporally related to
property chain axiom: overlaps with
property chain axiom: is part of
description: A overlaps with B iff there is some C that is part of both A and B. [S][R]

is about
type: ObjectProperty
sub property of: describes
inverse of: is subject of
description: is about is a relation between an information content entity and the entity that its primary subject.

is covalently connected to
type: ObjectProperty
type: SymmetricProperty
sub property of: is covalently connected to (transitive)
sub property of: is directly connected to
description: is covalently connected to is a relation between an atom and another atom.

is weakly interacting with
type: ObjectProperty
type: SymmetricProperty
sub property of: is weakly interacting with (transitive)
sub property of: is directly connected to

specifies
type: ObjectProperty
sub property of: is causally related with
sub property of: describes
inverse of: is specified by
description: A relation between an information content entity and a product that it (directly/indirectly) specifies

is specified by
type: ObjectProperty
sub property of: is causally related with
sub property of: is described by
description: a relation between a product and the information content entity that specifies it.

is manifested as
type: ObjectProperty
sub property of: is generically related with
inverse of: is manifestation of
description: is manifested as is a relation between an expression and its manifestations.
example: the english language version of 'war of the worlds' is manifested as a collection of english language versions of the book.

is causally related from
type: ObjectProperty
sub property of: is causally related with
description: a is causally related from b iff there is a causal chain of events from b to a
subset: core

realizes
type: ObjectProperty
sub property of: has output
inverse of: is realized in
description: realizes is a relation between a process and a realizable entity (role, function, disposition).
subset: core

is realized in
type: ObjectProperty
sub property of: is participant in
example: the role of a patient is realized in medical examination

satisfies
type: ObjectProperty
sub property of: has attribute
inverse of: is satisfied by
description: satisfies is a relation between an entity and the specification or objective that it conforms to.

is satisfied by
type: ObjectProperty
sub property of: is attribute of

has creator
type: ObjectProperty
sub property of: has source
inverse of: is creator of
description: has creator is a relation between an entity and that which created it.
equivalent to: dc:creator
example: the iPhone was created by Apple Inc
alternative: is created by
alternative: was created by

is creator of
type: ObjectProperty
sub property of: is source of
description: is creator of is a relation between a creator and an entity..
alternative: is created by

has component part
type: ObjectProperty
sub property of: has direct part
description: has component part is a relation between a whole and a component part where the component is instrinsic to the whole, and loss of the part would change the kind that it is.
example: a human has blood as a component part

has expression
type: ObjectProperty
sub property of: is generically related with
inverse of: is expression of
example: the story 'war of worlds' is expressed as every language edition of the book 'war of the worlds'

is expression of
type: ObjectProperty
sub property of: is generically related with
description: is expression of is a relation between more concrete expression of some conceptualization.
example: every language edition of 'war of the worlds' are expressions of the story of 'war of the worlds'

is broader than (t)
type: ObjectProperty
type: TransitiveProperty
sub property of: is similar to
inverse of: is narrower than (t)
domain: term
range: term
description: A is broader than B (t) iff for A is broader than B.
equivalent to: http://www.w3.org/2004/02/skos/core#narrowerTransitive

is narrower than (t)
type: ObjectProperty
type: TransitiveProperty
sub property of: is similar to
domain: term
range: term
description: A is narrower than B (t) iff for A is narrower than B.
equivalent to: http://www.w3.org/2004/02/skos/core#broaderTransitive

is generically related with
type: ObjectProperty
sub property of: is related to
description: A is generically related with B iff A is an abstract entity or an information content entity and B is a information content entity or a physical entity, respectively.

is manifestation of
type: ObjectProperty
sub property of: is generically related with

is narrower than
type: ObjectProperty
sub property of: is narrower than (t)
inverse of: is broader than
description: A is narrower than B iff the meaning of term A is narrower in scope than the meaning of term B
equivalent to: http://www.w3.org/2004/02/skos/core#broader

is broader than
type: ObjectProperty
sub property of: is broader than (t)
equivalent to: http://www.w3.org/2004/02/skos/core#narrower

is match to
type: ObjectProperty
type: SymmetricProperty
sub property of: is similar to
domain: term
range: term
description: A is match to B iff A and B are terms with similar (related, broad, close, exact) meanings
equivalent to: http://www.w3.org/2004/02/skos/core#relatedMatch

is exact match to
type: ObjectProperty
type: SymmetricProperty
sub property of: is match to
equivalent to: http://www.w3.org/2004/02/skos/core#exactMatch

is close match to
type: ObjectProperty
type: SymmetricProperty
sub property of: is match to
equivalent to: http://www.w3.org/2004/02/skos/core#closeMatch

is broad match to
type: ObjectProperty
type: SymmetricProperty
sub property of: is match to
equivalent to: http://www.w3.org/2004/02/skos/core#broadMatch

is dissimilar to
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of
description: is dissimilar to is a relation between two entities in which one is considered dissimilar to the other based on some criteria.

is opposite to
type: ObjectProperty
type: SymmetricProperty
sub property of: is dissimilar to
description: is opposite to is a relation between two entities in which one is diametrically opposed to the other.
example: hot is the opposite of cold; left is opposite of right

is version of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is variant of
description: is version of is a relation that holds between any two versions in which one is a subsequent or alternate version of (through a branch).

has parameter
type: ObjectProperty
sub property of: has input
inverse of: is parameter in
description: has parameter is a relation between a process and an information content entity which modulates the behaviour of some participant.
subset: sadi

is parameter in
type: ObjectProperty
sub property of: is input in
description: is parameter in is a relation between a data item and some data transformation process.

is described by
type: ObjectProperty
sub property of: is referred to by
inverse of: describes
description: is described by is a relation between one entity and another entity that provides a description (detailed account) of it.

is orthologous to
type: ObjectProperty
type: SymmetricProperty
sub property of: is homologous to
description: is orthologous to is a relation between two biological entities that share a common ancestor and occur in different species.

describes
type: ObjectProperty
sub property of: refers to
description: describes is a relation between one entity and another entity that it provides a description (detailed account of).
subset: core

has capability
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has realizable property
inverse of: is capability of
range: capability
description: has capability is a relation between an entity and the capability that it bears.
example: SIO has the capability to semantically integrate data.

refers to
type: ObjectProperty
sub property of: is related to
description: refers to is a relation between one entity and the entity that it makes reference to.
subset: core
subset: nlp+

is subject of
type: ObjectProperty
sub property of: is described by

is paralogous to
type: ObjectProperty
type: SymmetricProperty
sub property of: is homologous to
description: is paralogous to is a relation between two entities which indicates their common ancestry as a result of a gene duplication.

references
type: ObjectProperty
sub property of: refers to
description: references is a relation between one entity and the entity that it makes reference to by name, but is not described by it.
alternative: mentions
subset: core

is model of
type: ObjectProperty
sub property of: represents
inverse of: is modelled by
description: is model of is a relation between a model (an artifact) and the entity it purports to represent.
example: the architect builds a model that represents the building she envisions.

is modelled by
type: ObjectProperty
sub property of: is represented by

is xenologous to
type: ObjectProperty
type: SymmetricProperty
sub property of: is orthologous to
description: a relation between two entities which indicates their common ancestry but due to horizontal gene transfer.

has trigger
type: ObjectProperty
sub property of: is causally related to
inverse of: is trigger for
description: has trigger is a relation between a realizable and the factor that causes it to be realized.

is trigger for
type: ObjectProperty
sub property of: is causally related from

has basis
type: ObjectProperty
sub property of: has attribute
inverse of: is base for
domain: realizable entity
range: quality
description: has basis is a relation between a realizable entity and the quality that forms the basis for it.
example: the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization).

is base for
type: ObjectProperty
sub property of: is attribute of
domain: quality
range: realizable entity
description: is base for is a relation between a quality and the realizable entity that it is the basis for.
example: the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization).

is realizable property of
type: ObjectProperty
type: FunctionalProperty
sub property of: is property of
inverse of: has realizable property

has realizable property
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has property

is capability of
type: ObjectProperty
type: FunctionalProperty
sub property of: is realizable property of
domain: capability
description: is capability of is a relation between a capability and the entity that bears it.

is directly connected to
type: ObjectProperty
type: SymmetricProperty
sub property of: is connected to
description: A is directly connected to B iff there exists a path direclty between A and B.

transforms into
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related to
inverse of: is transformed from
description: A transitive temporal relation in which an entity mainstains identity from one state to another.

immediately transforms into
type: ObjectProperty
sub property of: transforms into
inverse of: is immediately transformed from
description: A temporal relation in which an entity mainstains identity from one state to another.

is transformed from
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related from
description: A transitive temporal relation in which an entity mainstains identity from one state to another.

is immediately transformed from
type: ObjectProperty
sub property of: is transformed from
description: A temporal relation in which an entity mainstains identity from one state to another.

in relation to
type: ObjectProperty
sub property of: refers to
inverse of: in relation from
description: in relation to is a comparative relation to indicate that the instance of the class holding the relation exists in relation to another entity.
subset: core

has identifier
type: ObjectProperty
sub property of: has attribute
inverse of: is identifier for
range: identifier
description: a relation between an entity and an identifier.

is identifier for
type: ObjectProperty
sub property of: is attribute of
domain: identifier
description: a relation between an identifier and an entity.
alternative: identifies

has unique identifier
type: ObjectProperty
type: InverseFunctionalProperty
sub property of: has identifier
inverse of: is unique identifier for
range: unique identifier
description: has unique identifier is an inverse functional relation between an entity and an identifier that uniquely identifies it.

is unique identifier for
type: ObjectProperty
type: FunctionalProperty
sub property of: is identifier for
domain: unique identifier
description: is unique identifier for is a relation between an identifier and an entity that it uniquely identifies

has time boundary
type: ObjectProperty
type: FunctionalProperty
sub property of: has boundary
range: time instant

has start time
type: ObjectProperty
type: FunctionalProperty
sub property of: has time boundary
inverse of: is start time of
range: time instant

has end time
type: ObjectProperty
type: FunctionalProperty
sub property of: has time boundary
inverse of: is end time of
range: time instant

is start time of
type: ObjectProperty
sub property of: is time boundary of
domain: time instant

is end time of
type: ObjectProperty
sub property of: is time boundary of
domain: time instant

exists at
type: ObjectProperty
sub property of: is spatiotemporally related to
range: time measurement
description: exists at is a relation between an entity and a time measurement.
subset: core

is mutual disposition of
type: ObjectProperty
type: SymmetricProperty
sub property of: is mutually related to
description: a is mutual disposition of b if and only if the realization of the disposition a necessarily causes the realization of the disposition b.

is greater than or equal to
type: ObjectProperty
type: TransitiveProperty
sub property of: is numerically comparable to
inverse of: is lesser than or equal to
description: is greater than or equal to is a comparison relation between two quantities in which the first has a value larger or equal to the second.

is mutually related to
type: ObjectProperty
type: SymmetricProperty
sub property of: is related to
description: a is mutually related to b if and only if the realization of the relation of a necessarily causes the realization of a relation to b.

is mutual role of
type: ObjectProperty
type: SymmetricProperty
sub property of: is mutually related to
description: a is mutual role of b if and only if the realization of role a necessarily causes the realization of role b.

is lesser than or equal to
type: ObjectProperty
type: TransitiveProperty
sub property of: is numerically comparable to
description: is greater than to is a comparison relation between two quantities in which the first has a value smaller or equal to the second.

is greater than
type: ObjectProperty
type: TransitiveProperty
sub property of: is greater than or equal to
inverse of: is lesser than
description: is greater than to is a comparison relation between two quantities in which the first has a value larger than the second.

is lesser than
type: ObjectProperty
type: TransitiveProperty
sub property of: is lesser than or equal to
description: is lesser than to is a comparison relation between two quantities in which the first has a value smaller than the second.

is comparable to
type: ObjectProperty
type: SymmetricProperty
sub property of: is related to
description: is comparable to is a relation between two entities that share at least one feature whose value can be compared.
subset: core

is numerically comparable to
type: ObjectProperty
type: SymmetricProperty
sub property of: is comparable to
domain: quantity
range: quantity
description: is numerically comparable to is a comparison relation between two quantities whose datatype value can be compared.

is equal to
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is numerically comparable to
description: is equal to is a comparison relation between two quantities whose value are exactly the same.

is inequal to
type: ObjectProperty
type: SymmetricProperty
sub property of: is numerically comparable to
description: is inequal to is a comparison relation between two quantities whose value are not the same.

has evidence
type: ObjectProperty
sub property of: references
inverse of: is evidence for
description: has evidence is a relation between a proposition and something that demonstrates the truth of the assertion.

is evidence for
type: ObjectProperty
sub property of: is referenced by

is refuted by
type: ObjectProperty
sub property of: has evidence
inverse of: is refuting evidence for
description: has evidence is a relation between a proposition and something that refutes (is incompatible with) the truth of the assertion.

is refuting evidence for
type: ObjectProperty
sub property of: is evidence for

measured at
type: ObjectProperty
sub property of: exists at
range: time measurement
description: measured at is a relation between a measurement value and the time measurement.
subset: core

in relation from
type: ObjectProperty
sub property of: is referred to by
description: a in relation from b is a comparative relation in a is the object of reference in a relation with b.

has frequency
type: ObjectProperty
sub property of: has measurement value
inverse of: is frequency of
description: has frequency is a relation that specifies the occurence of an object or event

is frequency of
type: ObjectProperty
sub property of: is measurement value of
description: is frequency of is a relation between a temporal unit and an object or event

has substrate
type: ObjectProperty
sub property of: has target
description: has substrate is a relation between a process and an object where the object is destroyed by its participation in the process.

is first part of
type: ObjectProperty
sub property of: is ordered part of
inverse of: has first part
description: is first part of is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.

has first part
type: ObjectProperty
sub property of: has ordered part
description: has first part is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.

has last part
type: ObjectProperty
sub property of: has ordered part
inverse of: is last part of
description: has last part is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.

is last part of
type: ObjectProperty
sub property of: is ordered part of
description: is last part of is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.

has ordered part
type: ObjectProperty
sub property of: has proper part
description: has ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.

is ordered part of
type: ObjectProperty
sub property of: is proper part of
description: is ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.

is specialization of
type: ObjectProperty
sub property of: is variant of
inverse of: is generalization of
description: is specialization of is a relation between a more specific instance (in terms of spatial/temporal localization & other attributres) than the other.
equivalent to: http://www.w3.org/ns/prov#specializationOf
example: a weather forecast for the city of London produced at a specific time is a specialization of a weather forecast for the city of London.

is generalization of
type: ObjectProperty
sub property of: is variant of
description: is generalization of is a relation between a more general instance (in terms of spatial/temporal localization & other attributres) than the other.

is alternate of
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of
description: is alternate of relates two specialized instances.
equivalent to: http://www.w3.org/ns/prov#alternateOf
example: two weather forecasts for the city of London produced at different times or by different organizations (etc) are alternates of each other, and instances of / specializations of forecasts for the city of London.

is mutual capability of
type: ObjectProperty
type: SymmetricProperty
sub property of: is mutually related to
description: a is mutual capability of b if and only if the realization of capability a necessarily causes the realization of capability b.

regulates
type: ObjectProperty
sub property of: is causally related to
inverse of: is regulated by
description: x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or extent of y

is regulated by
type: ObjectProperty
sub property of: is causally related from

results in
type: ObjectProperty
sub property of: has output
sub property of: is causally related to
inverse of: is result of

is result of
type: ObjectProperty
sub property of: is causally related from

affects
type: ObjectProperty
sub property of: has output
inverse of: is affected by

is affected by
type: ObjectProperty
sub property of: is participant in

is identical to
type: ObjectProperty
type: SymmetricProperty
sub property of: is comparable to
description: is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes.

is transitively related to
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
comment: not implemented in standard distribution
subset: ovopub

has data item
type: ObjectProperty
sub property of: refers to
inverse of: is data item in
domain: dataset
description: has data item is a relation between a dataset and any described / referrenced entity.
subset: core

is data item in
type: ObjectProperty
sub property of: refers to
range: dataset
description: 'is data item in' is a relation between an entity that is described or referenced in a dataset.
subset: core

has phenotype
type: ObjectProperty
sub property of: has attribute
inverse of: is phenotype of
description: has phenotype is a relation between an object and an observable/measurable characteristic.

is phenotype of
type: ObjectProperty
sub property of: is attribute of
description: is phenotype of is a relation between an observable/measurable characteristic and an object.

positively regulates
type: ObjectProperty
sub property of: regulates
description: x positively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect that increases the frequency, rate or extent of y

negatively regulates
type: ObjectProperty
sub property of: regulates
description: x negatively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an reduced effect on the frequency, rate or extent of y

is associated with
type: ObjectProperty
sub property of: is related to
description: x is associated with y when x and y are logically or statistically related to one another.

is correlated with
type: ObjectProperty
sub property of: is associated with
description: x is correlated with y when x holds a statistical relationship with y

encodes
type: ObjectProperty
sub property of: specifies
inverse of: is encoded by
description: A relation between two objects, in which the first object contains information that is used to produce the second object.
example: an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology)

is encoded by
type: ObjectProperty
sub property of: is specified by
description: A relation between two objects, in which the first object is produced from the information contained in the second object.

is transcribed into
type: ObjectProperty
sub property of: encodes
inverse of: is transcribed from
description: a relation between two information content entities in which one is transcribed into (an exact or similar kind) another through some process.
example: DNA is transcribed into RNA

is transcribed from
type: ObjectProperty
sub property of: is encoded by

is translated into
type: ObjectProperty
sub property of: encodes
inverse of: is translated from
example: RNA is translated into Protein
example: a relation between two information content entities in which one is translated into (a completely different kind of entity) another through some process.

is translated from
type: ObjectProperty
sub property of: is encoded by

is homologous to
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of
description: a relation between two entities which indicates their common ancestry.

has value
type: DatatypeProperty
type: FunctionalProperty
description: A relation between a informational entity and its actual value (numeric, date, text, etc).
subset: core
subset: nlp
subset: relations
subset: sadi

entity
type: Class
description: Every thing is an entity.
subset: core

material entity
type: Class
subclass of: object
subclass of: Restriction
  on property: has attribute
  some values from: mass
subclass of: Restriction
  on property: has proper part
  all values from: Class
    union of: material entity
    union of: spatial region
description: A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass.
subset: core

quality
type: Class
subclass of: attribute
subclass of: Restriction
  on property: is quality of
  some values from: entity
disjoint with: realizable entity
description: A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary.
subset: core

process
type: Class
subclass of: entity
subclass of: Restriction
  on property: has proper part
  all values from: process
subclass of: Restriction
  on property: exists at
  all values from: time interval
description: A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.
subset: core
subset: process+

social entity
type: Class
subclass of: information content entity
description: A social entity pertains to the interaction among individuals and groups.

social structure
type: Class
subclass of: social entity
subclass of: Restriction
  on property: has member
  all values from: object
description: A social structure is a social entity which consists of relationships between two or more entities.

organization
type: Class
subclass of: collective
description: An organization is a collective with a complex articulation of tasks, roles and responsibilities.

geographic position
type: Class
subclass of: position
description: A geographic position is the coordinate of an entity against some geographic coordinate system.

disposition
type: Class
subclass of: capability
subclass of: Restriction
  on property: has attribute
  some values from: probability measure
description: A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger).
example: solubility (to dissolve when put in fluid); fragility (disposition to break when dropped)
subset: core

information content entity
type: Class
subclass of: object
subclass of: Restriction
  on property: has proper part
  all values from: information content entity
description: information content entity is an object that requires some background knowledge or procedure to correctly interpret.
subset: core
subset: ice+

role
type: Class
subclass of: realizable entity
description: A role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance.
subset: core

function
type: Class
subclass of: capability
disjoint with: dysfunction
description: A function is a capability that satisfies some agentive objective, or (evolutionary) optimization.
subset: core

site
type: Class
subclass of: spatial region
description: A site is a spatial region bounded (in part or in whole) by material entities and may be occupied by material entities.
example: A nostril; the interior of the heart valve; the interior of a bottle.

material boundary
type: Class
subclass of: spatial boundary
subclass of: Restriction
  on property: is boundary of
  some values from: material entity
description: A material boundary is the boundary of a material entity which exists as a lower dimensional entity at exactly the location where its parts no longer extend into space. Every material entity has a boundary, and a boundary is the boundary of exactly 1 material entity.
example: the external surface of the window; the surface of the p52 protein

object quality
type: Class
subclass of: quality
subclass of: Restriction
  on property: is quality of
  some values from: object
description: An object quality is quality of an object.

process quality
type: Class
subclass of: quality
subclass of: Restriction
  on property: is quality of
  some values from: process
description: A process quality is quality that is associated with a process.

biopolymer sequence
type: Class
subclass of: primary structure descriptor
subclass of: Restriction
  on property: represents
  some values from: Class
    intersection of: molecular structure
    intersection of: Restriction
      on property: is attribute of
      some values from: biopolymer
subclass of: Restriction
  on property: describes
  some values from: biopolymer
subclass of: Restriction
  on property: has value
  some values from: string
description: A sequence is a primary structure descriptor in which each of the letters in the string represents a monomeric unit (residue) in which adjacent letters represent the connectivity between the monomeric units.

start date
type: Class
subclass of: time instant
description: A start date is a time instant pertaining to the date of the beginning of a process.

end date
type: Class
subclass of: time instant
description: An end date is a time instant pertaining to date of the end of a process.

process status
type: Class
subclass of: process quality
subclass of: Restriction
  on property: is attribute of
  some values from: process
description: process status is a process quality that describes the state of a process.

completed
type: Class
subclass of: process status
description: completed is that status of a process that successfully unfolds.

ongoing
type: Class
subclass of: process status
description: ongoing is the status of a process that is not yet complete.

predicted
type: Class
subclass of: hypothetical
description: predicted is the quality of an entity that is thought to exist, as evidenced by some rational procedure.

spatial quantity
type: Class
subclass of: dimensional quantity
subclass of: Restriction
  on property: is attribute of
  some values from: object
subclass of: Restriction
  on property: has measurement value
  some values from: quantity
description: A spatial quantity is a quantity obtained from measuring the spatial extent of an entity
alternative: physical dimensional quantity

1D extent quantity
type: Class
subclass of: spatial quantity
description: A quantity that extends in single dimension.

depth
type: Class
subclass of: 1D extent quantity
description: depth is the dimensional extent into a plane of a 3D projection of the object.

height
type: Class
subclass of: 1D extent quantity
description: height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference.

length
type: Class
subclass of: 1D extent quantity
description: length is the longer dimensional extent along a 2D projection of the object.

width
type: Class
subclass of: 1D extent quantity
description: width is the shorter dimensional extent perpendicular to a 2D projection of the object.

thickness
type: Class
subclass of: depth
description: thickness is the shortest dimensional extent of a 3D projection of an object.

2D extent quantity
type: Class
subclass of: spatial quantity
description: A quantity that extends in two dimensions.

area
type: Class
subclass of: 2D extent quantity
description: area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane.

length of perimeter
type: Class
subclass of: 2D extent quantity
description: A perimeter is a length of the outline that surrounds a two-dimensional shape.

circumference
type: Class
subclass of: length of perimeter
description: circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius.

3D extent quantity
type: Class
subclass of: spatial quantity
description: A quantity that extends in three dimensions.

volume
type: Class
subclass of: 3D extent quantity
description: volume is the quantity of three-dimensional space enclosed by some closed boundary.

compositional quality
type: Class
subclass of: object quality
description: composition quality is a quality that describes its composition or anatomy.

quantity
type: Class
equivalent class: Class
  union of: dimensionless quantity
  union of: dimensional quantity
subclass of: measurement value
subclass of: Restriction
  on property: is attribute of
  some values from: entity
subclass of: Restriction
  on property: is measurement value of
  some values from: entity
description: A quantity is an informational entity that gives the magnitude of a property.

shape
type: Class
subclass of: object quality
description: shape is the quality of a bearer that relates to its spatial extent.

position
type: Class
subclass of: measurement value
subclass of: Restriction
  on property: has attribute
  some values from: positional identifier
description: A measurement of a spatial location relative to a frame of reference or other objects.

orientation
type: Class
subclass of: position
description: orientation is an angle between the bearer and an axis, or the angle between the bearer and another object.

namespace
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: has member
  all values from: identifier
description: A namespace is an informational entity that defines a logical container for a set of symbols or identifiers.

data item
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: is participant in
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: realizes
      some values from: objective
description: A data item consists of information that has been collected/generated towards some purpose.

measurement value
type: Class
subclass of: number
subclass of: Class
  union of: Restriction
    on property: has value
    some values from: boolean
  union of: Restriction
    on property: has value
    some values from: dateTime
  union of: Restriction
    on property: has value
    some values from: double
  union of: Restriction
    on property: has value
    some values from: float
  union of: Restriction
    on property: has value
    some values from: integer
description: A measurement value is a quantitative description that reflects the magnitude of some attribute.

coordinate
type: Class
subclass of: position
description: A coordinate is a measurement of position in n-dimensional space.

cartesian coordinate
type: Class
subclass of: coordinate
subclass of: Restriction
  on property: is proper part of
  some values from: cartesian coordinate system
disjoint with: polar coordinate
description: A Cartesian coordinate is the signed distance of a point to some referent line.

polar coordinate
type: Class
subclass of: coordinate
subclass of: Restriction
  on property: is proper part of
  some values from: polar coordinate system
description: A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction.

unit of measurement
type: Class
subclass of: quantity
description: A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.

mathematical entity
type: Class
subclass of: information content entity
description: A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
subset: math+

plan
type: Class
subclass of: action specification
description: A plan is a set of intended actions, through which one expects to achieve a goal.

generic name
type: Class
subclass of: name
description: A generic name is the preferred name provided by manufacturer.

language entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has value
  some values from: Literal
description: A language entity implements some language specification for the visual interpretation and is part of some document.
subset: nlp+

visual language entity
type: Class
subclass of: language entity
description: A visual language entity is a language entity that is manifested within the spectrum of light and can be pereceived and processed by a visual system.

figure
type: Class
subclass of: media
disjoint with: figure part
description: A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities.
alternative: diagram

image
type: Class
subclass of: figure
description: An image is an affine projection of a visual entity to a two dimensional surface.
alternative: depiction

photograph
type: Class
subclass of: image
description: A photograph is an image created by light falling on a light-sensitive surface.
alternative: photo

statistical graph
type: Class
subclass of: chart
description: A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions.
alternative: chart

question
type: Class
subclass of: sentence
description: A question is a linguistic expression used to make a request for information.

publication
type: Class
subclass of: document
description: A publication is a document that has been made available by a publisher.

record
type: Class
subclass of: document
subclass of: Restriction
  on property: has unique identifier
  some values from: identifier
description: A record is a document containing a collection of statements about some entity.

dataset
type: Class
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    on property: has member
    all values from: data item
subclass of: data item
subclass of: Restriction
  on property: has concretization
  some values from: file
description: A dataset is a data item that is a collection of data items.
equivalent to: http://www.w3.org/ns/dcat#Dataset
alternative: data set

specification
type: Class
subclass of: description
subclass of: Restriction
  on property: specifies
  some values from: entity
subclass of: Restriction
  on property: has component part
  some values from: objective
subclass of: Restriction
  on property: has expression
  some values from: information content entity
description: A specification is a description of the essential technical attributes/requirements for an object or procedure, and may be used to determine that the object / procedure meets its requirements/attributes.

action specification
type: Class
subclass of: specification
subclass of: Restriction
  on property: specifies
  some values from: process
subclass of: Restriction
  on property: satisfies
  some values from: objective
subclass of: Restriction
  on property: is manifested as
  all values from: process
description: An action specification is a specification composed of a sequence of instructions to achieve some objective.
alternative: effective specification

biopolymer
type: Class
equivalent class: Class
  intersection of: organic polymer
  intersection of: Restriction
    on property: has direct part
    some values from: Class
      union of: lipid residue
      union of: amino acid residue
      union of: nucleotide residue
      union of: carbohydrate residue
subclass of: organic polymer
subclass of: Restriction
  on property: has direct part
  some values from: Class
    union of: lipid residue
    union of: amino acid residue
    union of: nucleotide residue
    union of: carbohydrate residue
description: A biopolymer is an organic polymer that are typically produced by the cells of living organisms.

algorithm
type: Class
subclass of: mathematical entity
description: An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function.

software entity
type: Class
subclass of: computational entity
description: A software entity is a computational entity that can be interpreted by or directly executed by a processing unit.

software method
type: Class
subclass of: software entity
description: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.

software module
type: Class
subclass of: software entity
description: A software module is software composed of a collection of software methods.

software library
type: Class
subclass of: software entity
description: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.

software application
type: Class
subclass of: software entity
description: A software application is software that can be directly executed by some processing unit.

software interpreter
type: Class
subclass of: software application
description: A software interpreter is a software application that executes some specified input software.

software script
type: Class
subclass of: software entity
description: A software script is software whose instructions can be executed using a software interpreter.

language
type: Class
subclass of: language entity
description: Language is a language entity which is the result of encoding and decoding information through systematic creation and usage of systems of symbols, each pairing a specific sign with an intended meaning, established through social conventions

symbol
type: Class
subclass of: representation
subclass of: Restriction
  on property: represents
  some values from: entity
subclass of: Restriction
  on property: is about
  some values from: entity
description: A symbol is a proposition about what an entity represents.

book
type: Class
subclass of: publication
description: A book is a publication composed of a large number of entries.

chapter
type: Class
subclass of: document section
description: A chapter is a document section of a book or thesis.

character
type: Class
subclass of: language entity
description: A character is a language symbol used to construct words.

novel
type: Class
subclass of: publication
description: A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism.

paragraph
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: has direct part
  some values from: sentence
description: A paragraph is a self-contained unit of written discourse consisting of one or more sentences.

document section
type: Class
subclass of: document component
subclass of: Restriction
  on property: is proper part of
  some values from: document
description: A document section is a component of a document.

capability
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: is attribute of
  some values from: Restriction
    on property: is agent in
    some values from: process
subclass of: Restriction
  on property: has basis
  some values from: quality
subclass of: Restriction
  on property: has trigger
  all values from: process
description: A capability is a realizable entity whose basis lies in one or more parts or qualities and reflects possibility of an entity to behave in a specified way under certain conditions or in response to a certain stimulus (trigger).
subset: capability+
subset: core

sentence
type: Class
subclass of: phrase
description: A sentence is a grammatical unit consisting of one or more words that bear minimal syntactic relation to the words that precede or follow it.

word
type: Class
subclass of: language entity
subclass of: Restriction
  on property: has part
  some values from: morpheme
subclass of: Restriction
  on property: has direct part
  some values from: character
description: A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language.

identifier
type: Class
subclass of: label
subclass of: Restriction
  on property: is identifier for
  some values from: entity
description: An identifier is a label that specifically refers to (identifies) an entity (instance/type).

name
type: Class
subclass of: label
subclass of: Restriction
  on property: has value
  some values from: string
description: A name is a label used to identify an entity.

preferred name
type: Class
subclass of: name
description: A preferred name is the name that is generally used by some organization.

common name
type: Class
subclass of: name
description: A common name is a name that is commonly used.

brand name
type: Class
subclass of: name
description: A brand name is a trademarked and marketed name of a product.

scientific name
type: Class
subclass of: name
description: A scientific name is a name given through scientific nomenclature.

magazine
type: Class
subclass of: periodical
description: A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports.
equivalent to: http://purl.org/ontology/bibo/Magazine

synonym
type: Class
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is similar to
    some values from: term
subclass of: term variant
description: A synonym is a word with the same or very similar meanings.

antonym
type: Class
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is opposite to
    some values from: term
subclass of: term variant
description: An antonym is a word with opposite or nearly opposite meaning.

hypernym
type: Class
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is broader than
    some values from: term
subclass of: term variant
description: A hypernym is a term with a broader meaning.

hyponym
type: Class
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is narrower than
    some values from: term
subclass of: term variant
description: A hyponym is a term with a narrower meaning.

homonym
type: Class
subclass of: term variant
subclass of: Restriction
  on property: is dissimilar to
  some values from: term
description: A homonym is a word that sounds the same but has different meaning.

workflow
type: Class
subclass of: algorithm
description: A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives.

ontology document
type: Class
subclass of: document
description: An ontology document is a document that contains an ontology.

pattern
type: Class
subclass of: mathematical entity
description: A pattern is a generalized representation of some repeatable concrete or informational item.

sequence motif
type: Class
subclass of: pattern
disjoint with: structural motif
description: A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein.

descriptor
type: Class
subclass of: term
description: A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document.

definition
type: Class
subclass of: description
description: A definition is a description that succintly characterizes an entity.

description
type: Class
subclass of: language entity
subclass of: Restriction
  on property: describes
  all values from: entity
description: A description is language entity in which elements of a language (formal or natural) are used to characterize an entity.

category
type: Class
subclass of: concept
description: A category is a class of entities having particular shared characteristics.

class
type: Class
subclass of: set
description: A class is a collection of sets which can be unambiguously defined by a property that all its members share.

web service
type: Class
subclass of: software application
description: A web service is a software application that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.

criterion
type: Class
subclass of: design specification
description: A criterion is a specification to describe properties used for evaluation.

inclusion criterion
type: Class
subclass of: criterion
disjoint with: exclusion criterion
description: An inclusion criterion is a criterion that must be present to satisfy some objective.

exclusion criterion
type: Class
subclass of: criterion
description: An exclusion criterion is a criterion that must be absent to satistify the objective.

parameter
type: Class
subclass of: independent variable
description: A parameter is variable whose value changes the characteristics of a system or a function.

monomer
type: Class
subclass of: submolecule
subclass of: Restriction
  on property: is direct part of
  some values from: biopolymer
description: A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer.

keyword
type: Class
subclass of: descriptor
description: A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval.

document
type: Class
subclass of: textual entity
description: A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate.

list
type: Class
subclass of: set
subclass of: Restriction
  on property: has member
  some values from: entity
description: A list is any enumeration of a set of items.

manuscript
type: Class
subclass of: document
description: A manuscript is a document prior to publication.

note
type: Class
subclass of: document
description: A note is a brief document.

patent
type: Class
subclass of: legal document
description: A patent is an information entity granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.

article
type: Class
subclass of: publication
description: An article is a publication that is stand-alone section of a larger work.

blog
type: Class
subclass of: publication
description: A blog is a publication accessible at some website and is typically about various experiences.

book volume
type: Class
subclass of: book
description: A book volume is a book that is part of a collection.

conference proceedings
type: Class
subclass of: book
description: A conference proceedings is a book composed of papers presented at a conference.

book series
type: Class
subclass of: collection of documents
description: A book series is a collection of books that have been sequentially published.

edited publication
type: Class
subclass of: publication
description: An edited publication is a publication that has been examined and potentially changed by an editor.

journal
type: Class
subclass of: periodical
description: A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published.
equivalent to: http://purl.org/ontology/bibo/Journal

manual
type: Class
subclass of: publication
description: A manual is a document that instructs on the usage of a device.

periodical
type: Class
subclass of: collection of documents
description: A periodical is a publication that appears on a regular schedule.
equivalent to: http://purl.org/ontology/bibo/Periodical

newspaper
type: Class
subclass of: periodical
description: A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising.
equivalent to: http://purl.org/ontology/bibo/Newspaper

technical report
type: Class
subclass of: publication
description: A technical report is a publication published by a school or other institution, usually numbered within a series.

thesis document
type: Class
subclass of: publication
description: A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments.

honor's thesis
type: Class
subclass of: thesis document
description: An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree.

master's thesis
type: Class
subclass of: thesis document
description: A Master's thesis is a thesis prepared as a requirement for a Master's degree.

phd thesis
type: Class
subclass of: thesis document
description: A PhD thesis is a thesis prepared as a requirement for a doctoral degree.

booklet
type: Class
subclass of: document
description: A booklet is a document that lacks a named publisher or sponsoring institution.

diary
type: Class
subclass of: document
description: A diary is a document which describes day-to-day experiences.

document component
type: Class
subclass of: textual entity
description: A bibliographic attribute is an attribute related to publications.

address
type: Class
subclass of: positional identifier
description: An address is a position that indicates the physical location of some entity using a social convention.

affiliation
type: Class
subclass of: social relation
description: An affiliation is a social relation which indicates the partnership between two or more entities.

citation
type: Class
subclass of: document component
description: A citation is a textual entity which denotes a source described in the bibliography or reference section of a document.

document title
type: Class
subclass of: title
description: A document title is a textual entity that summarizes the topic of the document in one sentence.

reference
type: Class
subclass of: document component
description: A reference is a textual entity that describes a single source used in the preparation or development of the work.

page range
type: Class
subclass of: interval
description: A page range denotes the start and end page in some document.

page total
type: Class
subclass of: count
description: A page total is a textual entity that is about the number of pages in some informational entity.

label
type: Class
subclass of: term
description: a label is a term that is associated with some entity

language label
type: Class
subclass of: label
description: A language label is a label that denotes the language of a textual entity.

first name
type: Class
subclass of: name
description: A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname.

last name
type: Class
subclass of: name
description: A last name (surname) is a name added to a given name and is part of a personal name and is often the family name.

personal name
type: Class
subclass of: name
description: A personal name is a name to identify an individual person and usually comprises of a first name and a last name.
alternative: full name

legal name
type: Class
subclass of: personal name
description: A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate.

title
type: Class
subclass of: label
description: A title is a textual entity that summarily describes some entity.

document version
type: Class
subclass of: version label
description: A document version is a version of a work in some sequence of derivative works.

abstract section
type: Class
subclass of: document section
description: An abstract section is a document section that provides brief summary of a document that explains the main argument(s), topic(s) or findings.

acknowledgements section
type: Class
subclass of: document section
description: An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work.

author contribution section
type: Class
subclass of: document section
description: An author contribution section is a document section that describes the contribution of the authors.

author section
type: Class
subclass of: document section
description: An author section is a document section that lists the contributing authors.

bibliography section
type: Class
subclass of: document section
description: A bibliography section is a document section that is composed of a list of references used in the development of the work.

copyright section
type: Class
subclass of: document section
description: A copyright section is a document section that contains a notice of copyright.

correspondence section
type: Class
subclass of: document section
description: A correspondence section is a document section that contains the details for contacting the corresponding author.

discussion section
type: Class
subclass of: document section
description: The discussion section is a document section containing a summary of the findings, a reflection on the significance of findings, comparison with related work, among others.

introduction section
type: Class
subclass of: document section
description: An introduction section is a document section that generally provides background, motivation and goals of the work.

materials and methods section
type: Class
subclass of: document section
description: The materials and methods section is a document section containing a description of the materials and methods used in the study.

materials section
type: Class
subclass of: document section
description: The materials section is a document section containing a description of the materials used in the study.

methods section
type: Class
subclass of: document section
description: The methods section is a document section containing a description of the methods used in the study.

results section
type: Class
subclass of: document section
description: The results section is a document section describing the main findings of the study.

table of contents
type: Class
subclass of: document section
description: The table of contents is a document section that lists all sections (and optionally subsections) in a sequential order along with their page number.

implies (->)
type: Class
subclass of: logical operator
description: Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B.

namespace label
type: Class
subclass of: label
description: A namespace label is a short name for a namespace.

logical operator
type: Class
subclass of: mathematical entity
description: A logical operator is a unary or binary relation to construct logical expressions.

conjunction (and)
type: Class
subclass of: logical operator
description: AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false.

proposition
type: Class
subclass of: description
subclass of: Restriction
  on property: has quality
  some values from: truth value
subclass of: Restriction
  on property: is about
  some values from: entity
description: A proposition is a sentence expressing something true or false.

dimensionless quantity
type: Class
subclass of: quantity
subclass of: Class
  complement of: Restriction
    on property: has unit
    some values from: unit of measurement
disjoint with: dimensional quantity
description: A dimensionless quantity is a quantity that has no associated unit.

dimensional quantity
type: Class
subclass of: quantity
subclass of: Restriction
  on property: has unit
  some values from: unit of measurement
description: A dimensional quantity is a quantity that has an associated unit.

argument
type: Class
subclass of: proposition
subclass of: Class
  intersection of: Restriction
    on property: has proper part
    some values from: premise
  intersection of: Restriction
    on property: has proper part
    some values from: conclusion
description: An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion.

premise
type: Class
subclass of: proposition
description: A premise is a proposition of an argument from which the conclusion is drawn.

conclusion
type: Class
subclass of: proposition
description: A conclusion is a proposition which is reached after considering the evidence, arguments or premises.

deductive argument
type: Class
subclass of: argument
description: A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises.

inductive argument
type: Class
subclass of: argument
description: An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises.

sound argument
type: Class
subclass of: valid argument
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: premise
    intersection of: Restriction
      on property: has quality
      some values from: true
description: A sound argument is a valid argument with true premises.

valid argument
type: Class
subclass of: argument
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: conclusion
    intersection of: Restriction
      on property: has quality
      some values from: false
description: A valid argument is an argument where the truth of the conclusion is a logical consequence of the premises and (consequently) its corresponding conditional is a necessary truth.

invalid argument
type: Class
subclass of: argument
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: conclusion
    intersection of: Restriction
      on property: has quality
      some values from: false
description: An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises.

truth value
type: Class
equivalent class: Class
  union of: true
  union of: false
subclass of: informational quality
description: truth value is a quality of information that is claimed/verified to be true or false.

true
type: Class
subclass of: truth value
subclass of: Restriction
  on property: has value
  has value: true
disjoint with: false
description: true is a truth value that indicates that it holds under all possible worlds.

false
type: Class
subclass of: truth value
subclass of: Restriction
  on property: has value
  has value: false
description: false is a truth value in that indicates that it is not true.

term
type: Class
subclass of: language entity
subclass of: Class
  union of: word
  union of: phrase
description: A term is a word or phrase used to denote one or more entities.

emotion
type: Class
subclass of: behaviour
description: An emotion is a process (experience) that arises internally or from an involuntary physiological response to a stimulus.
subset: emotion++

mass
type: Class
subclass of: spatial quantity
subclass of: Restriction
  on property: is attribute of
  some values from: material entity
description: mass is the quality of the amount of substance.

disjunction (or)
type: Class
subclass of: logical operator
description: OR is a logical operator that results in true whenever one or more of its operands are true.

negation (not)
type: Class
subclass of: logical operator
description: NOT is a logical operator in that has the value true if its operand is false.

exclusive disjunction (xor)
type: Class
subclass of: disjunction (or)
description: XOR, also called exclusive disjunction or (symbolized XOR, EOR, EXOR, or ⊕), is a type of logical disjunction on two operands that results in a value of true if exactly one of the operands has a value of true.

hypothesis
type: Class
subclass of: proposition
description: A hypothesis is a proposed explanation for a phenomenon.

academic organization
type: Class
subclass of: organization
description: An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement.

social relation
type: Class
subclass of: social entity
description: A social relation is a social entity that describes a relationship between two or more individuals or groups.

set
type: Class
subclass of: mathematical entity
subclass of: Restriction
  on property: has member
  all values from: entity
description: A set is a collection of entities, for which there may be zero members.

university
type: Class
subclass of: academic organization
description: A university is an institution of higher education and research which grants academic degrees in a variety of subjects and provides both undergraduate education and postgraduate education.

collection of documents
type: Class
subclass of: collection
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: document
description: A collection of documents is a non-zero set of documents.
equivalent to: http://purl.org/ontology/bibo/Collection

website
type: Class
subclass of: collection of documents
subclass of: Restriction
  on property: has direct part
  some values from: web page
description: A website is a collection of documents published on the World Wide Web.

movie
type: Class
subclass of: media
description: A movie is a series of images that are displayed in rapid succession to give the impression of movement.
alternative: film
alternative: moving pictures

excerpt
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is part of
  some values from: textual entity
description: An excerpt is a contiguous or discontiguous portion of a document.

quote
type: Class
subclass of: excerpt
subclass of: Restriction
  on property: is derived from
  some values from: textual entity
description: A quote is a excerpt that is attributed to a particular source.

geographic image
type: Class
subclass of: photograph
description: A geographic image is a photograph of some geographical area.

web page
type: Class
subclass of: document
description: A web page is a document that is published according to World Wide Web standards.

email
type: Class
subclass of: document
description: Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol.

process number
type: Class
subclass of: ordinal position
description: process number is a number associated with a process that denotes its ordinal position in a set of processes.

letter
type: Class
subclass of: document
description: A letter is a document that contains a personal communication from one part to another.

normality
type: Class
equivalent class: Class
  union of: normal
  union of: abnormal
subclass of: quality
description: normality is the quality in which the value may differ from normal or average

edition number
type: Class
subclass of: count
description: An edition number is count of a literary work edited and published, as by a certain editor or in a certain manner including being printed during some interval of time.

volume number
type: Class
subclass of: count
description: volume number is a count of a sequence of periodicals.

polymer
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: has direct part
    some values from: monomer
subclass of: molecule
subclass of: Restriction
  on property: has direct part
  some values from: monomer
description: A polymer is a molecule composed of a connected set of monomeric residues.

functional specification
type: Class
subclass of: specification
subclass of: Restriction
  on property: specifies
  some values from: Class
    union of: material entity
    union of: information content entity
description: A functional specification is a specification that describes the characteristics of an object.

design specification
type: Class
subclass of: functional specification
description: A design specification is a specification that provides precise and explicit information about the requirements for a product design.

spatial specification
type: Class
subclass of: functional specification
description: A specification for spatial location is an effective specification towards representation spatial position or spatial data.

longitude
type: Class
subclass of: geographic position
disjoint with: latitude
description: Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point.

latitude
type: Class
subclass of: geographic position
description: Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane

coordinate system
type: Class
subclass of: spatial specification
description: A coordinate system is a specification for spatial location that uses a set of numbers, or coordinates, to uniquely determine the position of a point or other geometric element.

cartesian coordinate system
type: Class
subclass of: coordinate system
description: A Cartesian coordinate system specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.

concept
type: Class
subclass of: term
description: A concept is term that refers to a generalization of a set of attributes or entities.

polar coordinate system
type: Class
subclass of: coordinate system
description: A polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.

positional identifier
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is attribute of
  some values from: position
description: A positional description is a description of location using some system or frame of reference.

cylindrical coordinate system
type: Class
subclass of: coordinate system
description: A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis.

spherical coordinate system
type: Class
subclass of: coordinate system
description: A spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.

OWL ontology
type: Class
subclass of: ontology document
description: An OWL ontology is an ontology as specified by the W3C OWL specification.

3D cartesian coordinate
type: Class
subclass of: cartesian coordinate
subclass of: Class
  intersection of: Restriction
    on property: has direct part
    qualified cardinality: 1
    on class: x cartesian coordinate
  intersection of: Restriction
    on property: has direct part
    qualified cardinality: 1
    on class: y cartesian coordinate
  intersection of: Restriction
    on property: has direct part
    qualified cardinality: 1
    on class: z cartesian coordinate
description: A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate.

objective
type: Class
subclass of: proposition
subclass of: Restriction
  on property: is specified by
  all values from: action specification
subclass of: Restriction
  on property: is realized in
  all values from: process
description: An objective is a proposition that indicates a planned or anticipated outcome.

realizable entity
type: Class
subclass of: attribute
subclass of: Restriction
  on property: is realizable property of
  some values from: entity
subclass of: Restriction
  on property: in relation to
  all values from: entity
description: A realizable entity is an attribute that is exhibited under some condition and is realized in some process.
subset: core

term variant
type: Class
equivalent class: Class
  intersection of: term
  intersection of: Restriction
    on property: is variant of
    some values from: term
description: A term variant is a term that is a variant of another term.

to modify
type: Class
subclass of: to actively interact with
description: to modify is the capability to change some entity.

to record
type: Class
subclass of: to actively interact with
description: to record is the capability to detect and transcribe information in a specified format on some physical medium.

to magnify
type: Class
subclass of: to change appearance
description: to magnify is the capability to increase the appearance of the size of an object.

to heat
type: Class
subclass of: to supply energy
description: to heat is a capability to increase the internal kinetic energy of a material.

to cool
type: Class
subclass of: to reduce energy
description: to cool is the capability to decrease the internal kinetic energy of a material.

to freeze
type: Class
subclass of: to cool
description: to freeze is the capability to decrease the internal kinetic energy of a material such that it changes state from a gas or liquid to a solid.

to separate
type: Class
subclass of: to modify
description: to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them.

to ionize
type: Class
subclass of: to modify electronically
description: to ionize is the capability to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.

to supply energy
type: Class
subclass of: to change energetically
description: to supply energy is the capability to transfer energy from a source to a sink.

to observe
type: Class
subclass of: to passively interact with
description: to observe is the capability to watch attentively.

dysfunction
type: Class
subclass of: capability
description: dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function.

fitness
type: Class
subclass of: object quality
description: fitness is the quality of an object with respect to some stated functions or evolutionary adaptation.

intent
type: Class
subclass of: desire
description: intent is a desire to realize a particular outcome.

purpose
type: Class
subclass of: reason
description: purpose is the reason for which something is done or created or for which something exists.

belief
type: Class
subclass of: proposition
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: true
    intersection of: Restriction
      on property: is quality of
      some values from: proposition
description: A belief is a proposition that is believed to be true.

number
type: Class
subclass of: scalar
alternative: rank 0 tensor
description: A number is a tensor of rank 0.

variable
type: Class
subclass of: mathematical entity
description: A variable is a value that may change within the scope of a given problem or set of operations.

equation
type: Class
subclass of: mathematical entity
description: An equation is a mathematical statement that asserts the equality of two expressions.

spatial region
type: Class
subclass of: object
subclass of: Restriction
  on property: has part
  all values from: spatial region
description: A spatial region is an object contained in some region of space.
example: The airspace above Ottawa airport; the band around the northern hemisphere between 50 degrees N and 60 degrees N; the spatial region occupied by a bottle.
alternative: region

to measure
type: Class
subclass of: to investigate
description: to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric.

to inject
type: Class
subclass of: to modify
description: to inject is the capability to administer a substance into some object through its external barrier.

to boil
type: Class
subclass of: to heat
description: to boil is the capability to increase the internal kinetic energy of a material such that it changes state from a solid or liquid to a gas.

to reduce energy
type: Class
subclass of: to change energetically
description: to reduce energy is the capability to remove energy from a source.

to supply electricity
type: Class
subclass of: to supply energy
description: to supply electricity is the capability to transfer electricity from a source to a sink.

to change materially
type: Class
subclass of: to modify
description: to change appearance is the capability to change the material composition of an object.

to demagnify
type: Class
subclass of: to change appearance
description: to demagnify is the capability to decrease the appearance of the size of an object.

to change appearance
type: Class
subclass of: to modify
description: to change appearance is the capability to change the visual attributes of an object.

perception
type: Class
subclass of: observing
description: perception is the organization, identification, and interpretation of sensory information in order to fabricate a mental representation through the process of transduction, which sensors in the body transform signals from the environment into encoded neural signals.

to contain
type: Class
subclass of: to change spatially
description: to contain is the capability to bound or constrain a physical entity in some site.

to immobilize
type: Class
subclass of: to contain
description: to immobilize is the capability to contain an entity in such a way that it may not move in space.

to filter
type: Class
subclass of: to separate
description: to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through.

to excite
type: Class
subclass of: to supply energy
description: to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons).

to emit
type: Class
subclass of: to reduce energy
description: to emit is the capability to release some physical entity (light, pollution, etc).

to change energetically
type: Class
subclass of: to modify
description: to change energetically is the capability to change the energetic aspects of an object.

to positively charge
type: Class
subclass of: to ionize
description: to positively charge is the capability to remove an electron or add a positively charged ion to a chemical entity.

to negatively charge
type: Class
subclass of: to ionize
description: to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity.

to assemble
type: Class
subclass of: to actively interact with
description: to assemble is the capability to combine entities together into a larger object that persists in time.

to extract
type: Class
subclass of: to separate
description: to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain.

to transport
type: Class
subclass of: to actively interact with
description: to transport is the capability to displace a material from one location to another.

time measurement
type: Class
subclass of: dimensional quantity
description: time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference).
comment: Time intervals are specified as date/datetime ranges.
example: the duration of my life; the duration of a surgical procedure, the moment of death

to change spatially
type: Class
subclass of: to modify
description: to change spatially is the capability to affect the physical movement of some entity.

patient
type: Class
subclass of: person
subclass of: Restriction
  on property: has role
  some values from: patient role
description: A patient is an individual that is the recepient of medical care.

doctor
type: Class
subclass of: medical practitioner
subclass of: Restriction
  on property: has role
  some values from: doctor role
description: A doctor is an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments.

to regulate
type: Class
subclass of: to modify
description: to regulate is to control or maintain the rate or speed of an object or process.
alternative: to modulate

file
type: Class
subclass of: media
description: A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding.
equivalent to: http://www.w3.org/ns/dcat#Distribution

to provide
type: Class
subclass of: to retrieve
description: to provide is the capability to make available some object to another that requires it.

nurse
type: Class
subclass of: medical practitioner
subclass of: Restriction
  on property: has role
  some values from: nurse role
description: A nurse is an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations.

study subject
type: Class
subclass of: person
description: A study subject is an individual that is the subject of the study.

x cartesian coordinate
type: Class
subclass of: cartesian coordinate
description: An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system.

y cartesian coordinate
type: Class
subclass of: cartesian coordinate
description: An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system.

z cartesian coordinate
type: Class
subclass of: cartesian coordinate
description: A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system.

study group
type: Class
subclass of: collective
description: A study group is a group of individuals that are subjects in an observational or intervention study.

professor
type: Class
subclass of: academic
description: A professor is an individual that is a scholarly teacher.

student
type: Class
subclass of: academic
description: A student is an individual who is attends an educational institution.

academic
type: Class
subclass of: person
description: An academic is an individual that participates in education and scholarship.

to increase the rate of formation
type: Class
subclass of: to regulate the rate of formation
description: to increase the rate of formation is to regulate the rate of formation in a manner that increases this rate relative to a reference process.

to investigate
type: Class
subclass of: to actively interact with
description: to investigate is the capability to uncover facts.

mutual disposition
type: Class
subclass of: disposition
description: A mutual disposition is a disposition that simulataneously invokes another disposition when realized.

anger
type: Class
subclass of: disgust
description: anger is disgust directed toward an equal status individual.

hate
type: Class
subclass of: disgust
description: Hate is a deep and emotional extreme dislike, directed against a certain object or class of objects.

love
type: Class
subclass of: positive emotion
description: love is an emotion of a strong affection and personal attachment.

geolegal region
type: Class
subclass of: geographic region
description: A geolegal region is a geographic region which has causal powers confered by a legal entity.
example: The 50 kph zones in Ottawa; the geographic region occupied by France.

geographic region
type: Class
subclass of: spatial region
description: A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth).
example: The spatial region occupied by the province of ontario; the spatial region occupied by a lake.

geopolitical region
type: Class
subclass of: geolegal region
description: a geopolitical region is a geographic region recognized by social or legal convention.
example: The geographic region bounded by Canada; the spatial region occupied by the US embassy in Ottawa.

time interval
type: Class
subclass of: time measurement
description: A time internval is a contiguous temporal region having some duration.

time instant
type: Class
subclass of: time measurement
description: A time instant is a temporal region which occurs instantaneously, e.g. having no duration.
example: at this moment; the moment at which a finger is detached in an industrial accident; the moment at which a child is born; the moment of death

table
type: Class
subclass of: figure
description: A table is a figure that consists of an ordered arrangement of columns and rows.

scatterplot
type: Class
subclass of: statistical graph
description: A scatterplot is a statistical 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.
alternative: scatter chart
alternative: scatter diagram
alternative: scatter graph

year
type: Class
subclass of: time interval
description: A year is a period of time taken by a planet to make one revolution around the sun.

month
type: Class
subclass of: time interval
description: A month is a period of time that divides the year.

day
type: Class
subclass of: time interval
description: A day is a period of 24 hours.

century
type: Class
subclass of: time interval
description: A century is a period of one hundred years.

millennium
type: Class
subclass of: time interval
description: A millenium is a period of 1000 years

hour
type: Class
subclass of: time interval
description: An hour is a period of 60 minutes.

minute
type: Class
subclass of: time interval
description: A minute is a period of 60 seconds.

second
type: Class
subclass of: time interval
description: A second (symbol: s) is the base unit of time in the International System of Units (SI) and is the second division of the hour by sixty, the first division by 60 being the minute.

informational quality
type: Class
subclass of: quality
subclass of: Restriction
  on property: is quality of
  some values from: information content entity
description: An informational quality is a quality that pertains to information.

2D cartesian point
type: Class
equivalent class: Class
  intersection of: point
  intersection of: Restriction
    on property: has component part
    all values from: Class
      union of: x cartesian coordinate
      union of: y cartesian coordinate
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: x cartesian coordinate
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: y cartesian coordinate
subclass of: point
description: A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates.

altitude
type: Class
subclass of: position
description: Altitude is a distance above sea level.

center of mass
type: Class
subclass of: position
description: The center of mass (aka barycenter) is the weighted average location of all the mass in a body or group of bodies.

3D cartesian point
type: Class
equivalent class: Class
  intersection of: point
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: x cartesian coordinate
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: y cartesian coordinate
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: z cartesian coordinate
subclass of: point
description: A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates.

1D cartesian point
type: Class
equivalent class: Class
  intersection of: point
  intersection of: Restriction
    on property: has component part
    all values from: z cartesian coordinate
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: z cartesian coordinate
subclass of: point
description: A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates.

line graph
type: Class
subclass of: statistical graph
description: A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments.
example: Graph 1 in http://tinyurl.com/opwnvm
alternative: line chart

bar graph
type: Class
subclass of: statistical graph
description: A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent.
example: Graphs 3,4,5 in http://tinyurl.com/opwnvm

horizontal bar graph
type: Class
subclass of: bar graph
description: A horizontal bar graph is a bar graph in which the rectangular bars are horizontally oriented in space.
example: Graph 3 in http://tinyurl.com/opwnvm

vertical bar graph
type: Class
subclass of: bar graph
description: A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space.
example: Graph 4,5 in http://tinyurl.com/opwnvm

stacked bar graph
type: Class
subclass of: bar graph
description: A stacked bar graph is a bar graph in which each rectangular bar is partioned by the categorical value of each series of data.
example: Graphs 6,7 in http://tinyurl.com/opwnvm

line-bar graph
type: Class
subclass of: statistical graph
description: A line-bar graph statistical graph that contains both lines and bars.
example: Graph 8 in http://tinyurl.com/opwnvm

figure part
type: Class
subclass of: media
subclass of: Restriction
  on property: is proper part of
  some values from: figure
description: A figure part is a part of a figure.

plot
type: Class
subclass of: figure part
disjoint with: legend
description: A plot is a part of a figure that corresponds to the spatial region between the set of axes.
example: The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm

axis
type: Class
subclass of: directed line segment
subclass of: Restriction
  on property: is component part of
  some values from: statistical graph
description: An axis is a line segment that is part of a statistical graph in which the position along the line corresponds to a numeric or categorical value.
comment: The value of a plotted geometric objects (e.g. point) can be obtained from the perpendicular projection of the position of the object onto the axis. Axis may also be associated with a textual description of what the values on the axis represents.
example: The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm

Cartesian coordinate axis
type: Class
subclass of: value axis
subclass of: Restriction
  on property: satisfies
  some values from: cartesian coordinate system
description: A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system.

x-axis
type: Class
subclass of: Cartesian coordinate axis
disjoint with: y-axis
disjoint with: z-axis
description: An x-axis is a Cartesian coordinate axis that is aligned with the horizon.
comment: In most figures, this axis represents categories, such as months, market segments, or other non-numeric data.
example: The horizontal axis in http://tinyurl.com/opwnvm
alternative: horizontal axis

y-axis
type: Class
subclass of: Cartesian coordinate axis
description: A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis.
alternative: vertical axis

z-axis
type: Class
subclass of: Cartesian coordinate axis
description: A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes.

category axis
type: Class
equivalent class: Class
  union of: primary category axis
  union of: secondary category axis
subclass of: axis
disjoint with: value axis
description: A category axis is an axis in which the position along the line is partioned into categories.
example: The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm

primary category axis
type: Class
subclass of: category axis
disjoint with: secondary category axis
description: A primary category axis is a category axis that either defines the sole value range or holds the larger set of categorical values specified by the secondary category axis.
example: The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm

secondary category axis
type: Class
subclass of: category axis
description: A secondary category axis is a category axis that defines a finer granular part (or subset) of the value range of the primary category axis.
example: The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm

value axis
type: Class
equivalent class: Class
  union of: left value axis
  union of: right value axis
  union of: top value axis
  union of: bottom value axis
subclass of: axis
description: A value axis is an axis in which the position along the line is partioned into numeric values.
comment: A value axis holds the properties of having a minimum and a maximum value, and is usually associated with tickmarks that indicate intervals along the axis.
example: The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm

left value axis
type: Class
subclass of: value axis
description: A left value axis is a value axis that is spatially positioned to the left of the plot area.
example: The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm

right value axis
type: Class
subclass of: value axis
description: A right value axis is a value axis that is spatially positioned to the right of the plot area.

scaled value axis
type: Class
subclass of: value axis
description: A scaled value axis is a value axis in which the value range was subject to a mathematic transformation.

linear value axis
type: Class
subclass of: scaled value axis
disjoint with: logarithmic value axis
description: A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range.

logarithmic value axis
type: Class
subclass of: scaled value axis
description: A logarithmic value axis is a scaled value axis that corresponds to a scaling factor of the logarithm of the value range.

data series
type: Class
subclass of: list
description: A data series is a data set composed of related values displayed in a statistical graph.
example: Example: The two series that correspond to "Seasonally adjusted" and "Trend" are composed of the seasonally adjusted value of permits in each month and values from a trend derived from some mathematical tranformation across those values, respectively, in Graph 1 of http://tinyurl.com/opwnvm

data point
type: Class
subclass of: point
subclass of: Restriction
  on property: denotes
  some values from: entity
description: A data point is a point that which corresponds to the projection of the values of measurement data against the axes of a statistical graph.

global maximal stationary point
type: Class
subclass of: local maximum stationary point
description: A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints.

global minimal stationary point
type: Class
subclass of: local minimum stationary point
description: A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints.

legend
type: Class
subclass of: figure part
description: A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities.
example: The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm

graph title
type: Class
equivalent class: Class
  intersection of: title
  intersection of: Restriction
    on property: is direct part of
    some values from: statistical graph
description: A graph title is a title that describes a graph.
example: Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm

primary title
type: Class
subclass of: title
description: A primary title is a title that should be first used in describing some entity.

secondary title
type: Class
subclass of: title
description: A secondary title is a title of lesser importance that should be used after the first title in describing some entity.
alternative: subtitle, alternative title

scientific data
type: Class
subclass of: data item
description: scientific data is data obtained from some scientific procedure.

primary graph title
type: Class
subclass of: primary title
subclass of: Restriction
  on property: is direct part of
  some values from: statistical graph
description: A primary graph title is a primary title that describes a statistical graph.
example: "Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm

secondary graph title
type: Class
subclass of: primary title
subclass of: Restriction
  on property: is direct part of
  some values from: statistical graph
description: A secondary graph title is a secondary title that describes a statistical graph.

biological quality
type: Class
subclass of: object quality
description: A biological quality is a quality held by a biological entity.

cellular quality
type: Class
subclass of: biological quality
subclass of: Restriction
  on property: is quality of
  some values from: cell
description: cellular quality is the quality of a cell

sequence variant role
type: Class
subclass of: variant role
description: A sequence variant role is a comparative role in which the composition of characters in a sequence differs when compared to another entity of similar type.

variant role
type: Class
subclass of: comparative role
description: A variant role is a comparative role in which the value of an attribute differs when compared to another entity

insertion variant role
type: Class
subclass of: sequence variant role
description: An insertion variant role is the role of an sequence that contains a sub-sequence that is considered to be an addition relative to the frame of reference.

deletion variant role
type: Class
subclass of: sequence variant role
description: A deletion variant role is the role of an sequence that lacks a sub-sequence relative to the frame of reference.

phrase
type: Class
subclass of: language entity
subclass of: Restriction
  on property: has direct part
  min qualified cardinality: 2
  on class: word
description: A phrase is a group of words functioning as a single unit in the syntax of a sentence.

human
type: Class
subclass of: multicellular organism
description: A human is a primates of the family Hominidae and are characterized by having a large brain relative to body size, with a well developed neocortex, prefrontal cortex and temporal lobes, making them capable of abstract reasoning, language, introspection, problem solving and culture through social learning.

mouse
type: Class
subclass of: multicellular organism
description: A mouse is a small mammal belonging to the order of rodents, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail.

rat
type: Class
subclass of: multicellular organism
description: A rat is a medium-sized, long-tailed rodent of the superfamily Muroidea.

worm
type: Class
subclass of: multicellular organism
description: A worm is a non-arthropod invertebrate animal that typically have a long cylindrical tube-like body and no legs.

e.coli
type: Class
subclass of: unicellular organism
description: Escherichia coli (e coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms.

to consume
type: Class
subclass of: to actively interact with
description: to consume is the capability to internalize a material entity.

clause
type: Class
subclass of: sentence
description: A clause consists of a subject and a predicate.

to actively interact with
type: Class
subclass of: to interact with
description: to actively interact with is the capability to interact with another entity in a way that requires physical contact.

person
type: Class
subclass of: specialized object
description: A person is an object that has certain capacities or attributes constituting personhood.

to decrease the rate of formation
type: Class
subclass of: to regulate the rate of formation
description: to decrease the rate of formation is to regulate the rate of formation in a manner that decreases this rate relative to a reference process.

polygon vertex
type: Class
subclass of: node
subclass of: Restriction
  on property: is component part of
  min qualified cardinality: 2
  on class: polygon edge
subclass of: Restriction
  on property: has component part
  qualified cardinality: 1
  on class: vertex normal
description: A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon.

polygon edge
type: Class
subclass of: line segment
subclass of: Restriction
  on property: is part of
  some values from: polygon
subclass of: Restriction
  on property: has component part
  qualified cardinality: 2
  on class: polygon vertex
description: A polygon edge is a line segment joining two polygon vertices.

polyhedral skeleton
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: has direct part
  some values from: polygon edge
description: A polyhedral skeleton is a collection of polygon edges.

polygonal face
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: is part of
  some values from: polygon
description: A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary.

polyhedral surface
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: has part
  some values from: polygonal face
description: A polyhedral surface is composed of polygonal faces.

polygon
type: Class
subclass of: geometric entity
description: A polygon is a planar entity that is bounded by a closed path or circuit, composed of a finite connected sequence3 of straight line segments.

geometric entity
type: Class
subclass of: information content entity
description: A geometric entity is an information content entity that pertains to the structure and topology of a space.
subset: geometry+

point
type: Class
subclass of: geometric entity
description: A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system.

endpoint
type: Class
subclass of: terminal point
description: An endpoint is a terminal point that is the last of an ordered pair of points.

start point
type: Class
subclass of: terminal point
description: A start point is a terminal point which is the first of an ordered pair of points.

model
type: Class
subclass of: representation
subclass of: Restriction
  on property: represents
  some values from: entity
description: A model is a representation of some thing.

line
type: Class
equivalent class: Class
  union of: line segment
  union of: ray
  union of: infinite line
subclass of: curve
description: A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points.

line segment
type: Class
subclass of: line
subclass of: Restriction
  on property: has component part
  qualified cardinality: 2
  on class: terminal point
description: A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points.

tick mark
type: Class
subclass of: line segment
description: A tick mark is a line segment that is spatially positioned perpendicular to the axis of a statistical graph and indicates the position of a specific numeric value (which may be indicated by an adjacent value label) on a value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value (which may be indicated by an adjacent category label) on the categorical axis.

major tick mark
type: Class
subclass of: tick mark
description: A major tick mark is a tick mark that indicates the position of a specific numeric value and is adjacent to its value label on the value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value indicated by an adjacent category label on the categorical axis.

minor tick mark
type: Class
subclass of: tick mark
description: A minor tick mark is a tick mark that indicates the position of a specific numeric value but has no adjacent value label, or is one of a pair of tick marks that delineates the boundary of a categorical value but has no adjacent category label on the categorical axis.

ray
type: Class
subclass of: line
description: A ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension.

quadrilateral
type: Class
subclass of: polygon
description: A quadrilateral is a polygon with composed of four points and four line segments, in which each point is fully connected to two other points.

rectangle
type: Class
subclass of: quadrilateral
description: A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair.

bar
type: Class
subclass of: rectangle
description: A bar is a rectangle that is located in the plot of a statistical graph in which its length is proportional to the values that it represents.

triangle
type: Class
subclass of: polygon
description: A triangle is a polygon composed of three points and three line segments, in which each point is fully connected to another point along through the line segment.

directed line segment
type: Class
subclass of: line segment
subclass of: Restriction
  on property: has component part
  qualified cardinality: 1
  on class: endpoint
subclass of: Restriction
  on property: has component part
  qualified cardinality: 1
  on class: start point
description: A directed line segment is a line segment that is contained by an ordered pair of endpoints (a start point and an endpoint).

arrowed line segment
type: Class
subclass of: directed line segment
subclass of: Restriction
  on property: has part
  some values from: triangle
subclass of: Restriction
  on property: has component part
  max qualified cardinality: 2
  on class: triangle
description: An arrowed line is a directed line segment in which one or both endpoints is tangentially part of a triangle that bisects the line.

single arrowed line segment
type: Class
subclass of: arrowed line segment
subclass of: Restriction
  on property: has component part
  qualified cardinality: 1
  on class: triangle
disjoint with: double arrowed line segment
description: A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line.

double arrowed line segment
type: Class
subclass of: arrowed line segment
subclass of: Restriction
  on property: has component part
  qualified cardinality: 2
  on class: triangle
description: A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line.

horizontal line
type: Class
subclass of: positionally oriented line
description: A horizontal line is a line that is positionally oriented with the horizon.

vertical line
type: Class
subclass of: positionally oriented line
description: A vertical line is a line that is positionally oriented perpendicular to the horizon.

trend line
type: Class
subclass of: statistical graph line
description: A trend line is a line, line segment or ray that is part of a statistical graph which indicates a statistical or visual direction across categorical or value data.

increasing line
type: Class
subclass of: trend line
description: An increasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is positive.

decreasing line
type: Class
subclass of: trend line
description: An decreasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is negative.

plateau line
type: Class
subclass of: trend line
description: An plateau line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is zero.

drop line
type: Class
subclass of: statistical graph line
description: A drop line is a statistical graph line that vertically or horizontally connects a data series line with a value axis in a statistical graph.

terminal point
type: Class
subclass of: point
description: A terminal point is a point that defines the finite extension of a line.

surface normal
type: Class
subclass of: vector line
description: A surface normal is a vector that is perpendicular to a flat surface.

positionally oriented line
type: Class
subclass of: line
description: A positionally oriented line is a line that is positioned against some axis of reference.

statistical graph line
type: Class
subclass of: line
description: A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data.

to regulate the rate of formation
type: Class
subclass of: to regulate
description: to regulate the rate of formation is to modify the rate at which an object is formed.

curvature
type: Class
subclass of: shape
description: curvature is a quality of a bearer that relates to the presence of curves, bends, or angles.

straight
type: Class
subclass of: curvature
description: straight is a quality of a bearer that is free of curves, bends, or angles.
see also: PATO:0002180 [for material entities]

infinite line
type: Class
subclass of: line
description: An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points.

vector line
type: Class
subclass of: ray
description: A vector line is a line which that is bounded by a startpoint and extends outwards along one dimension.

vertex normal
type: Class
subclass of: vector line
description: A vertext normal is the normalized average of the surface normals of the faces that contain that vertex.

to serve as
type: Class
subclass of: to actively interact with
description: to serve as is the capability to act in a manner corresponding to some role.

to serve as a host
type: Class
subclass of: to serve as
subclass of: Restriction
  on property: is capability of
  some values from: host
description: to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself.

to infect
type: Class
subclass of: to inject
description: to infect is the capability to administer a disease-causing organism into some object.

polyline
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: line segment
description: A polyline is a connected sequence of line segments.
alternative: polygonal chain, polygonal curve, polygonal path, piecewise linear curve

collection of points
type: Class
subclass of: geometric entity
subclass of: collection
subclass of: Restriction
  on property: has member
  all values from: point
description: A collection of points is a geometric entity that contains a non-zero set of geometric points.

to cause disease
type: Class
subclass of: to change materially
description: to cause disease is the capability to materially change a biological object in that it functions abnormally.

to reduce the activation energy
type: Class
subclass of: to change the activation energy
disjoint with: to increase the activation energy
description: to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond.
alternative: to activate

to increase the activation energy
type: Class
subclass of: to change the activation energy
description: to increase the activation energy is to require a larger amount of energy in order to form or break a chemical bond.
alternative: to inhibit

to change the activation energy
type: Class
subclass of: to change energetically
description: to change the activation energy is to change the amount of energy required to form or break a chemical bond.

normal
type: Class
subclass of: normality
disjoint with: abnormal
description: A quality that has a value that is normal or average.
equivalent to: PATO:0000461

abnormal
type: Class
subclass of: normality
description: A quality that has a value that is outside normal or average.

lipid residue
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: lipid
description: A lipid residue is a part of an organic molecule that was derived from a lipid molecule.

chemical synthesis
type: Class
subclass of: creating
subclass of: Restriction
  on property: has agent
  some values from: enzyme
subclass of: Restriction
  on property: has product
  some values from: chemical entity
description: chemical synthesis is synthesis of a chemical entity from physical precursors through one or more chemical interactions or reactions.

molecular orbital
type: Class
subclass of: chemical quality
description: A molecular orbital (or MO) is a mathematical function describing the wave-like behavior of an electron in a molecule.

passive transport
type: Class
subclass of: membrane transport
disjoint with: active transport
description: passive transport is the movement of a substance across a membrane and does not require chemical energy.

diffusion
type: Class
subclass of: passive movement
description: diffusion is motion of particles at temperatures above absolute zero.

diffusion equation
type: Class
subclass of: movement equation
subclass of: Restriction
  on property: specifies
  some values from: diffusion
description: A diffusion equation describes density fluctuations in a material undergoing diffusion.

movement equation
type: Class
subclass of: equation
description: A movement equation describes the displacement of an object in space over time.

ordinary differential equation
type: Class
subclass of: differential equation
description: An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable.

partial differential equation
type: Class
subclass of: differential equation
description: A partial differential equation (PDE) is a differential equation in which the unknown function is a function of multiple independent variables and the equation involves its partial derivatives.

differential equation
type: Class
subclass of: equation
description: A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders.

movement
type: Class
subclass of: process
description: movement is the process in which an object is spatially displaced.
subset: core

brownian motion
type: Class
subclass of: diffusion
description: Brownian motion is the seemlingly random movement of particles suspended in a fluid.

osmosis
type: Class
subclass of: diffusion
description: osmosis is the movement of water molecules through a selectively-permeable membrane down a water potential gradient.

passive movement
type: Class
subclass of: movement
description: passive movement is the process in which an object is spatially displaced without an expenditure of energy contained in molecular bonds.

active movement
type: Class
subclass of: movement
description: active movement is the process in which an object is spatially displaced using some chemical energy.

transporting
type: Class
subclass of: interacting
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: to transport
  intersection of: Restriction
    on property: realizes
    some values from: to be transported
description: transporting is a process in which one object physically moves another object from one location to another.

membrane transport
type: Class
subclass of: chemical transport
description: membrane transport is the movement of molecules across a membrane.

primary active transport
type: Class
subclass of: active transport
disjoint with: secondary active transport
description: primary active transport, also called direct active transport, directly uses energy to transport molecules across a membrane.

secondary active transport
type: Class
subclass of: active transport
description: secondary active transport or co-transport uses electrochemical potential difference created by pumping ions out of the cell to transport molecules across a membrane.

symport enabled secondary active transport
type: Class
subclass of: secondary active transport
disjoint with: antiport enabled secondary active transport
description: symport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in the same direction simultaneously.

antiport enabled secondary active transport
type: Class
subclass of: secondary active transport
description: antiport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in opposite directions simultaneously.

locomotion
type: Class
subclass of: active movement
description: The self-propelled movement of an object.
broader than: GO:0040011

birthing
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: biological entity
description: birthing is the process by which a biological organism is brought into existence.

dying
type: Class
subclass of: destroying
subclass of: Restriction
  on property: has substrate
  some values from: biological entity
description: dying is a process in which a biological entity ceases to exist.

idea
type: Class
subclass of: proposition
description: An idea is a proposition about some object of conceptual thought.

biological reproduction
type: Class
subclass of: reproducing
description: biological reproduction is the biological process by which one or more biological organisms are produced from their "parents".

creating
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has product
  some values from: object
description: creating is the process in which an entity comes into existence.
alternative: creation
alternative: development
alternative: formulation
alternative: production
alternative: synthesis

regulating
type: Class
equivalent class: Class
  union of: process maintenance
  union of: process up-regulation
  union of: process down-regulation
subclass of: interacting
description: regulating is a process that modulates the attributes of an object or process.
alternative: regulation

biosynthesis
type: Class
subclass of: chemical synthesis
description: biosynthesis is the synthesis of an organic compound in a living organism, usually aided by enzymes.

destroying
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has substrate
  some values from: object
description: destroying is a process in which something is broken down and/or ceases to exist.
alternative: destruction

chemical destruction
type: Class
subclass of: destroying
subclass of: Restriction
  on property: has target
  some values from: chemical entity
description: chemical destruction is destruction of a chemical entity to its chemical constituents through one ormore chemical interactions or reactions.

interacting
type: Class
subclass of: process
subclass of: Class
  intersection of: Restriction
    on property: realizes
    min qualified cardinality: 2
    on class: to interact with
  intersection of: Restriction
    on property: realizes
    min qualified cardinality: 2
    on class: to be interacted with
subclass of: Restriction
  on property: has participant
  some values from: object
description: interacting is a process characterized by the interaction between two or more entities.
subset: core

data transformation
type: Class
subclass of: information processing
subclass of: Restriction
  on property: has output
  some values from: data item
subclass of: Restriction
  on property: has input
  some values from: data item
description: data transformation is the process of applying an algorithmic procedure to some input data and producing some output data.

parameterized data transformation
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has parameter
  some values from: parameter
description: A parameterized data transformation is a data transformation whose behaviour may be modified by one or more parameters.

data storage device
type: Class
subclass of: device
description: A data storage device is a device that is capable of storing information.

solid state hard drive
type: Class
subclass of: hard disk drive
description: A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data.

hard disk drive
type: Class
subclass of: data storage device
description: A hard disk drive (HDD) is a non-volatile, random access device for digital data. It features rotating rigid platters on a motor-driven spindle within a protective enclosure. Data is magnetically read and written on the platter by read/write heads that float on a film of air above the platters.

structure
type: Class
subclass of: functional specification
description: structure is the specification that refers to the composition and arrangement of parts of an object.

computational entity
type: Class
subclass of: information content entity
description: A computational entity is an information content entity operated on using some computational system.

sound wave
type: Class
subclass of: wave
description: A sound wave is a mechanical wave that is an oscillation of pressure transmitted through a solid, liquid, or gas, composed of frequencies within the range of hearing.

curve
type: Class
subclass of: geometric entity
description: A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself.

regulation of process
type: Class
equivalent class: Class
  union of: regulation of process frequency
  union of: regulation of process duration
  union of: regulation of process spatial extent
  union of: regulation of object quantity
subclass of: regulating
subclass of: Restriction
  on property: regulates
  some values from: process
description: regulation of a process is a process that modulates the duration, frequency, spatial extent of a target process.

regulation of capability
type: Class
subclass of: regulating
subclass of: Restriction
  on property: affects
  some values from: capability
description: regulation of capability is the regulation of the ability of one party by another.

regulation of catalytic capability
type: Class
subclass of: regulation of capability
subclass of: Restriction
  on property: regulates
  some values from: to change materially
description: the regulation of the enzymatic activity.

representation
type: Class
equivalent class: Class
  intersection of: information content entity
  intersection of: Restriction
    on property: represents
    all values from: entity
subclass of: information content entity
subclass of: Restriction
  on property: is model of
  some values from: entity
description: A representation is a entity that in some way represents another entity (or attribute thereof).

ordinal position
type: Class
subclass of: linear position
description: A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities.
alternative: offset

attribute
type: Class
subclass of: entity
subclass of: Restriction
  on property: is attribute of
  some values from: entity
description: An attribute is a characteristic of some entity.
subset: core

collection
type: Class
subclass of: set
subclass of: Restriction
  on property: has member
  some values from: entity
description: A collection is a set for which there exists at least one member, although any member need not to exist at any point in the collection's existence.

empty set
type: Class
subclass of: set
subclass of: Restriction
  on property: has member
  qualified cardinality: 0
  on class: entity
description: An empty set is a set for which there are exactly 0 members.

standard
type: Class
subclass of: specification
subclass of: Restriction
  on property: has quality
  some values from: agreement
description: A standard is a socially-agreed upon specification.

regulatory authority
type: Class
subclass of: organization
description: A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity.

collective
type: Class
subclass of: social structure
description: A collective is a group of entities that share or are motivated by at least one common issue or interest, or work together on a specific project(s) to achieve a common objective.
alternative: group

formal specification
type: Class
subclass of: functional specification
description: A formal specification is a mathematical description of software or hardware that may be used to develop an implementation.

RDFS ontology
type: Class
subclass of: ontology document
description: An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS).

OBO ontology
type: Class
subclass of: ontology document
description: An OBO ontology is an ontology document as specified by the Open Biological Ontology community.

chemical functional group
type: Class
subclass of: submolecule
alternative: chemical group
description: A chemical functional group is a submolecule that confers specific chemical properties.

chemical structure
type: Class
subclass of: structure
description: chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure.

molecular structure
type: Class
subclass of: chemical structure
description: molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together.
alternative: molecular geometry

probability measure
type: Class
subclass of: dimensionless quantity
description: A probability measure is quantity of how likely it is that some event will occur.

to passively interact with
type: Class
subclass of: to interact with
description: to passively interact with is the capability to interact with another entity in a way that does not require physical contact.

increased
type: Class
subclass of: abnormal
disjoint with: decreased
description: A quality that has a value that is increased compared to normal or average.
equivalent to: PATO:0002300

process model
type: Class
subclass of: model
subclass of: Restriction
  on property: is model of
  some values from: process
disjoint with: object model
description: A process model is a representation of some process.

object model
type: Class
subclass of: model
description: An object model is a representation of an object.

information processing
type: Class
subclass of: procedure
description: information processing is a process that involves the generation or use of information.

wave
type: Class
subclass of: heterogeneous substance
description: A wave is a physical entity that travels through space and time, consist of oscillations or vibrations and may be accompanied by the transfer of energy.

textual entity
type: Class
subclass of: language entity
description: A textual entity is language entity that is manifested as a sequence of one or more distinct characters.

version label
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is identifier for
  some values from: Restriction
    on property: is variant of
    some values from: entity
description: A version label is a label for a particular form or variation of an earlier or original type.

software version label
type: Class
subclass of: version label
subclass of: Restriction
  on property: is identifier for
  some values from: software entity
description: A software version label is a version label for a piece of software.
example: major.minor[.build[.revision]]

hole
type: Class
subclass of: site
description: A hole is a site that is opening into or through something.

province
type: Class
subclass of: geopolitical region
subclass of: Restriction
  on property: is proper part of
  some values from: country
description: A province is a territorial unit, almost always an administrative division, within a country or state.

state
type: Class
subclass of: geopolitical region
description: A state is a set of governing and supportive institutions that have sovereignty over a definite territory and population.

territory
type: Class
subclass of: geopolitical region
description: A territory is a non-sovereign geographic region.

country
type: Class
subclass of: geopolitical region
description: A country is a region legally identified as a distinct entity in political geography.

city
type: Class
subclass of: geopolitical region
description: A city is a relatively large and permanent settlement.

township
type: Class
subclass of: geopolitical region
description: A township is a rural or sub-urban settlement.

sofware execution
type: Class
subclass of: information processing
description: software execution is the process of executing software on a computing device.

start time
type: Class
subclass of: time instant
description: A start time is a time instant pertaining to the time at which a process begins.

end time
type: Class
subclass of: time instant
description: An end time is a time instant pertaining to the time at which a process ends.

unique identifier
type: Class
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: is unique identifier for
    some values from: entity
subclass of: identifier
subclass of: Restriction
  on property: is unique identifier for
  some values from: entity
description: A unique identifier is an identifier that uniquely identifies some thing.

social role
type: Class
subclass of: role
description: A social role is a role that is ascribed to individuals in a community.

processual role
type: Class
subclass of: role
description: A processual role is a role that can only be realized in a process.

abstract role
type: Class
subclass of: role
description: An abstract role is a role whose basis lies in spatial/temporal or comparative relations.

justification
type: Class
subclass of: proposition
description: A justification is a proposition that defends, explains or excuses some argument.

academic department
type: Class
subclass of: academic organization
description: An academic department is a division of a university or school faculty devoted to a particular academic discipline.

institute
type: Class
subclass of: organization
description: institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective.

to be a part of
type: Class
subclass of: to be combined
description: to be a part of is the capability to be assembled into a larger structure that persists in time.

to associate
type: Class
subclass of: to actively interact with
description: to associate is the capability to physically interact with another object.

to be actively interacted with
type: Class
subclass of: to be interacted with
subclass of: Restriction
  on property: is mutually related to
  some values from: to actively interact with
disjoint with: to be passively interacted with
description: to be actively interacted with is the capability to be manipulated by some device or agent.

corporation
type: Class
subclass of: organization
description: A corporation is an organization that is granted a charter recognizing it as a separate legal entity.

to be passively interacted with
type: Class
subclass of: to be interacted with
subclass of: Restriction
  on property: is mutually related to
  some values from: to passively interact with
description: to be passively interacted with is the capability of an object to be observed.

to be recorded
type: Class
subclass of: to be observed
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to record
description: to be recorded is the capability of an object to be observed in such a way that information about it can be transcribed in a specified format on some physical medium.

to be observed
type: Class
subclass of: to be passively interacted with
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to observe
description: to be observed is the capability of an object to be perceived.

to disassemble
type: Class
subclass of: to change materially
description: to disassemble is to physically separate the parts of an object.

to disassociate
type: Class
subclass of: to modify
description: to disassociate is to cease or break association with some thing.

to interact with
type: Class
subclass of: capability
subclass of: Restriction
  on property: in relation to
  some values from: entity
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to be interacted with
description: to interact with is a capabililty that involves another object.

to be interacted with
type: Class
subclass of: capability
subclass of: Restriction
  on property: in relation to
  some values from: entity
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to interact with
description: to be interacted with is the capability of an object to be target of a physical interaction.

evolving
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: entity
description: evolving is a process that elicits change across successive generations in the inherited characteristics of biological populations.

positional role
type: Class
subclass of: abstract role
disjoint with: comparative role
description: A positional role is an abstract role which holds by comparing position to another object of reference.

design
type: Class
subclass of: functional specification
description: A specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints.

occupational role
type: Class
subclass of: social role
description: An occupational role is a social role that pertains to an organizational structure.

student role
type: Class
subclass of: academic role
subclass of: Restriction
  on property: is role of
  some values from: student
disjoint with: professor role
description: A student role is the role of an individual that is enrolled in courses at an academic institution.

professor role
type: Class
subclass of: academic role
subclass of: Restriction
  on property: is role of
  some values from: professor
subclass of: Restriction
  on property: is mutual role of
  some values from: student role
description: A professor role is the role of an individual that is involved in teaching of students (undergraduate and/or graduate) at a post-secondary academic institution.

academic role
type: Class
subclass of: occupational role
description: An academic role is a social role that pertains to the academic institution.

medical role
type: Class
subclass of: occupational role
description: A medical role is the role of an individual that is a participant in the delivery of medical care.

doctor role
type: Class
subclass of: medical role
description: A doctor role is the role of an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments.
alternative: physician

nurse role
type: Class
subclass of: medical role
description: A nurse role is the role of an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations.

patient role
type: Class
subclass of: medical role
description: A patient role is the role of an individual that is the recepient of medical care.

medical practitioner
type: Class
subclass of: person
description: A medical practioner is an individual that provides medical care.

dentist role
type: Class
subclass of: medical role
description: A dentist role is the role of an individual that that specializes in the diagnosis, prevention, and treatment of diseases and conditions of the oral cavity.

to translocate
type: Class
subclass of: to interact with
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to be translocated
disjoint with: to be translocated
description: to translocate is the capability to displace oneself from one location to another.
alternative: to move

to be translocated
type: Class
subclass of: to be interacted with
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to translocate
description: to be translocated is the capability to be physically displaced from one location to another
alternative: to be moved

comparative role
type: Class
subclass of: abstract role
description: A comparative role is an abstract role which holds by comparing some attribute of another object of reference.

to be compared
type: Class
subclass of: to be examined
description: to be compared is the capability of an object to be examined in order to note the similarities or differences among a set of objects.

to compare
type: Class
subclass of: to examine
description: to compare is the capability to examine in order to note the similarities or differences among a set of objects.

to examine
type: Class
subclass of: to observe
description: to examine is the capability to make detailed observation.

to be examined
type: Class
subclass of: to be observed
description: to be examined is the capability of an object to be observed in a detailed manner.

administrative role
type: Class
subclass of: occupational role
description: An administrative role is the role of an individual that performs administrative tasks for some organization.

secretary role
type: Class
subclass of: administrative role
description: A secretary role is the role of an individual that performs administrative tasks to support one or more individuals of the same organization.

chemical identifier
type: Class
subclass of: physical entity identifier
description: A chemical identifier is an identifier for a chemical entity

record identifier
type: Class
subclass of: informational entity identifier
subclass of: Restriction
  on property: is identifier for
  some values from: database entry
description: A record identifier is an identifier for a database entry.

physical entity identifier
type: Class
subclass of: identifier
description: A physical entity identifier is an identifier for a physical entity.

informational entity identifier
type: Class
subclass of: identifier
description: An informational entity identifier is an identifier for an informational entity.

molecular identifier
type: Class
subclass of: chemical identifier
description: A molecular identifier is an identifier for a molecular entity.

planning
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: Class
    union of: plan
    union of: design
description: planning is the agentive process of developing a plan that specifies a set of actions in order to meet a set of goals or objectives.

curve segment
type: Class
subclass of: curve
description: A curve segment is a part of a curve that consists of at least three points.

stationary point
type: Class
subclass of: data point
description: A stationary point is a point that is part of a curve in which the derivative at that point is zero, and hence its value is at least a local maximum or minimum.

local maximum stationary point
type: Class
subclass of: stationary point
description: A local maximum stationary point is a point that has a higher value in some axis than adjacent points.

local minimum stationary point
type: Class
subclass of: stationary point
description: A local minimum stationary point is a point that has a lower value in some axis than adjacent points.

learning
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: proposition
description: learning is the agentive process of acquiring knowledge.

comparing
type: Class
subclass of: interacting
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: to be compared
  intersection of: Restriction
    on property: realizes
    some values from: to compare
description: comparing is the process of examining a set of objects and determining their equality or inequality based on one or more features.
alternative: comparison

reasoning
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: Class
    intersection of: truth value
    intersection of: Restriction
      on property: is quality of
      some values from: proposition
description: reasoning is the agentive process of using knowledge to evaluate the truth value of a proposition.

investigation
type: Class
subclass of: procedure
subclass of: Restriction
  on property: has product
  some values from: object
subclass of: Restriction
  on property: realizes
  some values from: objective
description: investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study.
alternative: study

predicting
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: proposition
description: predicting is the process of formulating a proposition about a state of affairs which might be realized in the future.

database
type: Class
subclass of: computational entity
description: A database is a set of tables.

decreased
type: Class
subclass of: abnormal
description: A quality that has a value that is decreased compared to normal or average.
equivalent to: PATO:0002301

row
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: has proper part
  some values from: cell (informational)
subclass of: Restriction
  on property: has identifier
  some values from: identifier
description: A row represents a single, implicitly structured data item in a table.

column
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: specifies
  all values from: Class
    intersection of: cell (informational)
    intersection of: Restriction
      on property: has value
      some values from: Literal
    intersection of: Restriction
      on property: has value
      all values from: Literal
subclass of: Restriction
  on property: has attribute
  min qualified cardinality: 0
  on class: name
description: A column is a vertical sequence of cells in a cellular automata.

database table
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: is proper part of
  some values from: database
description: A database table is a set of named columns with zero or more rows composed of cells that contain column values and is part of a database.

cell (informational)
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: refers to
  some values from: entity
description: The minimal unit of a cellular automaton that can change state and has an associated behavior.

database entry
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: is proper part of
  some values from: database
description: A database entry is a single, implicitly structured data item in a table.
alternative: database record

database column
type: Class
subclass of: column
subclass of: Restriction
  on property: is proper part of
  some values from: database table
description: A database collumn is a column in a database table.

disordered
type: Class
subclass of: structural quality
subclass of: Restriction
  on property: is quality of
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has quality
      some values from: abnormal
disjoint with: rigid
description: disordered is a structural quality in which the parts of an object are non-rigid.

unique cell
type: Class
subclass of: cell (informational)
subclass of: Restriction
  on property: has attribute
  some values from: unique identifier
description: A unique cell is a cell that contains a unique value in the cellular automaton.

referencing cell
type: Class
subclass of: cell (informational)
description: A referenceing cell is a cell of a cellular automata that refers to another cell.

referent cell
type: Class
subclass of: cell (informational)
subclass of: Restriction
  on property: is referred to by
  some values from: cell (informational)
description: A referent cell is a cell that is the referent of some function or pointer.

database key
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: has component part
  some values from: column
subclass of: Restriction
  on property: has value
  some values from: Literal
description: A database key is an informational entity whose value is constructed from one or more database columns.

primary database key
type: Class
subclass of: database key
subclass of: Class
  complement of: Restriction
    on property: has value
    has value: null
subclass of: Restriction
  on property: is unique identifier for
  some values from: row
description: A primary database key is a database key that identifies every row of a table.

foreign database key
type: Class
subclass of: database key
subclass of: Restriction
  on property: references
  some values from: database key
description: A foreign database key is a database key that refers to a key in some table.

probability value
type: Class
subclass of: probability measure
subclass of: Restriction
  on property: has value
  some values from: Datatype
    on datatype: double
    with restrictions:
      min inclusive: 0.0
    with restrictions:
      max inclusive: 1.0
description: A p-value or probability value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true
alternative: p-value

street name
type: Class
subclass of: positional identifier
description: A street name is the token given to identify a particular street.

postal code
type: Class
subclass of: geographic position
description: A postal code is a geographic coordinate composed of a series of letters and/or digits appended to a postal address for the purpose of sorting mail.

apartment number
type: Class
subclass of: positional identifier
description: An apartment number is the number assigned to identify an apartment in a building of apartments.

uncertainty value
type: Class
subclass of: quantity
description: The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value.

standard deviation
type: Class
subclass of: quantity
description: A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value).

versioned record
type: Class
subclass of: record
description: A versioned record is a record for which there exists another variant based that was derived via modification of the facts.

object
type: Class
subclass of: entity
subclass of: Restriction
  on property: has proper part
  all values from: object
description: An object is an entity that is wholly identifiable at any instant of time during which it exists.
subset: core

to be a member of
type: Class
subclass of: to passively interact with
description: to be a member of is the capability to be considered a part of a collection.

to distort
type: Class
subclass of: to change appearance
description: to distort is the capability to change the appearance of an entity by some transformation.

primer
type: Class
subclass of: molecule
subclass of: Class
  intersection of: nucleic acid
  intersection of: Restriction
    on property: has capability
    some values from: Class
      intersection of: to bind to
      intersection of: Restriction
        on property: has capability
        some values from: to serve as a primer for DNA synthesis
      intersection of: Restriction
        on property: in relation to
        some values from: Class
description: A primer is a nucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.

to bind to
type: Class
subclass of: to associate
description: to bind to is the capability to physically interact with another object through a set of non-covalent interactions.

spatial boundary
type: Class
subclass of: spatial region
description: A spatial boundary is the closure minus the interior of a subset of a topological space.

hermaphrodite
type: Class
subclass of: intersex
disjoint with: male
description: hermaphrodite is a biological sex of an individual with both male and female sexual organs.
equivalent to: PATO:0001827

answer
type: Class
subclass of: description
description: An answer is a reply to a question.

verbal language entity
type: Class
subclass of: language entity
description: A verbal language entity is a language entity that is manifested through sound.

page number
type: Class
subclass of: count
description: A page number is the count of a page in a sequence of pages.

linear position
type: Class
subclass of: position
description: A linear position is the position of some object against a linear positioning system.

sequence element position
type: Class
subclass of: linear position
description: A sequence element position is the position of an element of a linear sequence.

non-protein coding RNA (ncRNA) gene
type: Class
subclass of: gene
description: A non-protein coding RNA (ncRNA) gene is a gene that encodes for a RNA transcript that is not further translated into a protein product.
equivalent to: http://purl.obolibrary.org/obo/SO_0001263
alternative: ncRNA gene

sequence start position
type: Class
subclass of: sequence element position
subclass of: start position
description: A sequence start position is the start position for a sequence of characters.

sequence end position
type: Class
subclass of: sequence element position
subclass of: end position
description: A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference.

count
type: Class
subclass of: dimensionless quantity
description: The number of elements of a finite set of objects.

chemical entity role
type: Class
subclass of: processual role
subclass of: Restriction
  on property: is role of
  some values from: chemical entity
description: A chemical role is a processual role held by a chemical entity.

catalytic role
type: Class
subclass of: regulator role
description: The role of a chemical participant that serves to increase the rate of reaction by lowering the activiation energy.

substrate role
type: Class
subclass of: reactant role
description: The role of a chemical entity that is modified in a chemical reaction.

product role
type: Class
subclass of: molecular entity role
subclass of: Restriction
  on property: is role of
  some values from: product
description: The role of a chemical entity present at the end of a chemical reaction.

cofactor role
type: Class
subclass of: molecular entity role
description: The role of a chemical entity involved in the mechanism for enzyme-mediated catalysis.

co-enzyme role
type: Class
subclass of: substrate role
subclass of: cofactor role
description: A co-factor role in which the chemical entity is modified during catalysis and must be regenerated.

prosthetic group role
type: Class
subclass of: co-enzyme role
description: A coenzyme role of a chemical entity that is covalently bonded to the enzyme.

co-substrate role
type: Class
subclass of: co-enzyme role
description: A co-enzyme role of a chemical entity that is transiently associated, and is regenerated in a separate reaction.

inhibitor role
type: Class
subclass of: regulator role
description: The role of a chemical entity that reduces the rate of reaction.

activator role
type: Class
subclass of: regulator role
description: The role of a chemical entity that increases the rate of reaction.

charged
type: Class
subclass of: charge quality
disjoint with: uncharged
description: The quality of having a charge.

uncharged
type: Class
subclass of: charge quality
description: The quality of not having a charge.

partial positive charge
type: Class
subclass of: partial charge
disjoint with: partial negative charge
description: A partial negative charge is a negative charge where the value of the charge is negative.

partial negative charge
type: Class
subclass of: partial charge
description: A partial positive charge is a partial charge where the value of the charge is positive.

partial charge
type: Class
equivalent class: Class
  union of: partial positive charge
  union of: partial negative charge
subclass of: charged
description: The quality of having a charge that is not a full multiple of 1 unit charge.

complete charge
type: Class
equivalent class: Class
  union of: positive charge
  union of: negative charge
subclass of: charged
description: A complete charge is a charge where the value of the charge is a multiple of 1.

URL
type: Class
subclass of: informational entity identifier
subclass of: Restriction
  on property: has value
  some values from: anyURI
description: A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource.
alternative: Uniform Resource Locator

affection
type: Class
subclass of: positive emotion
description: affection is an emotion characterized with a feeling or type of love for another living thing.

angst
type: Class
subclass of: anxiety
description: angst is the intense feeling of apprehension, anxiety or inner turmoil.

annoyance
type: Class
subclass of: negative emotion
description: Annoyance is an unpleasant emtion that is characterized by a abnormal or excessive sensitivity to some external stimulus.

anxiety
type: Class
subclass of: apprehension
description: anxiety is an emotion charactersized by intense feeling of fear and concern coupled with a physical response.

apathy
type: Class
subclass of: indifference
description: apathy is an emotion characterized by lack of interest, enthusiasm, or concern.

arousal
type: Class
subclass of: positive emotion
description: arousal is an emotion characterized by state of reactive to stimuli. It involves the activation of the reticular activating system in the brain stem, the autonomic nervous system and the endocrine system, leading to increased heart rate and blood pressure and a condition of sensory alertness, mobility and readiness to respond.

awe
type: Class
subclass of: positive emotion
description: awe is an emotion produced by that which is grand, sublime or powerful and is characterized by a combination of joy, fear and admiration/reverence/respect.

boldness
type: Class
subclass of: positive emotion
description: boldness is the trait of being willing to undertake things that involve risk or danger.

boredom
type: Class
subclass of: negative emotion
description: boredom is the emotion experience by those not interested in their surroundings or available activities.

contempt
type: Class
subclass of: disgust
description: contempt is disgust towards a lower status individual.

contentment
type: Class
subclass of: happiness
description: contentment is an emotion characterized by acknowledgement and satisfaction of the current state of affairs.

curiosity
type: Class
subclass of: desire
description: curiosity is the strong desire to know or learn something.

depression
type: Class
subclass of: sadness
description: depression is an unpleasant emotion linked to aversion to activity that can affect a person's thoughts, behavior, feelings and physical well-being. Depressed individuals may feel sad, anxious, empty, hopeless, worried, helpless, worthless, guilty, irritable, or restless.
alternative: depressed

desire
type: Class
subclass of: interest
description: desire is a strong emotion of wanting to have something or wishing for something to happen.

despair
type: Class
subclass of: sadness
description: despair is depression, hopelessness or lack of hope.

disappointment
type: Class
subclass of: negative emotion
description: disappointment is the feeling of dissatisfaction that follows the failure of expectations or hopes to manifest.
alternative: disappointed
alternative: disappointing

disgust
type: Class
subclass of: hostility
description: Disgust is a feeling of revulsion or profound disapproval aroused by something unpleasant or offensive.

dread
type: Class
subclass of: fear
description: dread is the instense negative emotion that induces fear and apprehension.

ecstasy
type: Class
subclass of: positive emotion
description: ecstacy is an emotion characterized by a heightened state of consciousness with total involvement of a subject.

positive emotion
type: Class
subclass of: emotion
subclass of: Restriction
  on property: has quality
  some values from: positive
description: A positive emotion is an emotion that feels good.

negative emotion
type: Class
subclass of: emotion
subclass of: Restriction
  on property: has quality
  some values from: negative
description: negative emotion is an emotion that does not feel good.

embarassment
type: Class
subclass of: negative emotion
description: Embarrassment is the emotion of intense discomfort with oneself, experienced upon having a socially unacceptable act or condition witnessed by or revealed to other.

envy
type: Class
subclass of: negative emotion
description: envy is an emotion that occurs when a person lacks another's (perceived) superior quality, achievement or possession and wishes that the other lacked it.

euphoria
type: Class
subclass of: happiness
description: euphoria is an emotion characterized by intense feelings of well-being, elation, happiness, ecstasy, excitement, and joy.

excitement
type: Class
subclass of: positive emotion
description: excitement is a positive emotion of feeling great enthusiasm and eagerness.

fear
type: Class
subclass of: apprehension
description: Fear is a negative emotion induced by a perceived threat that induces one to hide or move quickly away from the location of the perceived threat.

frustration
type: Class
subclass of: annoyance
description: Frustration is an emotion that arises from the perceived resistance to the fulfillment of individual will.

gratitude
type: Class
subclass of: positive emotion
description: Gratitude, thankfulness, gratefulness, or appreciation is a feeling, emotion or attitude in acknowledgment of a benefit that one has received or will receive.
alternative: appreciation
alternative: gratefulness
alternative: gratification
alternative: thankfullness

happiness
type: Class
subclass of: positive emotion
description: happiness is an emotion characterized by positive or pleasant emotions ranging from contentment to intense joy.

guilt
type: Class
subclass of: negative emotion
description: Guilt is the emotion borne from feeling responsible for the commission of an offense and arises out of public humiliation.
alternative: guilty

grief
type: Class
subclass of: sadness
description: grief is an emotion in response to loss, whether physical or abstract including death, unemployment, ill health or the end of a relationship.

hope
type: Class
subclass of: positive emotion
description: hope is an emotion of belief in a positive outcome related to events and circumstances in one's life.

hostility
type: Class
subclass of: negative emotion
description: Hostility is the intense negative emotion of being in conflict or opposition to someone or something.

hurt
type: Class
subclass of: negative emotion
description: hurt is an unpleasant feeling, emotion or sensation.

hysteria
type: Class
subclass of: negative emotion
description: Hysteria is an unmanageable emotion.

indifference
type: Class
subclass of: emotion
subclass of: Class
  intersection of: Class
    complement of: Restriction
      on property: has quality
      some values from: positive
  intersection of: Class
    complement of: Restriction
      on property: has quality
      some values from: negative
description: indifference is an emotion characterized by lack of interest, concern, or sympathy.

interest
type: Class
subclass of: positive emotion
description: interest is the emotion of wanting to know or learn about something or someone.

jealousy
type: Class
subclass of: envy
description: jealousy is an emotion and typically refers to the negative thoughts and feelings of insecurity, fear, and anxiety over an anticipated loss of something that the person values, particularly in reference to a human connection.

joy
type: Class
subclass of: happiness
description: joy is an emotion of intense happiness.

loathing
type: Class
subclass of: disgust
description: loathing is an intense dislike or disgust.

loneliness
type: Class
subclass of: negative emotion
description: Loneliness is an unpleasant emotion in which a person feels a strong sense of emptiness, yearning distress and solitude resulting from inadequate quantity or quality of social relationships.

lust
type: Class
subclass of: desire
description: lust is the strong desire for sex.

misery
type: Class
subclass of: sadness
description: misery is a feeling of great unhappiness, suffering and/or pain.

panic
type: Class
subclass of: fear
description: Panic is a sudden emotion of fear which is so strong as to dominate or prevent reason and logical thinking, replacing it with overwhelming feelings of anxiety and frantic agitation consistent with an animalistic fight-or-flight reaction.

passion
type: Class
subclass of: desire
description: passion is the intense desire for something.

pity
type: Class
subclass of: negative emotion
description: Pity is the emotion of sadness or sorrow for another.

pleasure
type: Class
subclass of: happiness
description: pleasure is an emotion of happy satisfaction and enjoyment.

pride
type: Class
subclass of: satisfaction
description: pride is an emotion of satisfaction of attachment toward one's own or another's choices and actions, or toward a whole group of people, and is a product of praise, independent self-reflection, or a fulfilled feeling of belonging.

rage
type: Class
subclass of: anger
description: Rage is a feeling of intense anger that is associated with the Fight-or-flight response.

regret
type: Class
subclass of: worry
description: regret is a feeling of sadness, repentance, or disappointment over something that has happened or been done.

remorse
type: Class
subclass of: regret
description: remorse is an emotion of personal regret felt by a person after he or she has committed an act which they deem to be shameful, hurtful, or violent.

sadness
type: Class
subclass of: negative emotion
description: sadness is emotional pain associated with, or characterized by feelings of disadvantage, loss, despair, helplessness, sorrow, and rage.
alternative: sad
alternative: unhappiness
alternative: unhappy

satisfaction
type: Class
subclass of: contentment
description: satisfaction is an emotion of fulfillment of one's wishes, expectations, or needs, or the pleasure derived from this.

shame
type: Class
subclass of: negative emotion
description: shame is the emotion borne from feeling responsible for the commission of an offense.

shock
type: Class
subclass of: negative emotion
description: shock is an emotion of sudden upset or surprise.

shyness
type: Class
subclass of: negative emotion
description: shyness is an emotion of apprehension, lack of comfort, or awkwardness experienced when in proximity to, approaching, or being approached by other individuals, especially in new situations or with unfamiliar individuals.

sorrow
type: Class
subclass of: sadness
description: sorrow is the emotion that is characterized by a long term state of intense sadness, distress and a degree of resignation (not accepting).

suffering
type: Class
subclass of: hurt
description: Suffering is the unpleasant emotion and aversion associated with the perception of harm or threat of harm in an individual.

surprise
type: Class
subclass of: positive emotion
description: surprise is a brief emotion experienced as the result of an unexpected event.

terror
type: Class
subclass of: dread
description: terror is the extreme feeling of fear.

wonder
type: Class
subclass of: surprise
description: wonder is an emotion of perceiving something very rare or unexpected, but not threatening.

worry
type: Class
subclass of: apprehension
description: worry is the emotion characterized by concer over a real or imaginary issue.

department chair role
type: Class
subclass of: academic role
description: A department chain role is the role of an individual that heads a department at a academic organization.

student advisor role
type: Class
subclass of: academic role
description: A student advisor role is the role of an individual employed at an academic organization that is involved in advising students.

undergraduate student advisor role
type: Class
subclass of: student advisor role
description: An undergraduate student advisor role is the role of an individual employed at an academic organization that is involved in advising undergraduate students.

graduate student advisor role
type: Class
subclass of: student advisor role
description: A graduate student advisor role is the role of an individual employed at an academic organization that is involved in advising graduate students.

reactant role
type: Class
subclass of: molecular entity role
description: The role of a chemical entity present at the beginning of a chemical reaction.

regulator role
type: Class
subclass of: molecular entity role
description: The role of a chemical entity that modifies the rate of reaction.

investigational role
type: Class
subclass of: processual role
description: An investigational role is a role held by participants involved in an investigation.

host role
type: Class
subclass of: chemical substance role
description: The role of an organism in providing resources to maintain the survival and/or reproduction of another organism.

subject role
type: Class
subclass of: investigational role
description: A subject role is the role of an individual that is the target of the study.

publishing role
type: Class
subclass of: occupational role
description: A publishing role is the role of an individual that is involved in the preparation and issue of creative works for consumption by a wider audience.

publisher role
type: Class
subclass of: publishing role
description: A publisher role is the role of an individual that prepares and issues creative works.

author role
type: Class
subclass of: publishing role
description: An author role is the role of an individual that creates a creative, written work.

buffer role
type: Class
subclass of: chemical substance role
subclass of: Restriction
  on property: is role of
  some values from: buffer
description: A buffer role is the role of a chemical substance which maintains a pH at a near constant value.

chemical substance role
type: Class
subclass of: chemical entity role
subclass of: Restriction
  on property: is role of
  some values from: chemical substance
description: A chemical substance role is a chemical entity role held by a chemical substance.

molecular entity role
type: Class
subclass of: chemical entity role
subclass of: Restriction
  on property: is role of
  some values from: molecule
description: A molecular entity role is a chemical entity role held by a molecule.

toxin role
type: Class
subclass of: poison role
description: A toxin role is a toxic role of a chemical substance that is poisonous and is produced by an organism.

toxic role
type: Class
subclass of: chemical substance role
description: A toxic role is the role of a chemical substance that is poisonous.

reagent role
type: Class
subclass of: chemical substance role
subclass of: Restriction
  on property: is role of
  some values from: reagent
description: A role of a chemical substance that participates in a chemical reaction as part of some scientific investigation.

to luminesce
type: Class
subclass of: to be actively interacted with
description: to luminesce is to emit light through cold body radiation

to fluoresce
type: Class
subclass of: to luminesce
description: to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation.

molecular tracer role
type: Class
subclass of: reactant role
description: A molecular tracer role is a reactant role of a molecular entity that serves as a marker for the presence, abundance, or location of a molecular target that it associates with.

association
type: Class
subclass of: mathematical entity
subclass of: Restriction
  on property: refers to
  min qualified cardinality: 2
  on class: entity
description: An assocation is a relationship between two or more entities derived by some informational analysis.

statistical association
type: Class
subclass of: association
description: A statistical association is any relationship between two measured quantities that renders them statistically dependent.

chromosome
type: Class
subclass of: molecular complex
subclass of: Restriction
  on property: has direct part
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has direct part
  some values from: protein
description: A chromosome is a molecular complex of circular or linear DNA and bound proteins.

top value axis
type: Class
subclass of: value axis
description: A top value axis is a value axis that is spatially positioned to the top of the plot area.

bottom value axis
type: Class
subclass of: value axis
description: A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area.

chart
type: Class
subclass of: figure
description: A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures.

map
type: Class
subclass of: chart
description: A map is a a visual representation of an area that depicts the relationship between elements of that space.

heatmap
type: Class
subclass of: chart
description: A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors.

streamgraph
type: Class
subclass of: stack graph
description: A streamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis.

boxplot
type: Class
subclass of: line-bar graph
description: A boxplot (box-and-whisker diagram) is a convenient way of graphically depicting groups of numerical data through their five-number summaries: the smallest observation (sample minimum), lower quartile (Q1), median (Q2), upper quartile (Q3), and largest observation (sample maximum).

geographic heatmap
type: Class
subclass of: heatmap
description: A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors.

histogram
type: Class
subclass of: chart
description: A histogram is a graphical representation of data which consists of tabular frequencies, shown as adjacent rectangles, over discrete intervals (bins) , with an area equal to the frequency of the observations in the interval.

measurement scale
type: Class
subclass of: functional specification
description: A measurement scale is a functional specification that specifies an allowed range of categories or values.

nomimal scale
type: Class
subclass of: measurement scale
description: A nominal scale of measurement only specifies a limited set of categories.

binary scale
type: Class
subclass of: measurement scale
description: A binary scale is a measurement scale that specifies a choice between two values.

numeric scale
type: Class
subclass of: measurement scale
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has value
      some values from: Literal
description: A numeric scale of measurement is one that only specifies numeric values.

decimal scale
type: Class
subclass of: numeric scale
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has value
      some values from: decimal
description: A decimal scale of measurement is one that only specifies decimal values.

integer scale
type: Class
subclass of: numeric scale
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has value
      some values from: integer
description: An integer scale of measurement is one that only specifies integer values.

modifying
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has output
  some values from: object
subclass of: Restriction
  on property: has target
  some values from: object
description: modifying is the process by which an entity gains or loses parts, qualities, roles, dispositions, functions, etc, but maintains their identity through these changes.
alternative: modification

reproducing
type: Class
subclass of: creating
subclass of: Class
  intersection of: Restriction
    on property: has input
    some values from: object
  intersection of: Restriction
    on property: has product
    some values from: object
description: reproducing is a process characterized by creation of an entity that is similar or exactly the same as the template from which it is derived.

independent variable
type: Class
subclass of: variable
description: An independent variable is a variable that may take on different values independent of other elements in a system.

dependent variable
type: Class
subclass of: variable
description: A dependent variable is one whose value changes as a consequence of changes in other values in the system.

Gantt chart
type: Class
subclass of: chart
description: A Gantt chart is a bar chart that illustrates a project schedule.

correlation
type: Class
subclass of: statistical association
description: A correlation is a statistical relationship involving dependence between two random variables or datasets.

television program
type: Class
subclass of: media
description: A television program is a audiovisual media that is produced and broadcast using a television.

radio receiver
type: Class
subclass of: communication device
description: A radio receiver is a communication device that receives its input from an antenna, uses electronic filters to separate a wanted radio signal from all other signals picked up by this antenna, amplifies it to a level suitable for further processing, and finally converts through demodulation and decoding the signal into a form usable for the consumer, such as sound, pictures, digital data, measurement values, navigational positions.

telephone
type: Class
subclass of: communication device
description: The telephone is a communications device that transmits and receives sounds, and are minimally composed of a microphone to speak into, a speaker'which reproduces the voice of the other person and a ringer which makes a sound to alert the owner when a call is coming in.

radar
type: Class
subclass of: device
description: A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects.

pie chart
type: Class
subclass of: mereological chart
description: A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents.

matrix chart
type: Class
subclass of: chart
description: A matrix chart summarizes a multidimensional data set in a grid.

network diagram
type: Class
subclass of: chart
description: A network diagram consists of a set of vertices connected by edges.

block histogram
type: Class
subclass of: histogram
description: A block histogram contains an x-axis that is divided into bins which correspond to value ranges. Each item in the data set is drawn as a rectangular block, and the blocks are piled into the bins to show how many values in each range.

bubble chart
type: Class
subclass of: chart
description: A bubble chart contains circles whose area corresponds to a value.

stack graph
type: Class
subclass of: statistical graph
description: A stack graph is a statistical graph which presents multiple series in which the distance between one series and another indicates the relative contribution to the total for any x-value.

treemap
type: Class
subclass of: mereological chart
description: A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value.

word tree
type: Class
subclass of: textual chart
description: A word tree is a chart that links phrases with contexts through a tree-like branching structure.

textual chart
type: Class
subclass of: chart
subclass of: Restriction
  on property: has direct part
  some values from: textual entity
description: A textual chart is a chart containing text.

tag cloud
type: Class
subclass of: textual chart
description: A tag cloud is a visualization of word frequencies.
alternative: word cloud

phrase net diagram
type: Class
subclass of: textual chart
description: A phrase net diagram illustrates the relationship between different words used in a text.

mereological chart
type: Class
subclass of: chart
description: A mereological chart is a chart that illustrates the parts in the context of the whole.

conversing
type: Class
subclass of: communicating
description: conversing a form of interactive, spontaneous communication between two or more agents who are following rules of etiquette.

numeric label
type: Class
subclass of: label
description: A numeric label is a number used as a label.

start position
type: Class
subclass of: linear position
description: A start position is the proximal position of an object relative to an origin in a linear system.

interval
type: Class
subclass of: mathematical entity
description: An interval is a set of real numbers that includes all numbers between any two numbers in the set.

tree diagram
type: Class
subclass of: directed acyclic graph
description: A tree diagram is a hierarchical network diagram in which a root vertex is connected to one or more other vertices through a directed edge, which in turn may be connected to other vertices.

flowchart
type: Class
subclass of: chart
description: A flowchart is a diagram that represents an algorithm or process, showing the steps as boxes of various kinds, and their order by connecting these with arrows.

venn diagram
type: Class
subclass of: chart
description: A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles.

dendrogram
type: Class
subclass of: tree diagram
description: A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering.

apprehension
type: Class
subclass of: negative emotion
description: apprehension is the negative emotion that something unpleasant will occur.

resentment
type: Class
subclass of: disgust
description: resentment is disgust directed toward a higher status individual.

pain
type: Class
subclass of: hurt
description: Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.

default parameter
type: Class
subclass of: parameter
description: A default parameter is a parameter which has a default value.

end position
type: Class
subclass of: linear position
description: An end position is the distal position of an object relative to an origin in a linear system.
alternative: stop position

sick
type: Class
subclass of: alive
description: sick is the status of a living organism that is behaving at a sub-optimal level.

environment
type: Class
subclass of: geographic region
description: An environment is a geographic region that hosts certain processes or objects.

device
type: Class
subclass of: heterogeneous substance
description: A device is usually a constructed tool.

communication device
type: Class
subclass of: device
description: A communication device is a device that facilitates the transmission of information through encoded in an audio or digital signal between a sender and a receiver.

existence quality
type: Class
subclass of: quality
description: existence quality is the quality of an entity that describe in what environment it is known to exist.

real
type: Class
subclass of: existence quality
disjoint with: fictional
disjoint with: virtual
description: real is the quality of an entity that exists in real space and time.

fictional
type: Class
subclass of: hypothetical
description: fictional is the quality of an entity that exists only in a creative work of fiction.

virtual
type: Class
subclass of: existence quality
description: virtual is the quality of an entity that exists only in a virtual setting such as a simulation or game environment.

not started
type: Class
subclass of: process status
description: not started is the status of a process that is predicted to exist but has not yet begun.

standard operating procedure
type: Class
subclass of: experimental protocol
description: A standard operating procedure is a specification approved for use in specific environments.

agreement quality
type: Class
equivalent class: Class
  union of: agreement
  union of: disagreement
subclass of: informational quality
description: agreement quality is a quality that exhibits the degree of consensus for some set of assertions.

agreement
type: Class
subclass of: agreement quality
disjoint with: disagreement
description: agreement is the result of consensus decision making when members of the group agree.

disagreement
type: Class
subclass of: agreement quality
description: agreement is the result of consensus decision making when members of the group do not all agree.

poison role
type: Class
subclass of: toxic role
subclass of: Restriction
  on property: is role of
  some values from: poison
description: A poison role is the role of a substance that causes some negative disturbance in an organism.

communicating
type: Class
subclass of: interacting
description: communicating is the process of conveying information through the exchange of thoughts, messages, or information, as by speech, visuals, signals, writing, or behaviour.
alternative: communication

observational study
type: Class
subclass of: experiment
subclass of: Restriction
  on property: has participant
  some values from: hypothesis
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: truth value
    intersection of: Restriction
      on property: is quality of
      some values from: hypothesis
description: observational study draws inferences about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator

syllable
type: Class
subclass of: verbal language entity
description: A syllable is a verbal entity of language having one vowel sound, with or without surrounding consonants, forming the whole or a part of a word.

consonant
type: Class
subclass of: verbal language entity
description: A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract.

vowel
type: Class
subclass of: verbal language entity
description: A vowel is a verbal entity of language that is pronounced with an open vocal tract so that there is no build-up of air pressure at any point above the glottis.

sign language
type: Class
subclass of: language
description: A sign language (also signed language) is a language that involves manual communication and body language to convey meaning. This can involve simultaneously combining hand shapes, orientation and movement of the hands, arms or body, and facial expressions to fluidly express a speaker's thoughts.

verbal language
type: Class
subclass of: language
description: A verbal language is a language that uses sounds to communicate.

written language
type: Class
subclass of: language
description: written language is a language that is communicated through a writing system.

gene-disease association
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  some values from: gene
subclass of: Restriction
  on property: refers to
  some values from: disease
description: A gene-disease association is an association between a gene and a disease.

genome
type: Class
subclass of: biological entity
description: A genome is a collection of nucleic acids.

protein coding gene
type: Class
subclass of: gene
description: A gene that contains an open reading frame which codes for a protein.
equivalent to: http://purl.obolibrary.org/obo/SO_0001217

functional rna coding gene
type: Class
subclass of: rna gene
description: A gene that codes for a functional RNA molecule.

predicted gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: has attribute
  some values from: predicted
description: A predicted gene is a gene that was identified through computational method but has not been experimentally validated.

pseudogene
type: Class
subclass of: nucleic acid part
description: A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated.
equivalent to: http://purl.obolibrary.org/obo/SO_0000336

sequence assembly
type: Class
subclass of: biopolymer sequence
description: A sequence assembly is a sequence that is produced as by the alignment of two or more sequences.

validated gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: has attribute
  some values from: real
description: An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods.

unsupported
type: Class
subclass of: existence quality
description: unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical)

chemical-disease association
type: Class
subclass of: association
subclass of: Class
  intersection of: Restriction
    on property: refers to
    some values from: chemical entity
  intersection of: Restriction
    on property: refers to
    some values from: disease
description: A chemical-disease association is an association between a chemical and a disease.

experiment
type: Class
subclass of: investigation
description: An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis.
alternative: study

suspended
type: Class
subclass of: process status
description: suspended is the status of a process that is no longer progressing towards completion.

cancelled
type: Class
subclass of: not started
description: cancelled is a process status in which the process, while planned to occur, will not occur.

aborted
type: Class
subclass of: process status
description: aborted is a process status in which a started process will not complete as intended.

literature curation
type: Class
subclass of: information processing
subclass of: Restriction
  on property: has output
  some values from: phrase
subclass of: Restriction
  on property: has input
  some values from: document
description: literature curation is the process of an agent selecting and extracting terms and phrases from a document.

procedure
type: Class
subclass of: process
subclass of: Restriction
  on property: is manifestation of
  some values from: action specification
subclass of: Restriction
  on property: realizes
  all values from: Class
    union of: capability
    union of: objective
description: A procedure is a process that attempts to achieve one or more objectives by following an established set of actions.

clinical trial
type: Class
subclass of: intervention study
subclass of: Restriction
  on property: is specified by
  some values from: experimental protocol
description: A clinical trial is an intervention trial to determine the safety and efficacy of medical interventions (e.g., drugs, diagnostics, devices, therapy protocols).

medical diagnosis
type: Class
subclass of: medical procedure
subclass of: Restriction
  on property: has output
  some values from: diagnostic opinion
subclass of: Restriction
  on property: has input
  some values from: Class
    intersection of: biological entity
    intersection of: Restriction
      on property: has quality
      some values from: disordered
description: A medical diagnosis (often simply termed diagnosis) refers to the process of attempting to determine or identify a possible disease or disorder.

differential diagnosis
type: Class
subclass of: medical procedure
description: A differential diagnosis (sometimes abbreviated DDx, ddx, DD, D/Dx, or ΔΔ) is a systematic diagnostic method used to identify the presence of an entity where multiple alternatives are possible (and the process may be termed differential diagnostic procedure), and may also refer to any of the included candidate alternatives (which may also be termed candidate condition).

diagnostic opinion
type: Class
subclass of: opinion
description: A diagnostic opinion is an opinion resulting from a medical diagnostic procedure.

opinion
type: Class
subclass of: belief
subclass of: Restriction
  on property: is product of
  some values from: medical diagnosis
description: An opinion is a belief that is the result of emotion or interpretation of facts.

chemical effect
type: Class
subclass of: chemical interaction
subclass of: Restriction
  on property: has agent
  some values from: drug
description: A chemical effect is a chemical interaction in which a chemical elicits a marked characteristic of a biological system.

drug drug interaction
type: Class
subclass of: chemical effect
subclass of: Restriction
  on property: has participant
  min qualified cardinality: 2
  on class: drug
description: A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response.

assay
type: Class
subclass of: procedure
subclass of: Restriction
  on property: has output
  some values from: Class
    intersection of: Class
      union of: measurement value
      union of: existence quality
    intersection of: Restriction
      on property: is attribute of
      some values from: entity
subclass of: Restriction
  on property: has input
  some values from: object
description: An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.
alternative: bioassay

toxicity
type: Class
equivalent class: Class
  union of: toxic
  union of: non toxic
subclass of: chemical quality
description: toxicity is the quality of a chemical substance to cause injury to an organism in a dose dependent manner.

toxic
type: Class
subclass of: toxicity
disjoint with: non toxic
description: toxic is the quality of a substance imparing the normal functioning of a system.

non toxic
type: Class
subclass of: toxicity
description: non toxic is the quality of a substance having no damaging effect to a system.

chemical quality
type: Class
subclass of: object quality
description: chemical quality is the quality of a chemical entity.

healthy
type: Class
subclass of: alive
description: healthy is an organismal state of complete physical, mental and social well-being.

age
type: Class
subclass of: dimensional quantity
description: age is the length of time that a person has lived or a thing has existed.

ethnicity
type: Class
subclass of: biological quality
description: ethnicity is the biological quality of membership in a social group based on a common heritage.

race
type: Class
subclass of: biological quality
description: race is a characteristic of an individual by heritable phenotypic characteristics, geographic ancestry, physical appearance, ethnicity, and social status.

ethnic group
type: Class
subclass of: human population
description: An ethnic group is a group of people whose members identify with each other through a common heritage, consisting of a common culture, including a shared language or dialect.

syndrome
type: Class
subclass of: description
description: A syndrome is composed of a set of several clinically recognizable features, signs (observed by someone other than the patient), symptoms (reported by the patient), phenomena or characteristics that often occur together.

ratio
type: Class
subclass of: dimensionless quantity
description: A ratio is a relationship between two numbers of the same kind expressed arithmetically as a dimensionless quotient of the two which explicitly indicates how many times the first number contains the second.

dose
type: Class
subclass of: dimensional quantity
description: A dose is the quantity of a chemical substance administered to a biological system.

effective dose
type: Class
subclass of: dose
description: effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population.

expected value
type: Class
subclass of: probability measure
description: An expected value (or e-value) is the weighted average of all possible values that a random variable can take on.

diagnostic test
type: Class
subclass of: medical procedure
description: A diagnostic test is a procedure performed to confirm, or determine the presence of disease in an individual suspected of having the disease, usually following the report of symptoms, or based on the results of other medical tests.
alternative: clinical laboratory test

medical screening
type: Class
subclass of: medical procedure
description: A medical screening is a medical test or series used to detect or predict the presence of disease in individuals at risk for disease within a defined group, such as a population, family, or workforce

medical procedure
type: Class
subclass of: procedure
description: A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder.

prognosis
type: Class
subclass of: proposition
description: A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence.

report
type: Class
subclass of: document
description: A report is a textual document made that present focused, salient content to a specific audience.

medical health record
type: Class
subclass of: record
description: A medical health record is a record of a single patient's medical history.

medical report
type: Class
subclass of: report
description: A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual.

peer reviewed article
type: Class
subclass of: article
subclass of: Restriction
  on property: has quality
  some values from: peer-reviewed
description: A peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication.

major version number
type: Class
subclass of: software version label
description: A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version.

minor version number
type: Class
subclass of: software version label
description: A minor version number is a version of a software that exhibits minor features or significant fix from a prior version.

revision number
type: Class
subclass of: software version label
description: A revision number is a version of a software in which bugs have been fixed from a prior version.

text quality
type: Class
subclass of: object quality
subclass of: Restriction
  on property: is quality of
  some values from: textual entity
description: text quality is the quality of a textual entity.

reviewed
type: Class
subclass of: written
description: reviewed is the quality of a textual entity that has been examined and commented on by another party.

peer-reviewed
type: Class
subclass of: reviewed
disjoint with: editor reviewed
description: peer-reviewed is the quality of a textual entity that has been examined and commented by a peer expert reviewer.

draft
type: Class
subclass of: written
description: draft is the quality of text that has not yet complete.
alternative: drafted

finalized
type: Class
subclass of: written
description: finalized is the quality of a textual entity that is in its final form.

editor reviewed
type: Class
subclass of: reviewed
description: editor reviewed is the quality of a textual entity that has been examined and commented on by an editor.

written
type: Class
subclass of: text quality
description: written is the quality of information that is embodied as visual glyphs in some material form.

morpheme
type: Class
subclass of: language entity
description: A morpheme is the smallest semantically meaningful unit in a language.

study design
type: Class
subclass of: experimental protocol
subclass of: Restriction
  on property: is manifested as
  all values from: Restriction
    on property: is part of
    some values from: investigation
description: A study design is a protocol for the proper execution of a study which normally requires a carefullly crafted research question or hypothesis and at least one variable under observation and observed values for that variable.
alternative: study protocol

recipe
type: Class
subclass of: action specification
description: A recipe is a set of instructions that describe how to prepare or make something.

experimental protocol
type: Class
subclass of: action specification
description: An experimental protocol is an action specification with respect to the design and implementation of experiments. In addition to providing a detailed set of procedures and lists of required equipment and instruments, experimental protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias.

viroid
type: Class
subclass of: non-cellular organism
description: A viroid is a molecule of RNA that does not code for and is not protected by a protein coat.

polar quality
type: Class
equivalent class: Class
  union of: polar
  union of: non-polar
subclass of: chemical quality
description: The quality of being polar or not polar.

polar
type: Class
subclass of: polar quality
disjoint with: non-polar
description: polar is the quality of having a dipole.

non-polar
type: Class
subclass of: polar quality
description: non-polar is the quality of not having a dipole.

intervention study
type: Class
subclass of: experiment
description: An intervention study has the objective of improving the condition of an individual or a group of individuals, and demonstrates the magnitude of that capability by comparing it to a control group.

sampling
type: Class
subclass of: interacting
subclass of: Class
  intersection of: Restriction
    on property: has output
    some values from: sample
  intersection of: Restriction
    on property: has input
    some values from: object
description: sampling is the act of obtaining a sample, whether through selection, collection or preparation.

sample
type: Class
subclass of: heterogeneous substance
subclass of: Class
  union of: Restriction
    on property: is member of
    some values from: collection
  union of: Restriction
    on property: is derived from
    some values from: object
description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.

data analysis
type: Class
subclass of: information processing
subclass of: Class
  intersection of: Restriction
    on property: has output
    some values from: proposition
  intersection of: Restriction
    on property: has input
    some values from: data item
description: data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making.

data collection
type: Class
subclass of: information processing
subclass of: Restriction
  on property: has product
  some values from: data item
description: data collection is the process of acquiring information.

reason
type: Class
subclass of: justification
description: A reason is a justification that specifies the motive for an action or a determination.

measuring
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has output
  some values from: measurement value
subclass of: Restriction
  on property: has input
  some values from: Class
    union of: quality
    union of: process
    union of: object
description: measuring is the process of determining the size, amount, or degree of (something) by using an instrument or device marked in standard units
alternative: measurement

observing
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has output
  some values from: entity
subclass of: Restriction
  on property: has input
  some values from: entity
description: observing is a process of passive interaction in which one entity makes note of attributes of one or more entities.
alternative: observation

character position
type: Class
subclass of: ordinal position
subclass of: Restriction
  on property: has value
  all values from: integer
description: The ordinal position of a character in a sequence of characters.
alternative: character offset

word start position
type: Class
subclass of: text span start position
subclass of: Restriction
  on property: is part of
  some values from: textual entity
description: The position of the first character in a word as an offset from the first character of the text in which it is found.

word end position
type: Class
subclass of: text span end position
description: word end position is the position of the last character in a word as an offset from the first character of the text in which it is found.

gesturing
type: Class
subclass of: communicating
description: gesturing is a form of non-verbal communication in which visible bodily actions communicate particular messages, either in place of speech or together and in parallel with spoken words. Gestures include movement of the hands, face, or other parts of the body.

planned
type: Class
subclass of: not started
description: planned is a process status for a process that has not yet started, but is referred to in a plan.

population
type: Class
subclass of: collective
description: A population is all the organisms that both belong to the same group or species and live in the same geographical area.

human population
type: Class
subclass of: population
description: A human population refers to a collection of human beings.

family
type: Class
subclass of: collective
description: A group of people affiliated by consanguinity, affinity, or co-residence.

community
type: Class
subclass of: collective
description: A community is a sizeable social unit that shares common values.

speculation
type: Class
subclass of: opinion
description: speculation is an opinion based on incomplete evidence.

study
type: Class
subclass of: investigation
subclass of: Restriction
  on property: realizes
  some values from: objective
subclass of: Restriction
  on property: is manifestation of
  some values from: study design
description: A study is a process that realizes the steps of a study design.

controlled observational cohort study
type: Class
subclass of: observational study
description: In a controlled observational cohort study, two groups of subjects are selected from two populations that are thought to differ in only one characteristic. The groups of subjects are studied for a specific period and contrasted at the end of the study period.

control group
type: Class
subclass of: study group
description: A control group is a group of individuals that are not subject to an intervention of interest, but rather serve as a baseline to compare the outcomes in the intervention group.

intervention group
type: Class
subclass of: study group
description: An intervention group is a group of individuals that are subject to an intervention.

control variable
type: Class
subclass of: variable
description: A control variable that is believed to alter the dependent or independent variables, but may not actually be the focus of the experiment. So that variable will be kept constant or monitored to try to minimise its effect on the experiment.
alternative: controlled variable
alternative: extraneous variable

text span start position
type: Class
subclass of: start position
description: text span start position is the position (offset) of the first character of a text span in relation the text it is from.

text span end position
type: Class
subclass of: end position
description: text span end position is the position (offset) of the last character of a text span in relation the text it is from.

text span
type: Class
subclass of: textual entity
subclass of: Class
  intersection of: Restriction
    on property: has attribute
    some values from: text span start position
  intersection of: Restriction
    on property: has attribute
    some values from: text span end position
description: A text span is a subset of contiguous sequence of characters of a textual entity.
alternative: selector

t-statistic
type: Class
subclass of: ratio
description: A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error.

microarray probe set identifier
type: Class
subclass of: molecular identifier
description: A microarray probe set identifier is an identifier for a set of probe pairs selected to represent expressed sequences on an array.

microarray experiment
type: Class
subclass of: experiment
description: A microarray experiment is an experiment that involves a microarray device to measure the expression of one or more genes.

gene expression value
type: Class
subclass of: dimensional quantity
description: A gene expression value is a measured value obtained from a gene expression experiment.

differential gene expression ratio
type: Class
subclass of: ratio
description: A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample.

genotype
type: Class
subclass of: functional specification
description: A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof).

vocabulary
type: Class
subclass of: functional specification
subclass of: formal specification
description: A vocabulary is a collection of terms.

t-statistic based increased differential gene expression
type: Class
subclass of: differential gene expression ratio
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: t-statistic
    intersection of: Restriction
      on property: has value
      some values from: Datatype
        on datatype: double
description: A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero.

t-statistic based decreased differential gene expression
type: Class
subclass of: differential gene expression ratio
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: t-statistic
    intersection of: Restriction
      on property: has value
      some values from: Datatype
        on datatype: double
description: A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero.

date of database submission
type: Class
subclass of: time instant
description: A date of database submission refers to the moment in time in which some information was submitted/received to a database system.

liquid solution
type: Class
subclass of: heterogeneous substance
description: A liquid solution is a heterogeneous substance in a liquid state.

to remove a covalent bond
type: Class
subclass of: to covalently modify
description: to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond.

to add a covalent bond
type: Class
subclass of: to covalently modify
description: to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond.

to modify electronically
type: Class
subclass of: to change energetically
description: to modify electronically is the capability to change the electronic properties of an object.

concentration
type: Class
subclass of: 3D extent quantity
subclass of: Restriction
  on property: is attribute of
  some values from: Class
    intersection of: chemical substance
    intersection of: Restriction
      on property: is proper part of
      some values from: heterogeneous substance
    intersection of: Restriction
      on property: in relation to
      some values from: chemical substance
description: concentration is the amount of substance per unit volume of a solution

pH
type: Class
subclass of: dimensionless quantity
description: pH is a measure of the activity of the (solvated) hydrogen ion.
comment: pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution.

homogeneous
type: Class
subclass of: compositional quality
disjoint with: heterogeneous
description: homogeneous is a quality that describes the uniform composition of an object.

heterogeneous
type: Class
subclass of: compositional quality
description: homogeneous is a quality that describes the varied composition of an object.

structural quality
type: Class
subclass of: object quality
description: A structural quality is a quality of an object that describes its structure.

rigid
type: Class
subclass of: structural quality
description: rigid is the quality of maintaining structural integrity (and not bending) under pressure.

bent
type: Class
subclass of: curvature
description: bent is the quality of a line being sharply curved or having an angle.

curved
type: Class
subclass of: curvature
description: curved is the quality of a line that deviates from straightness in a smooth, continuous fashion.

electronic structure
type: Class
subclass of: chemical structure
description: electronic structure is the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals.
example: the electron configuration of the neon atom is 1s2 2s2 2p6.
alternative: electronic configuration

crystal structure
type: Class
subclass of: molecular structure
description: A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid.

to interact and to be interacted with
type: Class
subclass of: mutual disposition
subclass of: Class
  intersection of: Restriction
    on property: has proper part
    some values from: to interact with
  intersection of: Restriction
    on property: has proper part
    some values from: to be interacted with
description: to interact and to be interacted with is a mutual disposition of interacting objects.

to gain a covalent bond
type: Class
subclass of: to be covalently modified
description: to gain a covalent bond is the capability of a chemical entity to have bonds added.

to lose a covalent bond
type: Class
subclass of: to be covalently modified
description: to lose a covalent bond is the capability of a chemical entity to have bonds removed.

to ingest
type: Class
subclass of: to consume
description: to ingest is the capability to take into the body by the mouth for digestion or absorption.

to produce
type: Class
subclass of: to actively interact with
description: to produce is the capability to create new objects

pathway
type: Class
subclass of: action specification
description: A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective.
alternative: biological pathway

centrality measure
type: Class
subclass of: quantity
description: A central tendency measure is a central value or a typical value for a probability distribution.

mean
type: Class
subclass of: centrality measure
description: A mean is the central tendency of a collection of numbers taken as the sum of the numbers divided by the size of the collection.
alternative: arithmeritic mean
alternative: average

median
type: Class
subclass of: centrality measure
description: A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half.

mode
type: Class
subclass of: centrality measure
description: A mode is the value that appears most often in a set of data.

sum
type: Class
subclass of: quantity
description: A sum is the result of adding a set of values together.

minimal value
type: Class
subclass of: quantity
subclass of: Restriction
  on property: is attribute of
  some values from: collection
description: A minimal value is smallest value of an attribute for the entities in the defined set.
alternative: min

maximal value
type: Class
subclass of: quantity
subclass of: Restriction
  on property: is attribute of
  some values from: collection
description: A maximal value is largest value of an attribute for the entities in the defined set.
alternative: max

member count
type: Class
subclass of: count
description: A count of the instances of a class or members in a collection.

union
type: Class
subclass of: list
disjoint with: intersection
description: A union is a list of all of the values of an attribute for the entities in the defined set.

intersection
type: Class
subclass of: list
description: An intersection is a list of only the values of an attribute for the entities in the defined set where all entities have that value.

sequence
type: Class
subclass of: list
subclass of: Restriction
  on property: has member
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
    intersection of: Restriction
      on property: refers to
      some values from: entity
alternative: ordered list
description: A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms).
example: For example, (M, A, R, Y) is a sequence of letters that differs from (A, R, M, Y), as the ordering matters, and (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence.

gene-disease association linked with causal mutation
type: Class
subclass of: gene-disease association linked with genetic variation
description: A gene-variant disease association in which a mutation in the gene/protein results in the development or maintenance of the disease.

therapeutic gene-disease association
type: Class
subclass of: gene-disease association
description: A gene disease association in which the gene is a therapeutic marker for the disease.
alternative: gene-disease association arising from a therapeutic role of the gene/protein

gene-disease biomarker association
type: Class
subclass of: gene-disease association
description: A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease.

gene-disease association linked with genetic variation
type: Class
subclass of: gene-disease association linked with genomic alterations
description: A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease.
alternative: gene variant-disease association

gene-disease association linked with altered gene expression
type: Class
subclass of: gene-disease biomarker association
description: A gene-disease association in which the disease phenotype is associated with an altered expression of the gene.

gene-disease association linked with post-translational modification
type: Class
subclass of: gene-disease biomarker association
description: A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product.
example: methylation or phosphorylation of protein product

regulation of transcription
type: Class
subclass of: regulation of biochemical process
description: A process that modulates the frequency, rate or extent of transcription.

regulation of translation
type: Class
subclass of: regulation of biochemical process
description: A process that modulates the frequency, rate or extent of translation.

regulation of molecular quantity
type: Class
subclass of: regulation of object quantity
description: A process that modulates the frequency, rate or extent of process involved in the creation or destruction of a molecule.

regulation of molecular production
type: Class
subclass of: regulation of molecular quantity
description: A process that modulates the frequency, rate or extent of process involved in the production of a molecule.

regulation of molecular degradation
type: Class
subclass of: regulation of molecular quantity
subclass of: Restriction
  on property: regulates
  some values from: chemical destruction
description: A process that modulates the frequency, rate or extent of process involved in the destruction of a molecule.

protein mediated regulation of translation
type: Class
subclass of: regulation of translation
subclass of: Restriction
  on property: has agent
  some values from: protein
description: A process mediated by a protein that modulates the frequency, rate or extent of translation.

rna mediated regulation of translation
type: Class
subclass of: regulation of translation
subclass of: Restriction
  on property: has agent
  some values from: RNA transcript
description: A process mediated by rna that modulates the frequency, rate or extent of translation.

process maintenance
type: Class
subclass of: regulation of process
description: The process of maintaining some the frequency, rate or extent of another process.

increased frequency of process from increased regulation
type: Class
subclass of: regulation of process frequency
description: The increase of regulation leads to a increased occurence of processes of the target type.

decreased frequency of process from increased regulation
type: Class
subclass of: regulation of process frequency
description: The increase of regulation leads to a decreased occurence of processes of the target process type.

regulation of process frequency
type: Class
subclass of: regulation of process
description: regulation of a process duration is a process that modulates the frequency of another process relative to some reference process.

regulation of process duration
type: Class
subclass of: regulation of process
description: regulation of a process duration is a process that modulates the duration of another process relative to some reference process.

increased duration of process from increased regulation
type: Class
subclass of: regulation of process duration
description: increased duration of process from increased regulation is a process in which the duration of the target process is increased as a result of increased regulation.

decreased duration of process from increased regulation
type: Class
subclass of: regulation of process duration
description: decreased duration of process from increased regulation is a process in which the duration of the target process is decreased as a result of increased regulation.

regulation of process spatial extent
type: Class
subclass of: regulation of process
description: regulation of a process spatial extent is a process that modulates the spatial extent of another process relative to some reference process.
example: heating the solution causes greater diffusion of a chemical.

increased spatial extent of process from increased regulation
type: Class
subclass of: regulation of process spatial extent
description: The increase of regulation leads to a increased spatial extent of the target process.

decreased spatial extent of process from decreased regulation
type: Class
subclass of: regulation of process spatial extent
description: The increase of regulation leads to a decreased spatial extent of the target process.

maintenance of spatial extent of process
type: Class
subclass of: regulation of process spatial extent
description: maintenance of spatial extent of process is a regulation of a process' spatial extent within some specified parameter.

maintenance of duration of process
type: Class
subclass of: regulation of process duration
description: maintenance of duration of process is a process that regulates a target process to maintain its duration within an expected interval.

maintenance of frequency of process
type: Class
subclass of: regulation of process frequency
description: maintenance of frequency of process is a process that regulates the number of occurences of a target process type to a specified number or interval.

regulation of object quantity
type: Class
subclass of: regulation of process
subclass of: Restriction
  on property: regulates
  some values from: quantity
description: regulation of a participant quantity is the regulation of a process in which the quantity of its partcipants is changed.

increased object production from increased regulation
type: Class
subclass of: regulation of object production
description: increased regulation leads to an increase in the number of target objects of a specified type.

decreased object production from increased regulation
type: Class
subclass of: regulation of object production
description: increased regulation leads to a decrease in the number of target objects of a specified type.

increased object consumption from increased regulation
type: Class
subclass of: regulation of object consumption
description: increased regulation leads to an increase in the consumption of an object of specified type.

decreased object consumption from increased regulation
type: Class
subclass of: regulation of object consumption
description: increased regulation leads to an decrease in the consumption of an object of specified type.

regulation of object consumption
type: Class
subclass of: regulation of object quantity
description: A process that modulates the frequency, rate or extent of process involved in the consumption of an object.

regulation of object production
type: Class
subclass of: regulation of object quantity
description: regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is increased.

maintenance of quantity of object production
type: Class
subclass of: regulation of object production
description: maintenance of quantity of object production is a regulation of object production in which the number of objects produced is held more or less constant.

maintenance of level of object consumption
type: Class
subclass of: regulation of object consumption
description: regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is maintained at a steady level.

number of objects produced
type: Class
subclass of: count
description: number of objects produced is a count of objects that were produced in some process.

number of objects consumed
type: Class
subclass of: count
description: number of objects consumed is a count of objects that were consumed in some process.

difference in number of objects produced
type: Class
subclass of: count
description: A difference in number of objects produced is a count of the number of objects produced with respect to a second variable (space, time, etc)

increase in number of objects produced
type: Class
subclass of: difference in number of objects produced
description: An increase in the number of objects produced is the positive value of a difference in number of objects produced.

decrease in number of objects produced
type: Class
subclass of: difference in number of objects produced
description: An decrease in the number of objects produced is the negative value of a difference in number of objects produced.

user account
type: Class
subclass of: computational entity
description: user account allows a user to authenticate to system services and be granted authorization to access them.

annotation
type: Class
subclass of: description
subclass of: Restriction
  on property: in relation to
  some values from: entity
description: An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information.

comment
type: Class
subclass of: proposition
description: A comment is a verbal or written remark often related to an added piece of information, or an observation or statement.

audio recording
type: Class
subclass of: media
description: An audio recording is an electrical or mechanical inscription and re-creation of sound waves, such as spoken voice, singing, instrumental music, or sound effects.

issue
type: Class
subclass of: edited publication
subclass of: Restriction
  on property: is proper part of
  some values from: periodical
description: An issue is a single instance of a periodically published journal, magazine, or newspaper.

slideshow
type: Class
subclass of: media
subclass of: Restriction
  on property: has proper part
  some values from: slide
description: A slideshow is a visual presentation of information contained within a collection of slides.

database cross-reference
type: Class
subclass of: association
description: A database cross-reference is an association between one data item and another.
alternative: dbxref

exact cross-reference
type: Class
subclass of: database cross-reference
description: An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source).

double stranded DNA
type: Class
subclass of: double stranded nucleic acid
subclass of: Restriction
  on property: has proper part
  qualified cardinality: 2
  on class: deoxyribonucleic acid
disjoint with: double stranded RNA
description: double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids.

nucleic acid strand
type: Class
equivalent class: Class
  union of: positive nucleic acid strand
  union of: negative nucleic acid strand
subclass of: nucleic acid
subclass of: Restriction
  on property: is proper part of
  some values from: double stranded nucleic acid
description: A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex.

positive nucleic acid strand
type: Class
subclass of: nucleic acid strand
description: The positive nucleic acid strand refers to the strand that is to be read 5' to 3'.
alternative: forward strand

negative nucleic acid strand
type: Class
subclass of: nucleic acid strand
description: The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'.
alternative: reverse strand

double stranded nucleic acid
type: Class
subclass of: molecular complex
subclass of: Restriction
  on property: has proper part
  qualified cardinality: 2
  on class: nucleic acid
description: double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids.

double stranded RNA
type: Class
subclass of: double stranded nucleic acid
subclass of: Restriction
  on property: has proper part
  qualified cardinality: 2
  on class: ribonucleic acid
description: double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids.

full agreement
type: Class
subclass of: agreement
description: full agreement is the result of consensus decision making when members of the group unanimously agree.

mass spectrometry experiment
type: Class
subclass of: experiment
description: A mass spectrometry experiment is an experiment that involves the use of a mass spectrometer.

full disagreement
type: Class
subclass of: disagreement
description: full agreement is the result of consensus decision making when members of the group unanimously disagree.

ribosomal RNA gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
description: A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule.
equivalent to: http://purl.obolibrary.org/obo/SO_0001637
alternative: rRNA gene

statement
type: Class
subclass of: proposition
description: A statement is a proposition that is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts.

slope
type: Class
subclass of: ratio
description: A slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline. Slope is normally described by the ratio of the "rise" divided by the "run" between two points on a line.

software process identifier
type: Class
subclass of: informational entity identifier
description: A software process identifier is an identifier for a software process in some operating system.

hypothetical
type: Class
subclass of: existence quality
description: hypothetical is the quality of an entity that is conjectured to exist.

database row
type: Class
subclass of: row
subclass of: Restriction
  on property: is proper part of
  some values from: database table
description: A database row is a row that is part of a database table.

SADI semantic web service
type: Class
subclass of: semantic web service
description: a SADI semantic web service is a semantic web service that follows the SADI specification
subset: sadi

semantic web service
type: Class
subclass of: web service
description: a semantic web service is a web service that provides a formal, machine understanble description of its functionality.

REST web service
type: Class
subclass of: web service
description: a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification.

SOAP web service
type: Class
subclass of: web service
description: a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP).

web service invocation
type: Class
subclass of: sofware execution
description: A web service invocation involves the execution of a web service.

SADI web service invocation
type: Class
subclass of: web service invocation
subclass of: Restriction
  on property: has agent
  some values from: SADI semantic web service
description: A SADI web service invocation is the excution of a SADI web service.
subset: sadi

media
type: Class
subclass of: information content entity
description: media are audo/visual/audiovisual modes of communicating information for mass consumption.

behaviour
type: Class
subclass of: process
description: Behaviour is the set of actions and mannerisms made by systems (biological or otherwise) in response to stimuli or inputs, whether internal or external, conscious or subconscious, overt or covert, and voluntary or involuntary.
subset: behaviour+
subset: core

history
type: Class
subclass of: description
description: history is a sequence of past events.

structural motif
type: Class
subclass of: pattern
description: A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms).

consensus
type: Class
subclass of: agreement
description: consensus is an acceptable resolution, one that can be supported, even if not the preferred outcome for each individual.

increased molecular degradation from increased regulation
type: Class
subclass of: regulation of molecular degradation
description: A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation.

decreased molecular degradation from decreased regulation
type: Class
subclass of: regulation of molecular degradation
description: A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation.

increased molecular degradation from decreased regulation
type: Class
subclass of: regulation of molecular degradation
description: A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation.

decreased molecular degradation from increased regulation
type: Class
subclass of: regulation of molecular degradation
subclass of: Restriction
  on property: has quality
  some values from: increased
subclass of: Restriction
  on property: results in
  some values from: Class
    intersection of: chemical destruction
    intersection of: Restriction
      on property: has quality
      some values from: decreased
description: A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation.

increased molecular production from increased regulation
type: Class
subclass of: regulation of molecular production
description: A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation.

decreased molecular production from increased regulation
type: Class
subclass of: regulation of molecular production
description: A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation.

increased molecular production from decreased regulation
type: Class
subclass of: regulation of molecular production
description: A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation.

decreased molecular production from decreased regulation
type: Class
subclass of: regulation of molecular production
description: A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation.

increased chemical destruction
type: Class
subclass of: chemical destruction
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is greater than
      some values from: Class
        intersection of: count
        intersection of: Restriction
subclass of: Restriction
  on property: has quality
  some values from: increased
description: increased chemical destruction is a process in which there is an increase in the amount of chemical destroyed relative to some reference process

decreased chemical destruction
type: Class
subclass of: chemical destruction
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is greater than
      some values from: Class
        intersection of: count
        intersection of: Restriction
subclass of: Restriction
  on property: has quality
  some values from: increased
subclass of: Restriction
  on property: in relation to
  some values from: chemical destruction
description: decreased chemical destruction is a process in which there is a decrease in the amount of chemical destroyed relative to some reference process

assertional qualifier
type: Class
equivalent class: Class
  union of: positive
  union of: negative
subclass of: quality
description: An assertional qualifier is the quality of affirmation, either being positive or negative.

positive
type: Class
subclass of: assertional qualifier
disjoint with: negative
description: positive is an assertional qualifier that expresses the validity or truth of a basic assertion.

negative
type: Class
subclass of: assertional qualifier
description: negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion.

intensity
type: Class
subclass of: quality
description: intensity is a quality that represents the strength or degree of something.

mild
type: Class
subclass of: intensity
description: mild is a qualitative intensity value that is more intense than weak, but less intense than moderate.

moderate
type: Class
subclass of: intensity
description: moderate is a qualitative intensity value that is more intense than mild, but less intense than strong.

severe
type: Class
subclass of: intensity
description: severe is a qualitative intensity value that is more intense than strong, but less intense than fatal.

fatal
type: Class
subclass of: intensity
description: fatal is a qualitative intensity value that is more intense than severe, leading to the death/non-functioning of a system.

strong
type: Class
subclass of: intensity
description: strong is a qualitative intensity value that is more intense than moderate, but less intense than severe.

weak
type: Class
subclass of: intensity
description: weak is a qualitative intensity value that is more intense than none, but less intense than mild.

to test a hypothesis
type: Class
subclass of: to examine
description: to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence.

to characterize
type: Class
subclass of: to describe
description: to characterize is the capability to classify the attributes or features of an entity against a reference classification.

to describe
type: Class
subclass of: to passively interact with
description: to describe is the capabilty to communicate facts about an entity.

5' splice site
type: Class
subclass of: splice site
description: The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised.

3' splice site
type: Class
subclass of: splice site
description: The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised.

amino acid
type: Class
subclass of: organic molecule
description: An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom.

cis regulatory element
type: Class
subclass of: nucleic acid part
description: A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects.

trans-regulatory element
type: Class
subclass of: nucleic acid part
description: A trans-regulatory element is a DNA sequence associated with the regulation of a gene located outside the genomic region supporting the corresponding structural DNA region of the trans-regulatory element (i.e., a different DNA strand or different chromosome).

small cytoplasmic RNA (scRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: small cytoplasmic RNA (scRNA)
description: A small cytoplasmic RNA (scRNA) gene is a gene that encodes a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
equivalent to: http://purl.obolibrary.org/obo/SO_0001266

small nuclear RNA (snRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: small nuclear RNA (snRNA)
description: A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule.
equivalent to: http://purl.obolibrary.org/obo/SO_0001268

small nucleolar RNA (snoRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: small nucleolar RNA (snoRNA)
description: A small nucleolar RNA (snoRNA) gene is a gene that encodes a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
equivalent to: http://purl.obolibrary.org/obo/SO_0001267

transfer RNA (tRNA) gene
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: transfer RNA (tRNA)
description: A transfer RNA (tRNA) gene is a gene that codes for a tRNA used in the translation of a messenger RNA (mRNA) to produce a protein product.
equivalent to: http://purl.obolibrary.org/obo/SO_0001272
alternative: solube RNA (sRNA) gene
alternative: tRNA gene

small cytoplasmic RNA (scRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
subclass of: Restriction
  on property: is encoded by
  some values from: small cytoplasmic RNA (scRNA) gene
description: A small cytoplasmic RNA (scRNA) molecule is a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
alternative: scRNA

transfer RNA (tRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
description: A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product.
alternative: tRNA

small nuclear RNA (snRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
description: A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell.
alternative: snRNA

small nucleolar RNA (snoRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
description: A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
alternative: snoRNA

non-protein coding RNA (ncRNA)
type: Class
subclass of: RNA transcript
description: A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product.

data collection device
type: Class
subclass of: device
description: A data collection device is a device that collects information about one or more objects.

mass spectrometer
type: Class
subclass of: data collection device
description: A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field.
similar to: http://purl.obolibrary.org/obo/OBI_0000049

microarray device
type: Class
subclass of: data collection device
description: A microarray device is a device that identifies the binding of a target substance to a physically immobile substrate placed in an array or lattice.
alternative: microarray platform
similar to: http://purl.obolibrary.org/obo/OBI_0000052

to identify
type: Class
subclass of: to investigate
description: to identify is the capability to determine the identity of something.

nmr device
type: Class
subclass of: data collection device
description: A nuclear magnetic resonance (NMR) device is a device that applies a magnetic field to perturb nuclei with an odd number of protons and/or of neutrons in order to hav them absort and re-emit electromagnetic radiation.
equivalent to: http://purl.obolibrary.org/obo/OBI_0000566
alternative: nuclear magnetic resonance device

catalog
type: Class
subclass of: collection
description: A catalog is a systemic collection of items of the same type.
alternative: registry

likelihood
type: Class
subclass of: quantity
description: Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome.

log likelihood
type: Class
subclass of: likelihood
description: Log likelihood is the natural logarithm of the likelihood function

standard score
type: Class
subclass of: probability measure
description: A standard score is the (signed) number of standard deviations an observation or datum is above the mean.
alternative: z-value, z-score, normal score, standardadized variable.

interval
type: Class
subclass of: set
description: an interval is a set of real numbers with the property that any number that lies between two numbers in the set is also included in the set.
example: The set of all numbers x satisfying 0<=x<=1 is an interval which contains 0 and 1, as well as numbers between them.

open interval
type: Class
subclass of: left open interval
subclass of: right open interval
description: an open interval is an interval that does not include its endpoints.
example: (0,1) is an open interval that is greater than 0 and less than 1.

closed interval
type: Class
subclass of: right closed interval
subclass of: left closed interval
description: A closed interval is an interval that includes its endpoints, and is denoted with square brackets.
example: [0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1.

chemical-pathway association
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  some values from: pathway
subclass of: Restriction
  on property: refers to
  some values from: chemical entity
description: a chemical-pathway association is an association between a chemical and a pathway.
alternative: drug-pathway association

left open interval
type: Class
subclass of: interval
description: a left open interval is an interval in which there is no element that is smaller than all other elements.

right open interval
type: Class
subclass of: interval
description: a right open interval is an interval in which there is no element that is greater than all other elements.

right closed interval
type: Class
subclass of: interval
description: a right closed interval is an interval in which there is a real number that is larger than all of its elements.

left closed interval
type: Class
subclass of: interval
description: a left closed interval is an interval in which there is a real number that is smaller than all its elements.

pharmacokinetic pathway
type: Class
subclass of: metabolic pathway
description: a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule.

pharmacodynamic pathway
type: Class
subclass of: regulatory pathway
description: a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway.

chemical-gene assocation
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  some values from: chemical entity
subclass of: Restriction
  on property: refers to
  some values from: gene
description: a chemical-gene assocation is an assocation between a chemical and a gene.

set item
type: Class
subclass of: mathematical entity
subclass of: Restriction
  on property: is member of
  some values from: set
description: set item is an item in a set.

collection item
type: Class
subclass of: set item
subclass of: Restriction
  on property: is member of
  some values from: collection
description: a collection item is an item in a collection.

list item
type: Class
subclass of: set item
subclass of: Restriction
  on property: refers to
  some values from: entity
subclass of: Restriction
  on property: is ordered part of
  some values from: list
description: a list item is an item in a list.

ordered list item
type: Class
subclass of: list item
subclass of: Class
  intersection of: list item
  intersection of: Restriction
    on property: has attribute
    some values from: ordinal position
  intersection of: Restriction
    on property: is part of
    some values from: list
description: an ordered list item is an item in an ordered list.

anatomical entity
type: Class
equivalent class: Class
  intersection of: Class
    union of: material entity
    union of: spatial region
  intersection of: Restriction
    on property: is direct part of
    some values from: biological entity
subclass of: specialized object
description: an anatomical entity is an object that is a structural part (material or immaterial) of a biological entity.

zygosity
type: Class
subclass of: biological quality
description: zygosity is the quality pertaining to the allelic complement of a biological system at a single locus on the DNA.

homozygous
type: Class
subclass of: zygosity
description: homozygous is the quality of a biological organism in which there are two identical alleles at a given locus.

heterozygous
type: Class
subclass of: zygosity
description: homozygous is the quality of a biological organism in which there are two different alleles at a given locus.

hemizygous
type: Class
subclass of: zygosity
description: hemizygous is the quality of a biological organism in which, based on the ploidy of the organism, there is half the number of alleles than normal at a given locus.

nullizygous
type: Class
subclass of: zygosity
description: nullizygous is the quality of a biological organism in which there are no allelles at a given locus.

parental transmission
type: Class
subclass of: biological quality
description: parental transmition is the quality of a biological organism in which the (genetic) material is transmitted from a parental unit.

maternally transmitted
type: Class
subclass of: parental transmission
disjoint with: paternally transmitted
description: maternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the maternal line.

paternally transmitted
type: Class
subclass of: parental transmission
description: paternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the paternal line.

helicity
type: Class
subclass of: structural quality
description: helicity is the quality of being helical

circularly helical
type: Class
subclass of: helicity
description: a circularly helical quality is the quality of a helix that is connected in a circle or loop.

left-handed helical
type: Class
subclass of: helicity
disjoint with: right-handed helical
description: left-handed helical quality is the quality in which a clockwise screwing motion moves the helix towards the observed along the line of sight along the helix's axis.

right-handed helical
type: Class
subclass of: helicity
description: right-handed helical quality is the quality in which a clockwise screwing motion moves the helix away from the observed along the line of sight along the helix's axis.

coding frame offset
type: Class
subclass of: chemical quality
description: a coding frame offset is a numeric value that indicates the number of bases from a reference start codon position.

coding sequence
type: Class
subclass of: nucleic acid sequence
description: a coding sequence is a sequence of nucleotides which encode a RNA or protein product..

humiliation
type: Class
subclass of: hurt
description: Humiliation is the abasement of pride, which creates mortification or leads to a state of being humbled or reduced to lowliness or submission.

hunger
type: Class
subclass of: negative emotion
description: hunger is the craving for food.

discouragement
type: Class
subclass of: negative emotion
description: Discouragement is the emtion of having lost confidence or enthusiasm.
alternative: discouraged

satisfaction
type: Class
subclass of: positive emotion
description: satisfaction is the emotion of fulfillling one's wishes, expectations, or needs.
alternative: contentment
alternative: pleasure

suicidal
type: Class
subclass of: negative emotion
description: suicidal is the emotion of being deeply unhappy or depressed with thoughts of killing one's self.

irritability
type: Class
subclass of: negative emotion
description: irritability is the negative emotion of quick excitability to annoyance, impatience, or anger.
alternative: irritable

indecision
type: Class
subclass of: negative emotion
description: indecision is the emotion of being unable to choose between two or more possible courses of action.
alternative: indecisiveness

temporal qualifier
type: Class
subclass of: informational quality
description: a temporal qualifier is pertains to the frequency of the event of interest.

never
type: Class
subclass of: temporal qualifier
description: never refers to in none of the occasions.
alternative: none of the time

some of the time
type: Class
subclass of: temporal qualifier
description: some refers to in the minority of occasions
alternative: some of the time

most of the time
type: Class
subclass of: temporal qualifier
description: most refers to in the majority of occasions
alternative: most of the time

always
type: Class
subclass of: temporal qualifier
description: always indicates that the event occurs at all times.
alternative: all of the time

quality descriptor
type: Class
subclass of: informational quality

very poor quality
type: Class
subclass of: quality descriptor

poor quality
type: Class
subclass of: quality descriptor

neither good nor poor quality
type: Class
subclass of: quality descriptor

good quality
type: Class
subclass of: quality descriptor

very good quality
type: Class
subclass of: quality descriptor

quantity modifier
type: Class
subclass of: informational quality

ovopub
type: Class
subclass of: computational entity
description: An ovopub is an information content entity that contains and links to one or more resources and/or statements, including those describing its provenance, and is itself a dereferenceable resource.
subset: ovopub+

collection ovopub
type: Class
subclass of: ovopub
disjoint with: assertion ovopub
description: A collection ovopub is an ovopub that contains and links to one or more assertion subgraphs and/or ovopubs, as well as statements describing its provenance. It is used to share a specific set of items or restrict a search to the resources contained therein.

assertion ovopub
type: Class
subclass of: ovopub
description: An assertion ovopub is an ovopub that contains and links to an assertion subgraph with one or more statements that may be true or false, as well as statements describing its provenance.

none quantifier
type: Class
subclass of: quantity modifier

a little quantifier
type: Class
subclass of: quantity modifier

moderately quantifier
type: Class
subclass of: quantity modifier

mostly quantifier
type: Class
subclass of: quantity modifier

completely quantifier
type: Class
subclass of: quantity modifier

satisfaction qualifier
type: Class
subclass of: informational quality

very dissatisfied qualifier
type: Class
subclass of: satisfaction qualifier

dissatisfied qualifier
type: Class
subclass of: satisfaction qualifier

neither satisfied or dissatisfied qualifier
type: Class
subclass of: satisfaction qualifier

satisfied qualifier
type: Class
subclass of: satisfaction qualifier

excellent quality
type: Class
subclass of: quality descriptor

date of issue
type: Class
subclass of: time instant
description: the date at which an information content entity was made public.

author list
type: Class
subclass of: ordered list
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: list item
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
    intersection of: Restriction
      on property: refers to
      some values from: Class
        union of: organization
        union of: person
description: an ordered list of authors.

ordered list
type: Class
subclass of: list
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: list item
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
description: an ordered list is a list in which items are sequentially ordered.

middle name
type: Class
subclass of: name
description: a middle name is a name assigned to an individual that is not the first or last name.

middle initial
type: Class
subclass of: middle name
description: a middle initial is an abbreviated middle name.

telephone number
type: Class
subclass of: informational entity identifier
description: a telephone number is an identifier used to connect to a physical device capable of transfering voice or data over a network.

cellular phone number
type: Class
subclass of: telephone number
description: a cellular phone number is a number to connect to a mobile device

fax number
type: Class
subclass of: telephone number
description: a fax number is a number to connect to fax device

IP number
type: Class
subclass of: informational entity identifier
description: an IP number is an number to connect to a device on the internet.
alternative: IP address

email address
type: Class
subclass of: informational entity identifier
description: an email address is an identifier to send mail to particular electronic mailbox.

work phone number
type: Class
subclass of: telephone number
description: a work phone number is the number to connect to an phone at a place of work.

home phone number
type: Class
subclass of: telephone number
description: a home phone number is the number to connect to an phone at a place of residence.

status descriptor
type: Class
subclass of: informational quality
description: status descriptor is a descriptor for the state of a process or object.

protein expression value
type: Class
subclass of: dimensional quantity
description: A protein expression value is a quantity obtained from a protein expression experiment.

copy number variation
type: Class
subclass of: count
description: copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state.
alternative: CNV

single nucleotide polymorphism
type: Class
subclass of: nucleotide residue
alternative: SNP
alternative: SNV
alternative: single nucleotide variation
description: a single nucleotide variation (SNV) is a nucleotide residue that is a variant compared to some reference nucleic acid sequence.

metadata
type: Class
subclass of: data item
description: metadata is data that provides information about data.

diagnosis
type: Class
subclass of: conclusion
description: A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.

directed acyclic graph
type: Class
subclass of: network diagram
alternative: dag
description: a directed acyclic graph or DAG is a network digram that contains directed edges in which nodes may have multiple parents, but there are no cycles.

arc
type: Class
subclass of: curve
description: an arc is a closed segment of a differentiable curve.

edge
type: Class
subclass of: line
description: an edge is a line connecting two graph vertices.

node
type: Class
subclass of: point
description: a node or vertex is a point in a graph.
alternative: vertex

epimer
type: Class
subclass of: stereoisomer
description: An epimer is a stereoisomer that differs in configuration at only one stereogenic center.

epimer association
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  qualified cardinality: 2
  on class: epimer

mereological quality
type: Class
subclass of: object quality
description: a mereological quality is a quality of an entity vis-a-vis containment or parthood

empty
type: Class
subclass of: containment quality
description: empty is the quality of not containing some thing

full
type: Class
subclass of: containment quality
description: full is the quality of contain an entity such that there is no more space for any additional entity.

containment quality
type: Class
subclass of: mereological quality
description: a containment quality is a quality of being able to contain another entity.

gene-disease association linked with modifying mutation
type: Class
subclass of: gene-disease association linked with genetic variation
description: A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease.

gene-disease association linked with susceptibility mutation
type: Class
subclass of: gene-disease association linked with genetic variation
description: A gene-disease association in which a germline mutation in the gene predisposes to the development of the disease, and it is necessary but not sufficient for the manifestation of the disease.

gene-disease association linked with germline causal mutation
type: Class
subclass of: gene-disease association linked with causal mutation
description: A gene-variant disease association in which a germline mutation in the gene/protein results in the development or maintenance of the disease, and it may be passed on to offspring.

gene-disease association linked with somatic causal mutation
type: Class
subclass of: gene-disease association linked with causal mutation
description: A gene-variant disease association in which a somatic mutation in the gene/protein results in the development or maintenance of the disease, and it may not be passed on to offspring.

gene-disease association linked with somatic modifying mutation
type: Class
subclass of: gene-disease association linked with modifying mutation
description: A gene-variant disease association in which a somatic mutation in the gene modifies the clinical presentation of the disease, and it may not be passed on to offspring.

gene-disease association linked with germline modifying mutation
type: Class
subclass of: gene-disease association linked with modifying mutation
description: A gene-variant disease association in which a germline mutation in the gene modifies the clinical presentation of the disease, and it may be passed on to offspring.

fusion gene-disease association
type: Class
subclass of: gene-disease association linked with genomic alterations
description: A gene-disease association in which the fusion between two different genes (promotor and/or other coding DNA regions) is associated with the disease.

gene-disease association linked with chromosomal rearrangement
type: Class
subclass of: gene-disease association linked with genomic alterations
description: A gene-disease association in which the gene is included in a chromosomal rearrangement associated with a particular manifestation of the disease.

gene-disease association linked with genomic alterations
type: Class
subclass of: gene-disease biomarker association
description: a gene-disease association that is linked with some genomic alteration

DisGeNET disease specificity
type: Class
subclass of: ratio
description: DisGeNET Disease specificity is a measure of disease coverage. It is calculated from the negative base 2 log of the ratio of number of diseases associated to the total number of diseases. The measure is described here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#specificity

DisGeNET Pleiotropy Index
type: Class
subclass of: ratio
description: The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100. The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy

specialized object
type: Class
equivalent class: Class
  intersection of: object
  intersection of: Restriction
    on property: has realizable property
    some values from: realizable entity
subclass of: object

week
type: Class
subclass of: time interval
description: A week is a period of 7 consecutive days.

specific gravity
type: Class
subclass of: ratio
description: Specific gravity is the ratio of the density of a substance to the density of a reference substance; equivalently, it is the ratio of the mass of a substance to the mass of a reference substance for the same given volume.

information encoding
type: Class
subclass of: information translation

speech
type: Class
subclass of: communicating
description: speech is the expression of thoughts and feelings by sound.

to retrieve
type: Class
subclass of: to actively interact with
description: the capability to retrieve a (digitial/physical/mental) object from a location.

information translation
type: Class
subclass of: information processing

information decoding
type: Class
subclass of: information translation

to store
type: Class
subclass of: to actively interact with
description: to store is the capability to place an object into a medium in which it can be retrieved in the future.

to encode information
type: Class
subclass of: to actively interact with
description: the capability to encode information in a different representation

to maintain information
type: Class
subclass of: to actively interact with
description: the capability to maintain information such that it can be retrieved in the future.

to decode information
type: Class
subclass of: to actively interact with
description: the ability to reverse an encoding operation

rate of change
type: Class
subclass of: dimensional quantity
description: The amount of change accumulated per unit time.

information maintenance
type: Class
subclass of: process maintenance
alternative: regulation of information
description: the regulation or maintenance of information

frequency
type: Class
subclass of: rate of change
description: Frequency is the number of occurrences of a repeating event per unit time

speed
type: Class
subclass of: rate of change
description: Speed is the rate of change of an object's position.

velocity
type: Class
subclass of: speed
description: The rate of change of an object's position and the direction of that change

slide
type: Class
subclass of: media
description: A slide is an visual representation meant to communicate some information.

statute
type: Class
subclass of: legal document
description: A statute is a formal written enactment of a legislative authority that governs a state, city or country.

legislation
type: Class
subclass of: legal document
description: A legal document proposing or enacting a law or a group of laws.

legal document
type: Class
subclass of: document
description: A legal document is a formally executed written document that can be formally attributed to its author, records and formally expresses a legally enforceable act, process, or contractual duty, obligation, or right, and therefore evidences that act, process, or agreement.

brief
type: Class
subclass of: legal document
description: A brief is a written legal document used in various legal adversarial systems that is presented to a court arguing why one party to a particular case should prevail.

book section
type: Class
equivalent class: Class
  intersection of: document section
  intersection of: Restriction
    on property: is proper part of
    some values from: book
subclass of: document section
subclass of: Restriction
  on property: is proper part of
  some values from: book

bill
type: Class
subclass of: legal document
description: A bill is proposed legislation under consideration by a legislature.

versioned dataset
type: Class
subclass of: dataset
subclass of: Restriction
  on property: has attribute
  some values from: version label
description: a versioned dataset is a dataset with a particular release date or release number.

analyte
type: Class
subclass of: chemical substance
description: an analyte is a substance or chemical constituent of interest in an analytical procedure.

protein domain
type: Class
subclass of: amino acid polymer submolecule
description: A protein domain is a part of a protein that maintains its structure and function independently of the rest of the protein.

protein family
type: Class
subclass of: collection
description: a protein family is a collection of proteins that share a common evolutionary origin, reflected by their related function and similarity in composition or structure.

genomic sequence variant
type: Class
subclass of: nucleic acid part
description: a genomic sequence variant is part of a nucleic acid which is compositionally different than another reference genomic part.
alternative: variant

unigene cluster
type: Class
subclass of: collection
description: a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region.
alternative: cluster of transcripts

gene symbol
type: Class
subclass of: scientific name
description: a gene symbol is a short name assigned to a gene.

statement of consequence
type: Class
subclass of: statement
description: a statement of consequence is a statement concerning the result or effect of an action or condition.

notation
type: Class
subclass of: specification
description: a notation is a series or system of written symbols used to represent numbers, amounts, or elements.

chemical notation
type: Class
subclass of: notation
description: a notation to describe a chemical entity

InCHI notation
type: Class
subclass of: chemical notation

sequence variation notation
type: Class
subclass of: notation

hgvs notation
type: Class
subclass of: sequence variation notation
description: The HGVS (human genome variation society) notation is a notation to specify a sequence variation in dna, rna, proteins, and other biomolecules.

protein coding sequence
type: Class
subclass of: gene component
description: A protein coding sequence (CDS) is the region of DNA that is translated to form proteins. The CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery.
alternative: CDS
alternative: coding sequence

ontology
type: Class
subclass of: formal specification
description: an ontology is a formal specification of entities, their attributes and relationships.

biologic
type: Class
subclass of: pharmaceutical drug
description: A biologic, also known as a biologic medical product, biological, or biopharmaceutical, is any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources.

post-translational modification
type: Class
subclass of: amino acid polymer submolecule
description: a post-translational modification is a part of a protein that was added, removed, or modified as a result of a chemical reaction after synthesis.

evidence
type: Class
subclass of: proposition
description: evidence is the body of facts or information indicating whether a belief or proposition is true or valid.

carbohydrate
type: Class
subclass of: organic polymer
subclass of: Restriction
  on property: has direct part
  min qualified cardinality: 2
  on class: carbohydrate residue
alternative: oligosaccharide
alternative: saccharide
description: a carbohydrate is an organic molecule composed of two or more monosaccharides.

terminology
type: Class
subclass of: vocabulary
description: A terminology is a set of terms used for a specified application.

microRNA (miRNA)
type: Class
subclass of: non-protein coding RNA (ncRNA)
description: A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.
alternative: miRNA

medical intervention
type: Class
subclass of: medical procedure
description: a medical intervention is a medical procedure to treat (to cure or alleviate) a health condition.

chemical exposure
type: Class
subclass of: chemical interaction
description: chemical exposure is a process to expose one or more individuals to a chemical substance.

subcellular entity
type: Class
subclass of: biological entity
subclass of: Restriction
  on property: is part of
  some values from: cell

intersex
type: Class
subclass of: biological sex
disjoint with: female
description: intersex is a biological sex characterised by birth with genitalia and/or secondary sexual characteristics of indeterminate sex, or which combine features of both sexes.

density
type: Class
subclass of: 3D extent quantity
description: Density (volumetric mass density) is the quantity of mass per unit volume of a substance.

surface area
type: Class
subclass of: area
description: The surface area of a is a measure of the total area that the surface of the object occupies.

aspect ratio
type: Class
subclass of: ratio
description: The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions.

object relational quality
type: Class
subclass of: object quality
description: object relational quality refers to a quality in relation to one or more objects

synthetic quality
type: Class
subclass of: object relational quality
description: synthetic quality is the quality of a manufactured object that has similar properties as naturally occuring objects.

sample quality
type: Class
subclass of: object relational quality
description: sample quality is the quality of an object that is drawn from a larger population.

replica quality
type: Class
subclass of: object relational quality
description: replica quality is the quality of an object that is an exact copy of another object.

percentage
type: Class
subclass of: ratio
description: A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%".

quantile
type: Class
subclass of: dimensionless quantity
description: A quantile is a quantity that divides the range of a probability distribution into continuous intervals with equal probabilities, or dividing the observations in a sample in the same way.

percentile
type: Class
subclass of: quantile
description: A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals.

duplicate role
type: Class
subclass of: comparative role
description: a duplicate role is a comparative role that holds when one item is an exact copy of another in a specific set.

replicate role
type: Class
subclass of: comparative role
description: a replicate role is a comparative role that holds when one item is a reproduction, facsimile, or a copy of another.

replicate
type: Class
subclass of: collection item
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: replicate role
    intersection of: Restriction
      on property: in relation to
      some values from: object
description: a replicate is an object that is a facsimile, reproduction, or copy of another item.

a collection of replicates
type: Class
subclass of: collection
subclass of: Restriction
  on property: has member
  some values from: replicate
description: a collection of replicates is a collection composed of items that are a facsimile, reproduction, or copy of other items in the collection.
alternative: replicates

duplicate
type: Class
subclass of: collection item
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: duplicate role
    intersection of: Restriction
      on property: in relation to
      some values from: object
description: a duplicate is an object that is an exact copy of another item

a collection of duplicates
type: Class
subclass of: collection
subclass of: Restriction
  on property: has member
  some values from: duplicate
description: a collection of duplicates is a collection composed of items that are an exact copy of other items in the collection.
alternative: duplicates

chemical salt
type: Class
subclass of: heterogeneous substance
description: a chemical salt is a heterogenous substance composed of an ionic assembly of cations and anions.
alternative: salt

strong chemical salt
type: Class
subclass of: chemical salt
description: a strong chemical salt is a chemical salt that is composed of strong electrolytes. Strong chemical salts contain Na,K,NH4 or NO3, CIO4, CH3COO.

weak chemical salt
type: Class
subclass of: chemical salt
description: a weak chemical salt is a chemical salt composed of weak eletrolytes.

peptide
type: Class
subclass of: amino acid polymer
description: a peptide is an organic polymer composed of between two and fifty amino acids.

oligopeptide
type: Class
subclass of: amino acid polymer
description: an oligopeptide is an organic polymer composed of fewer than 10 or 15 amino acids.

amino acid polymer
type: Class
subclass of: organic polymer
subclass of: Restriction
  on property: has direct part
  min qualified cardinality: 2
  on class: amino acid residue
description: an amino acid polymer is an organic polymer composed of two or more amino acid residues.

ingredient
type: Class
equivalent class: Class
  intersection of: chemical substance
  intersection of: Restriction
    on property: derives into
    some values from: chemical substance
subclass of: chemical substance
description: an ingredient is a chemical substance that forms part of a mixture.

tensor
type: Class
subclass of: mathematical entity
description: a tensor is a n-dimensional array.

vector
type: Class
subclass of: rank nonzero tensor
subclass of: Restriction
  on property: is part of
  some values from: vector space
subclass of: Restriction
  on property: has proper part
  all values from: scalar
alternative: rank 1 tensor
description: a vector is a rank 1 tensor that is described by n-dimension of scalars.

scalar
type: Class
subclass of: tensor
alternative: rank 0 tensor
description: a scalar is a rank 0 tensor and is an element of a field that is used to define a vector space.

vector space
type: Class
subclass of: mathematical entity
subclass of: Restriction
  on property: has member
  min qualified cardinality: 0
  on class: vector
description: a vector space is a set of vectors.

matrix
type: Class
subclass of: rank nonzero tensor
subclass of: Restriction
  on property: has proper part
  all values from: vector
alternative: rank 2 tensor
description: a matrix is a rank 2 tensor. It is represented as a rectangular array or table of numbers, symbols, or expressions arranged in rows and columns.

rank nonzero tensor
type: Class
subclass of: tensor
subclass of: Restriction
  on property: has proper part
  all values from: Class
    intersection of: tensor
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
description: a rank nonzero tensor is a tensor with a rank greater than zero.

organism
type: Class
equivalent class: Class
  union of: cellular organism
  union of: non-cellular organism
subclass of: biological entity
description: A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not).

cell
type: Class
subclass of: biological entity
description: A cell is a biological entity that is contained by a plasma membrane.

tissue
type: Class
subclass of: biological entity
subclass of: Restriction
  on property: has direct part
  some values from: cell
description: A tissue is a mereologically maximal collection of cells that together perform some function.

organ
type: Class
subclass of: biological entity
description: An organ is a collection of tissues joined in structural unit to serve a common function.

chemical entity
type: Class
subclass of: material entity
description: A chemical entity is a material entity that pertains to chemistry.
equivalent to: CHEBI:23367
example: atom, ion, molecule, chemical substance,
subset: chemical+

weak submolecular component
type: Class
subclass of: submolecular entity
disjoint with: strong submolecular component
description: A weak submolecular component is a submolecular component that weakly connects submolecular components.

polypeptide
type: Class
subclass of: amino acid polymer
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: amino acid residue
disjoint with: nucleic acid
description: A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length.

nucleic acid
type: Class
subclass of: organic polymer
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: nucleotide residue
description: A nucleic acid is an organic polymer composed of a sequence of nucleotide residues.

ribonucleic acid
type: Class
subclass of: nucleic acid
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: ribonucleotide residue
disjoint with: deoxyribonucleic acid
description: A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues.

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: deoxyribonucleotide residue
description: A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues.

lipid
type: Class
subclass of: organic molecule
description: A lipid is a water-insoluable organic molecule.

chemical interaction
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has participant
  some values from: chemical entity
description: A chemical interaction is a biochemical process in which chemical entities interact through some set of attractive forces.
equivalent to: biopax:Interaction

primary structure descriptor
type: Class
subclass of: biomolecular structure descriptor
description: A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology.

protein sequence
type: Class
subclass of: biopolymer sequence
subclass of: Restriction
  on property: is attribute of
  some values from: polypeptide
subclass of: Restriction
  on property: represents
  some values from: Class
    intersection of: molecular structure
    intersection of: Restriction
      on property: is attribute of
      some values from: polypeptide
description: A protein acid sequence is the character representation of the molecular structure of a protein.
alternative: amino acid sequence
alternative: polypeptide sequence

nucleic acid sequence
type: Class
subclass of: biopolymer sequence
subclass of: Restriction
  on property: is attribute of
  some values from: nucleic acid
subclass of: Restriction
  on property: represents
  some values from: Class
    intersection of: molecular structure
    intersection of: Restriction
      on property: is attribute of
      some values from: nucleic acid
description: A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid.

ribonucleic acid sequence
type: Class
subclass of: nucleic acid sequence
subclass of: Restriction
  on property: is about
  some values from: ribonucleic acid
description: A ribonucleic acid sequence is a symbolic representation of the sequence of ribonucleic acid residues in a ribonucleic acid.
alternative: RNA sequence

deoxyribonucleic acid sequence
type: Class
subclass of: nucleic acid sequence
subclass of: Restriction
  on property: is about
  some values from: deoxyribonucleic acid
description: A deoxyribonucleic acid sequence is a symbolic representation of the sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid.
alternative: DNA sequence

biological data
type: Class
subclass of: scientific data
description: biological data is scientific data relevant to biology.

submolecular entity
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: is part of
  some values from: chemical entity
description: A submolecular entity is a part of a molecule or a particle smaller than a molecule.

secondary structure descriptor
type: Class
subclass of: biomolecular structure descriptor
description: A secondary structure descriptor describes local topological patterns in a biopolymer.

tertiary structure descriptor
type: Class
subclass of: biomolecular structure descriptor
description: A tertiary structure descriptor describes 3D topological patterns in a biopolymer.

quaternary structure
type: Class
subclass of: biomolecular structure descriptor
description: A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex.

genetic polymorphism
type: Class
subclass of: nucleic acid part
description: genetic polymorphism is the description of a difference in genetic composition at some location.

genetic data
type: Class
subclass of: biological data
description: genetic data is data pertaining to genetics.

biological sex
type: Class
subclass of: biological quality
description: biological sex is the quality of a biological organism based on reproductive function or organs.

monosaccharide
type: Class
subclass of: organic molecule
description: A monosaccharide is an organic molecule that consists of a single polyhydroxy aldehyde or ketone group.

PDB chain identifier
type: Class
subclass of: molecular identifier
description: A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank .

PDB record identifier
type: Class
subclass of: record identifier
description: A PDB record identifier is an identifier for a PDB generated record.

hydrogen bond
type: Class
subclass of: weak submolecular component
description: A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom.

cation pi interaction
type: Class
subclass of: ionic interaction
description: A cation pi interaction is an ionic interaction between the localized negative charge of π orbital electrons, located above and below the plane of an aromatic ring, and a positive charge.

gene
type: Class
subclass of: nucleic acid part
description: A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript.
equivalent to: biopax:Gene
equivalent to: http://purl.obolibrary.org/obo/SO_0000704

biochemical reaction
type: Class
subclass of: catalyzed reaction
subclass of: Class
  intersection of: catalyzed reaction
  intersection of: Restriction
    on property: has agent
    some values from: enzyme
  intersection of: Restriction
    on property: has target
    some values from: substrate
  intersection of: Restriction
    on property: has product
    some values from: product
description: A biochemical reaction is a biochemical process that involves the conversion of at least one chemical participant (target) into another (product) by an enzyme (agent).
equivalent to: biopax:BiochemicalReaction
equivalent to: biopax:Conversion

chemical element
type: Class
subclass of: homogeneous substance
subclass of: Restriction
  on property: has direct part
  all values from: atom
description: A chemical element is a (effectively) homogeneous substance composed of one type of atom.

drug
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has capability
  some values from: Class
    intersection of: to regulate
    intersection of: Restriction
      on property: in relation to
      some values from: biological entity
description: A drug is a chemical substance that contains one or more active ingredients that regulate one or more biological processes.

pharmaceutical drug
type: Class
subclass of: drug
subclass of: Restriction
  on property: has direct part
  some values from: active ingredient
description: A pharmaceutical preparation is a chemical substance that is approved for use in the medical diagnosis, cure, treatment, or prevention of disease.
alternative: medicine

binding site
type: Class
subclass of: molecular site
description: A binding site is a molecular site which when occupied with particular ligands leads to structural transformations that initiatiate new moelcular processes.

active site
type: Class
subclass of: molecular site
description: An active site is a molecular site in which a chemical event occurs (structural transformation or conformational change).

haplotype
type: Class
subclass of: genomic sequence variant
description: A haplotype is one of a set of genomic sequence variants.

protein
type: Class
subclass of: amino acid polymer
subclass of: Restriction
  on property: has direct part
  some values from: amino acid residue
subclass of: Restriction
  on property: has component part
  some values from: polypeptide
description: A protein is an organic polymer that is composed of one or more linear polymers of amino acids.
equivalent to: CHEBI:36080

atom
type: Class
subclass of: chemical entity
description: An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons.

base pair
type: Class
subclass of: weak submolecular component
description: A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases.

biological entity
type: Class
subclass of: heterogeneous substance
subclass of: Restriction
  on property: is part of
  some values from: organism
description: A biological entity is a heterogeneous substance that contains genomic material or is the product of a biological process.
subset: chemical-

strong submolecular component
type: Class
subclass of: submolecular entity
description: A strong submolecular component is a submolecular component that strongly connects submolecular components.

male
type: Class
subclass of: biological sex
disjoint with: female
description: male is a biological sex of an individual with male sexual organs.
equivalent to: PATO:0000384

molecular site
type: Class
subclass of: site
description: A moleclar site is a spatial region bounded (in part or in whole) by a molecule and may be occupied by other material entities (e.g. drugs).

allosteric site
type: Class
subclass of: binding site
description: An allosteric site is a binding site that when bound to particular ligand changes the conformational state and affects its functionality.

biological fluid
type: Class
subclass of: biological entity
subclass of: Restriction
  on property: is derived from
  some values from: biological entity
description: A biological fluid is a fluid of biological origin.

female
type: Class
subclass of: biological sex
description: female is a biological sex of an individual with female sexual organs.

evolutionary lineage
type: Class
subclass of: history
description: evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species.

cell line
type: Class
subclass of: biological entity
description: A cell line is a collection of genetically identifical cells.

strain
type: Class
subclass of: organism
subclass of: Restriction
  on property: is variant of
  some values from: organism
description: A strain is a genetic variant or kind of microorganism.

phenotype
type: Class
subclass of: biological quality
description: A phenotype is an observable characteristic of an individual.

life status
type: Class
equivalent class: Class
  union of: alive
  union of: dead
subclass of: biological quality
description: life status is the quality of whether something is alive or dead.

alive
type: Class
subclass of: life status
disjoint with: dead
description: alive is the state of a biological organism that exhibits biological functions.

dead
type: Class
subclass of: life status
description: dead is the quality of an object in which there is a cessation of all biological functions.

family history
type: Class
subclass of: history
description: family history is the systematic narrative and research of past events relating to a specific family, or specific families.

generation number
type: Class
subclass of: count
description: generation number is a count of the number of biological reproduction events elapsed from some starting reference point.

5' untranslated region
type: Class
subclass of: gene component
description: The five prime untranslated region (5' UTR) is a section of messenger RNA (mRNA) and the DNA that codes for it that starts at the +1 position (where transcription begins) and ends one nucleotide before the start codon (usually AUG) of the coding region.

bioinformatic data
type: Class
subclass of: biological data
description: bioinformatic data is data genereated or used for computer-based investigations of biological phenomena.

sequence alignment
type: Class
subclass of: collection
description: A sequence alignment is the character-based alignment of sequences using some method.

multiple sequence alignment
type: Class
subclass of: sequence alignment
description: A multiple sequence alignment is a sequence alignment involving more than two sequences.

pairwise sequence alignment
type: Class
subclass of: sequence alignment
description: A pairwise sequence alignment is the alignment of exactly 2 sequences.

3' untranslated region
type: Class
subclass of: gene component
description: A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon.

organic submolecule
type: Class
subclass of: submolecule
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: carbon atom
  intersection of: Restriction
    on property: has part
    some values from: oxygen atom
subclass of: Restriction
  on property: is part of
  some values from: organic molecule
description: An organic submolecule is connected region of a molecule.

organic molecule
type: Class
subclass of: molecule
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: carbon atom
  intersection of: Restriction
    on property: has part
    some values from: hydrogen atom
description: An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur)

open reading frame
type: Class
subclass of: gene component
subclass of: Class
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: start codon
  intersection of: Restriction
    on property: has component part
    qualified cardinality: 1
    on class: stop codon
subclass of: Restriction
  on property: is transcribed into
  some values from: Class
    intersection of: RNA transcript
    intersection of: Restriction
      on property: is translated into
      some values from: polypeptide
description: An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon.

amino acid residue
type: Class
subclass of: amino acid polymer submolecule
subclass of: Restriction
  on property: is derived from
  some values from: amino acid
description: An amino acid residue is a submolecule of an amino acid that is part of a larger molecule.

nucleotide residue
type: Class
subclass of: nucleic acid part
description: A nucleotide residue is a part of a molecule that derives from a nucleotide.

poison
type: Class
subclass of: drug
description: A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity.

active ingredient
type: Class
subclass of: A pharmaceutical ingredient is a part of a pharmaceutical preparation.
description: An active ingredient is a molecular entity that exhibits biological activity.

operon
type: Class
subclass of: nucleic acid part
subclass of: Restriction
  on property: is proper part of
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has component part
  some values from: gene
subclass of: Restriction
  on property: is transcribed into
  some values from: RNA transcript
description: An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA.
similar to: SO:0000178

gene regulatory component
type: Class
subclass of: gene component
subclass of: Restriction
  on property: has function
  some values from: to regulate
description: A gene regulatory component is a gene component that exerts a regulatory function.

gene enhancer
type: Class
subclass of: gene regulatory component
description: A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster.

inactive ingredient
type: Class
subclass of: A pharmaceutical ingredient is a part of a pharmaceutical preparation.
description: Aninactive ingredient is a molecular entity that does not exhibit biological activity.

to serve as a template for molecular synthesis
type: Class
subclass of: to serve as
description: to serve as a template for molecular synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which another molecule may be produced.

to serve as a template for protein synthesis
type: Class
subclass of: to serve as a template for molecular synthesis
description: to serve as a template for protein synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a protein may be produced.

to serve as a template for RNA synthesis
type: Class
subclass of: to serve as a template for molecular synthesis
description: to serve as a template for RNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which an RNA molecule may be produced.

to serve as a template for DNA synthesis
type: Class
subclass of: to serve as a template for molecular synthesis
description: to serve as a template for DNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a DNA molecule may be produced.

deoxyribonucleic acid template
type: Class
subclass of: deoxyribonucleic acid
subclass of: Restriction
  on property: has function
  some values from: Class
    union of: to serve as a template for RNA synthesis
    union of: to serve as a template for DNA synthesis
description: A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription.

deoxyribonucleic acid primer
type: Class
subclass of: primer
subclass of: deoxyribonucleic acid
subclass of: Restriction
  on property: has function
  some values from: to serve as a template for DNA synthesis
description: A deoxyribonucleic acid primer is a deoxyribonucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.

to serve as a primer for DNA synthesis
type: Class
subclass of: to serve as
description: to serve as a primer for DNA synthesis is the capability of a short nucleic acid to bind to the 5' end of single strand of DNA template and help initiate DNA replication.

RNA transcript component
type: Class
subclass of: nucleic acid part
subclass of: Restriction
  on property: is part of
  some values from: messenger RNA
subclass of: Restriction
  on property: is proper part of
  some values from: RNA transcript
description: An RNA transcript component is a region of an RNA transcript.

mature mRNA
type: Class
subclass of: messenger RNA
subclass of: Class
  complement of: Restriction
    on property: has proper part
    some values from: intron
subclass of: Class
  complement of: Restriction
    on property: derives into
    some values from: RNA transcript
subclass of: Restriction
  on property: is derived from
  some values from: RNA transcript
subclass of: Restriction
  on property: is translated into
  some values from: protein
description: A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.

pre-mRNA
type: Class
subclass of: messenger RNA
subclass of: Restriction
  on property: derives into
  some values from: mature mRNA
description: Precursor mRNA (pre-mRNA) is a single strand of messenger ribonucleic acid (mRNA) that is synthesized from a DNA template throught transcription.

mRNA splice variant
type: Class
subclass of: messenger RNA
subclass of: Restriction
  on property: is derived from
  some values from: Class
    intersection of: messenger RNA
    intersection of: Restriction
      on property: has direct part
      some values from: splice site
description: An mRNA splice variant is an mRNA molecule that varies from another mRNA molecule of the same gene origin but having a different final sequence due to differences in its assembly from splice sites.

messenger RNA
type: Class
subclass of: RNA transcript
subclass of: Restriction
  on property: encodes
  some values from: protein
description: A messenger RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.

dna gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: is proper part of
  some values from: deoxyribonucleic acid
disjoint with: rna gene
description: A gene that is located on DNA.

rna gene
type: Class
subclass of: gene
subclass of: Restriction
  on property: is proper part of
  some values from: ribonucleic acid
description: A gene that is located on RNA.

allele
type: Class
subclass of: gene
subclass of: Restriction
  on property: is variant of
  some values from: gene
description: An allele is one of a set of sequence variants of a gene.

ploidy
type: Class
subclass of: cellular quality
description: ploidy is the cellular quality relating to the amount of DNA contained in a cell.

chemical transport
type: Class
subclass of: transporting
subclass of: Restriction
  on property: has participant
  some values from: chemical entity
description: chemical transport is the directed movement of a chemical entity by some agent (e.g. transporter).
equivalent to: biopax:Transport

active transport
type: Class
subclass of: membrane transport
description: active transport is the movement of a substance across a membrane against its concentration gradient (from low to high concentration) and requires chemical energy.
equivalent to: biopax:TransportWithBiochemicalReaction

molecular complex formation
type: Class
subclass of: chemical synthesis
subclass of: Restriction
  on property: has product
  some values from: molecular complex
description: molecular complex formation is the process of forming a molecular complex from its constituent parts.

molecular complex dissociation
type: Class
subclass of: chemical destruction
subclass of: Restriction
  on property: has target
  some values from: molecular complex
description: molecular complex disassociation is the process of dissambly of a molecular complex into its constitutent parts.

regulation of biochemical process
type: Class
subclass of: regulation of process
description: regulation of biochemical process is a process that changes the frequency, rate or extent of a target biochemical process.

biochemical activation
type: Class
subclass of: regulation of catalytic capability
subclass of: Restriction
  on property: realizes
  some values from: to decrease the rate of formation
disjoint with: biochemical inhibition
description: biochemical activation is a molecular interaction that increases the catalytic rate of the target enzyme.

biochemical inhibition
type: Class
subclass of: regulation of catalytic capability
subclass of: Restriction
  on property: realizes
  some values from: to increase the activation energy
description: biochemical inhibition is a molecular interaction that decreases the catalytic rate of the target enzyme.

process up-regulation
type: Class
subclass of: regulation of process
disjoint with: process down-regulation
description: process up-regulation is a process that increases the frequency, rate or extent of one or more processes in relation to a reference state.
alternative: positive regulation

process down-regulation
type: Class
subclass of: regulation of process
description: process down-regulation is a process that decreases the frequency, rate or extent of one or more processes in relation to a reference state.
alternative: negative regulation

medical data
type: Class
subclass of: biological data
description: medical data is data of interest to medicine.

disease
type: Class
subclass of: biological quality
subclass of: Restriction
  on property: is quality of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has quality
      some values from: abnormal
description: disease is the outward manifestation of one or more disorders.

transcription
type: Class
subclass of: biosynthesis
subclass of: Restriction
  on property: has output
  some values from: Class
    intersection of: ribonucleic acid
    intersection of: Restriction
      on property: is transcribed from
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has input
  some values from: deoxyribonucleic acid
description: transcription is the process of creating a complementary RNA copy of a sequence of DNA.

translation
type: Class
subclass of: biosynthesis
subclass of: Restriction
  on property: has input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has product
  some values from: polypeptide
description: translation is the process of producing a polypeptide from a ribonucleic acid by a ribosome.

molecular modification
type: Class
subclass of: chemical reaction
description: Molecular modification is chemical alteration of a known and previously characterized lead compound for the purpose of enhancing its usefulness as a drug. This could mean enhancing its specificity for a particular body target site, increasing its potency, improving its rate and extent of absorption, modifying to advantage its time course in the body, reducing its toxicity, changing its physical or chemical properties (like solubility) to provide desired features.

metabolism
type: Class
subclass of: chemical interaction
description: Metabolism is the set of chemical processes that occur within a living organism in order to maintain life.

catabolism
type: Class
subclass of: metabolism
disjoint with: anabolism
description: Anabolism is the set of metabolic processes that take apart larger chemical entities units into smaller chemical entities.

anabolism
type: Class
subclass of: metabolism
description: Anabolism is the set of metabolic processes that construct larger chemical entities units from smaller chemical entities.

carbohydrate residue
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: carbohydrate
subclass of: Restriction
  on property: is derived from
  some values from: monosaccharide
description: A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule.

nucleic acid part
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: nucleic acid
subclass of: Restriction
  on property: has direct part
  some values from: nucleotide residue
description: A nucleic acid part is a component of a nucleic acid.

deoxyribonucleotide residue
type: Class
subclass of: nucleotide residue
disjoint with: ribonucleotide residue
description: A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide.

ribonucleotide residue
type: Class
subclass of: nucleotide residue
description: A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide.

A pharmaceutical ingredient is a part of a pharmaceutical preparation.
type: Class
equivalent class: Class
  intersection of: ingredient
  intersection of: Restriction
    on property: is part of
    some values from: pharmaceutical drug
subclass of: ingredient
subclass of: Restriction
  on property: is proper part of
  some values from: pharmaceutical drug
label: pharmaceutical ingredient

to covalently modify
type: Class
subclass of: to change materially
description: to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms.

chemical complex
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is weakly interacting with
    some values from: material entity
description: A chemical complex is a chemical substance composed of a weakly connected molecules and ions in a known stoichiometry.

enzyme
type: Class
equivalent class: Class
  intersection of: Class
    union of: protein
    union of: protein complex
  intersection of: Restriction
    on property: has function
    some values from: Class
      intersection of: to covalently modify
      intersection of: Restriction
        on property: is realized in
        some values from: chemical reaction
      intersection of: Restriction
        on property: in relation to
        some values from: chemical entity
subclass of: protein
subclass of: Class
  union of: protein
  union of: protein complex
description: An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction.

catalyst
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has capability
  some values from: to regulate the rate of formation
subclass of: Restriction
  on property: has capability
  some values from: to reduce the activation energy
description: A catalyst is a molecule that has the capability to reduce the activation energy of a reaction and hence increase the overall rate of reaction.

chemical reaction
type: Class
subclass of: chemical interaction
subclass of: Class
  intersection of: Restriction
    on property: has proper part
    some values from: chemical synthesis
  intersection of: Restriction
    on property: has proper part
    some values from: chemical destruction
description: A chemical reaction is a process that leads to the transformation of one set of chemical substances to another.

organic polymer
type: Class
equivalent class: Class
  intersection of: organic molecule
  intersection of: Restriction
    on property: has direct part
    some values from: monomer
  intersection of: Restriction
    on property: has direct part
    some values from: organic submolecule
subclass of: organic molecule
subclass of: Restriction
  on property: has direct part
  some values from: organic submolecule
description: An organic polymer is an organic molecule composed of connected set of monomeric units.

to modify conformation of
type: Class
subclass of: to modify
description: to modify conformation of is to affect the spatial arrangement of an entity.

to cleave
type: Class
subclass of: to disassemble
description: to cleave is to split or sever an object along a natural line or grain.

to combine
type: Class
subclass of: to change materially
description: to combine is the capability to modify a set of objects in a way that the object is merged with another object to form a new object or substance.

to breathe
type: Class
subclass of: capability
description: to breathe is the capability to inhale and exhale air into the body during respiration.

to conformationally activate
type: Class
subclass of: to modify conformation of
description: to conformationally activate is to modify the conformation of an entity in such a way that it becomes activated or functional.

to conformationally inhibit
type: Class
subclass of: to modify conformation of
description: to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited.

to oxidize
type: Class
subclass of: to modify oxidation state of
description: to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity.

to reduce
type: Class
subclass of: to modify oxidation state of
description: to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity.

to modify oxidation state of
type: Class
subclass of: to modify electronically
description: to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion.

substrate
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: derives into
    some values from: product
  intersection of: Restriction
    on property: is target in
    some values from: chemical reaction
subclass of: target
description: A substrate is a molecule that is consumed in the course of a biochemical reaction.

product
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: is output of
    some values from: chemical reaction
  intersection of: Restriction
    on property: is derived from
    some values from: substrate

to be modified
type: Class
subclass of: to be actively interacted with
description: to be modified is the capability to be actively interacted with in such a way that it leads to a physical reconfiguration.

to be cleaved
type: Class
subclass of: to be modified
description: to be cleaved is the capability to be modified in a way that splits one part of the object from the other.

to be covalently modified
type: Class
subclass of: to be modified
description: to be covalently modified is the capability of a chemical entity to have bonds added or removed

to be combined
type: Class
subclass of: to be modified
description: to be combined is the capability to be modified in a way that the object is merged with another object to form a new object or substance.

to be transported
type: Class
subclass of: to be actively interacted with
description: to be transported is the disposition to undergo motion.

to be electronically modified
type: Class
subclass of: to be modified
description: to be electronically modified is the capability of a chemical entity to have electrons added or removed.

to gain an electron
type: Class
subclass of: to be electronically modified
description: to gain an electron is the capability of a chemical entity to receive an electron.

to lose an electron
type: Class
subclass of: to be electronically modified
description: to lose an electron is the capability of a chemical entity to lose an electron.

to be activated
type: Class
subclass of: to be conformationally changed
description: to be activated is the capability to be modified in such a way that the conformational change leads to an increase in another capability.

to be inhibited
type: Class
subclass of: to be conformationally changed
description: to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability.

to be conformationally changed
type: Class
subclass of: to be modified
description: to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed.

multicellular organism
type: Class
subclass of: cellular organism
subclass of: Restriction
  on property: has proper part
  min qualified cardinality: 2
  on class: cell
disjoint with: unicellular organism
description: A multi-cellular organism is an organism that consists of more than one cell.

unicellular organism
type: Class
subclass of: cell
subclass of: cellular organism
subclass of: Class
  complement of: Restriction
    on property: is proper part of
    some values from: biological entity
description: A unicellular organism is a organism that is composed of a single cell.

cellular organism
type: Class
equivalent class: Class
  union of: multicellular organism
  union of: unicellular organism
subclass of: organism
disjoint with: non-cellular organism
description: A cellular organism is an organism that contains one or more cells.

non-cellular organism
type: Class
subclass of: organism
description: A non-cellular organism is an organism that does not contain a cell.

virus
type: Class
subclass of: non-cellular organism
description: A virus is a non-cellular organism that can replicate only inside the living cells of an organism.

drug regulatory authority
type: Class
subclass of: regulatory authority
description: A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals.

specialized material entity
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has realizable property
    some values from: realizable entity
subclass of: specialized object
description: A specialized material entity is a material entity that is defined by having some quality, role or capability.

reagent
type: Class
subclass of: heterogeneous substance
description: A reagent is a substance that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs.

specimen
type: Class
subclass of: sample
description: A specimen is a portion of material for use in testing, examination, or study.

pathogen
type: Class
subclass of: organism
description: A pathogen or infectious agent is a microorganism that causes disease in its host.

host
type: Class
subclass of: organism
description: A host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter.

buffer
type: Class
subclass of: liquid solution component
description: A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base.

solvent
type: Class
subclass of: liquid solution component
description: A solvent is a substance that can dissolve other substances (solutes).

solute
type: Class
subclass of: liquid solution component
description: A solute is a substance that becomes dissolved in a solvent.

antigen
type: Class
subclass of: molecule
description: An antigen is a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor.

receptor
type: Class
subclass of: signal transducer
description: A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal.

target
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: is target in
    some values from: process

centrifugation pellet
type: Class
subclass of: centrifugation substance
disjoint with: supernatant
description: A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge.

supernatant
type: Class
subclass of: centrifugation substance
description: A supernatent is a liquid substance that remains after centrifugation.

centrifugation substance
type: Class
subclass of: chemical substance
description: A centrifugation substance is a substance that is the target or product of centrifugation.

liquid solution component
type: Class
subclass of: heterogeneous substance
description: A liquid solution component is a part of a liquid solution.

evaluation role
type: Class
subclass of: investigational role
description: An evaluation role is a processual role held by an entity during some evaluation.

placebo
type: Class
subclass of: heterogeneous substance
description: A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient.

test role
type: Class
subclass of: evaluation role
description: A test role is the role of an individual that is a participant in the study and is the target of the intervention.

control role
type: Class
subclass of: evaluation role
description: A control role is the role of an individual that is part of a study, but is not subject to the intervention that is to be tested.

ligand
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Class
    intersection of: Restriction
      on property: is direct part of
      some values from: molecular complex
    intersection of: Restriction
      on property: is weakly interacting with
      some values from: molecule
description: A ligand is a molecule that is part of a complex by weakly interacting with another molecule.

low barrier hydrogen bond
type: Class
subclass of: hydrogen bond
description: A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms.

activator
type: Class
subclass of: molecular regulator
description: A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality.

inhibitor
type: Class
subclass of: molecular regulator
description: A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality.

molecular regulator
type: Class
subclass of: molecule
subclass of: Restriction
  on property: has capability
  some values from: Class
    intersection of: to regulate
    intersection of: Restriction
      on property: in relation to
      some values from: chemical entity
description: A molecular regulator is a molecule that regulates the function of another chemical entity.

signal transducer
type: Class
subclass of: molecule
description: A signal transducer is a molecule that responds to and amplifies a signal in a signalling system.

signal
type: Class
subclass of: molecule
description: A signal is an object that initiates a sequence of events.

messenger
type: Class
subclass of: signal transducer
description: A mesenger is a molecule involved in either signal detection or signal propagation from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.

second messenger
type: Class
subclass of: messenger
description: A second messenger is a molecule that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.

submolecule
type: Class
subclass of: submolecular entity
subclass of: Restriction
  on property: is component part of
  some values from: molecule
subclass of: Restriction
  on property: has component part
  some values from: atom
description: A submolecule is any part of a molecule.

charge quality
type: Class
equivalent class: Class
  union of: charged
  union of: uncharged
subclass of: chemical quality
description: charge quality is the quality pertaining to electric charge.

intron
type: Class
subclass of: gene component
subclass of: Restriction
  on property: is proper part of
  some values from: gene
description: An intron is a region of a gene that is removed from the final protein open reading frame.

gene component
type: Class
subclass of: nucleic acid part
subclass of: Restriction
  on property: is proper part of
  some values from: gene
description: A gene component is a component of a gene.

exon
type: Class
subclass of: gene component
description: An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing.

gene promoter
type: Class
subclass of: gene regulatory component
description: A gene promoter is a region of DNA that initiates transcription of a particular gene.

start codon
type: Class
subclass of: RNA transcript component
disjoint with: stop codon
description: A start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon is almost always preceded by an untranslated region 5' UTR.

stop codon
type: Class
subclass of: RNA transcript component
subclass of: Restriction
  on property: is part of
  some values from: messenger RNA
description: A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.

RNA transcript
type: Class
subclass of: ribonucleic acid
subclass of: Restriction
  on property: is transcribed from
  some values from: Class
    union of: deoxyribonucleic acid
    union of: Restriction
      on property: is part of
      some values from: deoxyribonucleic acid
description: An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template.

splice site
type: Class
subclass of: RNA transcript component
description: A splice site is a region required for the excision of an intron and connection to another exon.

molecular pocket
type: Class
subclass of: molecular site
description: A molecular pocket is a site on a molecule that appears as a depression into the structure.

acid
type: Class
subclass of: liquid solution component
description: An acid is a molecular entity in solution capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).

base
type: Class
subclass of: liquid solution component
description: A base is a molecular entity dissolved in a solvent that is capable of accepting a proton (Bronsted base) or forming a covalent bond with a hydron (Lewis base) .

isomer
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: is variant of
    some values from: molecule
description: An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity.

ion
type: Class
equivalent class: Class
  intersection of: Class
    union of: atom
    union of: molecule
  intersection of: Restriction
    on property: has quality
    some values from: charge quality
subclass of: chemical entity
description: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge.

cation
type: Class
equivalent class: Class
  intersection of: ion
  intersection of: Restriction
    on property: has quality
    some values from: positive charge
description: An anion is an atom or molecule with a net positive electrical charge.

anion
type: Class
equivalent class: Class
  intersection of: ion
  intersection of: Restriction
    on property: has quality
    some values from: negative charge
description: An anion is an atom or molecule with a net negative electrical charge.

polar solvent
type: Class
subclass of: solvent
subclass of: Restriction
  on property: has quality
  some values from: polar
disjoint with: nonpolar solvent
description: A polar solvent is a solvent that exhibits a polar quality.

nonpolar solvent
type: Class
subclass of: solvent
subclass of: Restriction
  on property: has quality
  some values from: non-polar
description: A non-polar solvent is a solvent that exhibits a non-polar quality.

positive charge
type: Class
subclass of: complete charge
disjoint with: negative charge
description: A positive charge is a charge where the value is positive.

heterogeneous substance
type: Class
subclass of: chemical substance
disjoint with: homogeneous substance
description: A heterogeneous substance is a chemical substance that is composed of more than one different kind of component.

homogeneous substance
type: Class
subclass of: chemical substance
description: A homogeneous substance is a substance that is composed of a uniform type of entity.

negative charge
type: Class
subclass of: complete charge
description: A negative charge is a charge where the value is negative.

antibody
type: Class
subclass of: protein complex
description: An antibody (also known as immunoglobulins, abbreviated Ig) are gamma globulin proteins that are used by the immune system to identify and neutralize foreign objects. They are typically made of two large heavy chains and two small light chains.

alpha helix
type: Class
subclass of: amino acid polymer submolecule
description: An alpha helix is structural region of a protein that is characterized by 3.6 residues per turn, a translation of 1.5 angstroms along the helical axis in which backbone N-H groups form a hydrogen bond to the backbone carboxyl group of the amino acid four residues prior.

beta strand
type: Class
subclass of: amino acid polymer submolecule
description: A beta strand is structural region of a protein that is characterized by a roughly planar sequence of amino acid residues forming hydrogen bonds between the N-O and the C=O of another part of the peptide and having their side chains perpendicular to the planar axis.

amino acid polymer submolecule
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: amino acid polymer
description: An amino acid polymer submolecule is a submolecule of an amino acid polymer.

ionic interaction
type: Class
subclass of: weak submolecular component
description: An ionic interaction is a weak submolecular interaction between a charged submolecules.

protein complex
type: Class
subclass of: molecular complex
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 2
  on class: polypeptide
description: A protein complex is a molecular complex composed of at least two polypeptide chains.

single bond
type: Class
subclass of: covalent bond
description: A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared.

double bond
type: Class
subclass of: covalent bond
description: A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared.

triple bond
type: Class
subclass of: covalent bond
description: A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared.

aromatic bond
type: Class
subclass of: covalent bond
description: An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared.

disulfide bond
type: Class
subclass of: single bond
description: A disulfide bond is a bond between two sulfur atoms.

dipole-dipole interaction
type: Class
subclass of: weak submolecular component
description: A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms.

van der Waals interaction
type: Class
subclass of: weak submolecular component
description: van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole.

base stack
type: Class
subclass of: weak submolecular component
description: A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces.

molecular complex
type: Class
subclass of: chemical complex
subclass of: Restriction
  on property: has direct part
  some values from: molecule
description: A molecular complex is a chemical complex composed of at least one weakly interacting molecule.

acid-base reaction
type: Class
subclass of: chemical reaction
description: An acid-base reaction is a chemical reaction between an acid and a base.

catalyzed reaction
type: Class
subclass of: chemical reaction
subclass of: Restriction
  on property: has agent
  some values from: catalyst
description: A catalyzed reaction is a chemical reaction that is facilitated by a catalyst.

redox reaction
type: Class
subclass of: chemical reaction
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: to oxidize
      intersection of: Restriction
        on property: is disposition of
        some values from: molecule
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: to reduce
      intersection of: Restriction
        on property: is disposition of
        some values from: molecule
description: A redox reaction is a chemical reaction in which there is a net movement of electrons from one reactant to another.

inorganic reaction
type: Class
subclass of: chemical reaction
description: An inorganic reaction is a chemical reaction that involves the transformation of inorganic molecules.

decomposition reaction
type: Class
subclass of: inorganic reaction
description: A decomposition reaction is an inorganic reaction in which molecule is fragmented into submolecules or atoms.

displacement reaction
type: Class
subclass of: inorganic reaction
description: A displacement reaction is an inorganic reaction in which a elementary substance displaces and sets free a constituent atom from a molecule.

double displacement reaction
type: Class
subclass of: displacement reaction
description: A double displacement reaction is a displacement reaction in which two molecules swap ions, effectively displacing each other to form two new molecules.

single displacement reaction
type: Class
subclass of: displacement reaction
description: A single displacement reaction where one atom is transferred out of one molecule and into another.

synthesis reaction
type: Class
subclass of: inorganic reaction
description: A synthesis reaction is an inorganic reaction in which two or more molecules are chemically bonded together to produce a single product.

organic reaction
type: Class
subclass of: chemical reaction
description: An organic reaction is a chemical reaction involving at least one organic molecule.

isomerization reaction
type: Class
subclass of: chemical reaction
description: An isomerization reaction is a chemical reaction in which a molecule is converted into its isomer.

addition reaction
type: Class
subclass of: organic reaction
description: An addition reaction is an organic reaction where two or more molecules combine to form a larger one. Addition reactions are limited to chemical compounds that have multiply-bonded atoms: * Molecules with carbon-carbon double bonds or triple bonds * Molecules with carbon - hetero double bonds like C=O or C=N

polar addition reaction
type: Class
subclass of: addition reaction
description: A polar addition reaction is an addition reaction involving polar residues.

non-polar addition reaction
type: Class
subclass of: addition reaction
description: A non-polar addition reaction is an addition reaction involving non-polar residues.

free radical addition
type: Class
subclass of: non-polar addition reaction
description: A free radical addition is a non-polar addition reaction involving free radicals.

nucleophilic addition reaction
type: Class
subclass of: polar addition reaction
description: A nucleophilic addition reaction is an addition reaction where a pi bond is removed by the creation of two new covalent bonds by the addition from a nucleophile.

electrophilic addition reaction
type: Class
subclass of: polar addition reaction
description: An electrophilic addition reaction is a polar addition reaction where a pi bond is removed by the creation of two new covalent bonds.

biochemical pathway
type: Class
subclass of: chemical reaction pathway
description: A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome.

chemical reaction pathway
type: Class
subclass of: pathway
subclass of: Restriction
  on property: specifies
  some values from: Restriction
    on property: has proper part
    some values from: chemical reaction
subclass of: Restriction
  on property: is model of
  some values from: process
subclass of: Restriction
  on property: has member
  all values from: chemical reaction
description: A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product.

chemical synthesis pathway
type: Class
subclass of: chemical reaction pathway
description: A chemical synthesis pathway is a pathway involved in the assembly of a chemical.

chemical degradation pathway
type: Class
subclass of: chemical reaction pathway
description: A chemical degradation pathway is a pathway involved in the disassembly of a chemical.

3d structure model
type: Class
subclass of: tertiary structure descriptor
description: A 3D structure model is a representation of the spatial arrangement of one or more chemical entities.

sequence profile
type: Class
subclass of: pattern
description: A sequence profile is provides the preference for a character at each position of an abstracted sequence.

metabolic pathway
type: Class
subclass of: biochemical pathway
disjoint with: regulatory pathway
description: A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products.

regulatory pathway
type: Class
subclass of: biochemical pathway
description: A regulatory pathway is a series of biochemical reactions that lead to the increase or decrease of activity of participating molecular components.

medical history
type: Class
subclass of: history
description: A medical history is a record of the events of a recipient of medical care.

binary compound
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has direct part
  qualified cardinality: 2
  on class: molecule
description: A binary compound is a mereological maximum sum of two kinds of weakly connected entities.

stereoisomer
type: Class
subclass of: isomer
description: A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms.

diastereomer
type: Class
subclass of: stereoisomer
description: A diastereomer is a stereoisomer that is not a mirror image of its isomer.

enantiomer
type: Class
subclass of: stereoisomer
description: An enantiomer is a stereoisomer that is a mirror image of its isomer.

optical isomer
type: Class
subclass of: stereoisomer
description: An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light.

structural isomer
type: Class
subclass of: isomer
description: A structural isomer is an isomer in which the atoms are joined together in different ways.

ring
type: Class
equivalent class: Class
  union of: heterocyclic ring
  union of: homocyclic ring
subclass of: chemical functional group
subclass of: Restriction
  on property: has component part
  min qualified cardinality: 3
  on class: atom
description: A ring is a submolecule with a circular topology.

aromatic ring
type: Class
subclass of: ring
description: An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring.

heterocyclic ring
type: Class
subclass of: ring
disjoint with: homocyclic ring
description: A heterocyclic ring is a ring containing a hetero atom.

homocyclic ring
type: Class
subclass of: ring
description: A homocyclic ring is a ring where the atoms are of a single type.

ionic compound
type: Class
subclass of: binary compound
subclass of: Restriction
  on property: has direct part
  qualified cardinality: 1
  on class: cation
subclass of: Restriction
  on property: has direct part
  qualified cardinality: 1
  on class: anion
description: An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions.

allotrope
type: Class
subclass of: chemical element
description: An allotrope is a structural variant of a chemical element.

carbon allotrope
type: Class
subclass of: allotrope
subclass of: Restriction
  on property: has direct part
  all values from: carbon atom
description: A carbon allotrope is a chemical substance composed of carbon.

diamond
type: Class
subclass of: carbon allotrope
description: diamond is a carbon allotrope in which each carbon atom in diamond is covalently bonded to four other carbons in a tetrahedron. These tetrahedrons together form a 3-dimensional network of puckered six-membered rings of atoms.

graphite
type: Class
subclass of: carbon allotrope
description: graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon.

fullerene
type: Class
subclass of: carbon allotrope
description: fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube.

aggregated carbon nanorods
type: Class
subclass of: carbon allotrope
description: aggregate of carbon nanorods is an allotrope of carbon considered to be the least compressible material known, as measured by its isothermal bulk modulus; aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), while a conventional diamond has a modulus of 442 GPa. ADNRs are also 0.3% denser than regular diamond.

amorphous carbon
type: Class
subclass of: carbon allotrope
description: amorphous carbon is an allotrope of carbon that does not have any crystalline structure. As with all glassy materials, some short-range order can be observed, but there is no long-range pattern of atomic positions.

carbon nanofoam
type: Class
subclass of: carbon allotrope
description: carbon nanofoam is an allotrope of carbon that consists of a low-density cluster-assembly of carbon atoms strung together in a loose three-dimensional web. Each cluster is about 6 nanometers wide and consists of about 4000 carbon atoms linked in graphite-like sheets that are given negative curvature by the inclusion of heptagons among the regular hexagonal pattern.

chaoite
type: Class
subclass of: carbon allotrope
description: chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white.

glassy carbon
type: Class
subclass of: carbon allotrope
description: glassy carbon is an allotrope of carbon which is widely used as an electrode material in electrochemistry, as well as for high temperature crucibles and as a component of some prosthetic devices.

ionsdaleite
type: Class
subclass of: carbon allotrope
description: ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond.

boron atom
type: Class
subclass of: atom
see also: CHEBI:27560

carbon atom
type: Class
subclass of: atom
see also: CHEBI:27594

hydrogen atom
type: Class
subclass of: atom
see also: CHEBI:49637

helium atom
type: Class
subclass of: atom
see also: CHEBI:30217

lithium atom
type: Class
subclass of: atom
see also: CHEBI:30145

beryllium atom
type: Class
subclass of: atom
see also: CHEBI:30501

nitrogen atom
type: Class
subclass of: atom
see also: CHEBI:25555

oxygen atom
type: Class
subclass of: atom
see also: CHEBI:25805

fluorine atom
type: Class
subclass of: atom
see also: CHEBI:24061

neon atom
type: Class
subclass of: atom
see also: CHEBI:33310

sodium atom
type: Class
subclass of: atom
see also: CHEBI:26708

magnesium atom
type: Class
subclass of: atom
see also: CHEBI:25107

aluminium atom
type: Class
subclass of: atom
see also: CHEBI:28984

silicon atom
type: Class
subclass of: atom
see also: CHEBI:27573

phosphorus atom
type: Class
subclass of: atom
see also: CHEBI:28659

sulfur atom
type: Class
subclass of: atom
see also: CHEBI:26833

chlorine atom
type: Class
subclass of: atom
see also: CHEBI:23116

argon atom
type: Class
subclass of: atom
see also: CHEBI:49475

potassium atom
type: Class
subclass of: atom
see also: CHEBI:26216

calcium atom
type: Class
subclass of: atom
see also: CHEBI:22984

scandium atom
type: Class
subclass of: atom
see also: CHEBI:33330

titanium atom
type: Class
subclass of: atom
see also: CHEBI:33341

vanadium atom
type: Class
subclass of: atom
see also: CHEBI:27698

chromium atom
type: Class
subclass of: atom
see also: CHEBI:28073

manganese atom
type: Class
subclass of: atom
see also: CHEBI:18291

iron atom
type: Class
subclass of: atom
see also: CHEBI:18248

cobalt atom
type: Class
subclass of: atom
see also: CHEBI:27638

nickel atom
type: Class
subclass of: atom
see also: CHEBI:28112

copper atom
type: Class
subclass of: atom
see also: CHEBI:28694

zinc atom
type: Class
subclass of: atom
see also: CHEBI:27363

gallium atom
type: Class
subclass of: atom
see also: CHEBI:49631

germanium atom
type: Class
subclass of: atom
see also: CHEBI:30441

arsenic atom
type: Class
subclass of: atom
see also: CHEBI:27563

selenium atom
type: Class
subclass of: atom
see also: CHEBI:27568

bromine atom
type: Class
subclass of: atom
see also: CHEBI:22927

krypton atom
type: Class
subclass of: atom
see also: CHEBI:49696

rubidium atom
type: Class
subclass of: atom
see also: CHEBI:33322

strontium atom
type: Class
subclass of: atom
see also: CHEBI:33324

yttrium atom
type: Class
subclass of: atom
see also: CHEBI:33331

zirconium atom
type: Class
subclass of: atom
see also: CHEBI:33342

niobium atom
type: Class
subclass of: atom
see also: CHEBI:33344

molybdemum atom
type: Class
subclass of: atom
see also: CHEBI:28685

technetium atom
type: Class
subclass of: atom
see also: CHEBI:33353

ruthenium atom
type: Class
subclass of: atom
see also: CHEBI:30682

rhodium atom
type: Class
subclass of: atom
see also: CHEBI:33359

palladium atom
type: Class
subclass of: atom
see also: CHEBI:33363

silver atom
type: Class
subclass of: atom
see also: CHEBI:30512

cadmium atom
type: Class
subclass of: atom
see also: CHEBI:22977

indium atom
type: Class
subclass of: atom
see also: CHEBI:30430

tin atom
type: Class
subclass of: atom
see also: CHEBI:27007

antimony atom
type: Class
subclass of: atom
see also: CHEBI:30513

tellurium atom
type: Class
subclass of: atom
see also: CHEBI:30452

iodine atom
type: Class
subclass of: atom
see also: CHEBI:24859

xenon atom
type: Class
subclass of: atom
see also: CHEBI:49957

caesium atom
type: Class
subclass of: atom
see also: CHEBI:30514

barium atom
type: Class
subclass of: atom
see also: CHEBI:32594

lanthanum atom
type: Class
subclass of: atom
see also: CHEBI:33336

hafnium atom
type: Class
subclass of: atom
see also: CHEBI:33343

tantalum atom
type: Class
subclass of: atom
see also: CHEBI:33348

tungsten atom
type: Class
subclass of: atom
see also: CHEBI:27998

rhenium atom
type: Class
subclass of: atom
see also: CHEBI:49882

osmium atom
type: Class
subclass of: atom
see also: CHEBI:30687

iridium atom
type: Class
subclass of: atom
see also: CHEBI:49666

platinum atom
type: Class
subclass of: atom
see also: CHEBI:33364

gold atom
type: Class
subclass of: atom
see also: CHEBI:29287

mercury atom
type: Class
subclass of: atom
see also: CHEBI:25195

thallium atom
type: Class
subclass of: atom
see also: CHEBI:49920

lead atom
type: Class
subclass of: atom
see also: CHEBI:25016

bismuth atom
type: Class
subclass of: atom
see also: CHEBI:33301

polonium atom
type: Class
subclass of: atom
see also: CHEBI:33313

astatine atom
type: Class
subclass of: atom
see also: CHEBI:30415

radon atom
type: Class
subclass of: atom
see also: CHEBI:33314

francium atom
type: Class
subclass of: atom
see also: CHEBI:33323

radium atom
type: Class
subclass of: atom
see also: CHEBI:33325

actinium atom
type: Class
subclass of: atom
see also: CHEBI:33337

rutherfordium atom
type: Class
subclass of: atom
see also: CHEBI:33346

dubnium atom
type: Class
subclass of: atom
see also: CHEBI:33349

seaborgium atom
type: Class
subclass of: atom
see also: CHEBI:33351

bohrium atom
type: Class
subclass of: atom
see also: CHEBI:33355

hassium atom
type: Class
subclass of: atom
see also: CHEBI:33357

meitnerium atom
type: Class
subclass of: atom
see also: CHEBI:33361

darmstadtium atom
type: Class
subclass of: atom
see also: CHEBI:33367

roentgenium atom
type: Class
subclass of: atom
see also: CHEBI:33368

copernicium atom
type: Class
subclass of: atom
see also: CHEBI:33517

unutrium atom
type: Class
subclass of: atom

ununquadium atom
type: Class
subclass of: atom

ununpentium atom
type: Class
subclass of: atom

ununhexium atom
type: Class
subclass of: atom

ununseptium atom
type: Class
subclass of: atom

ununoctium atom
type: Class
subclass of: atom

cerium atom
type: Class
subclass of: atom
see also: CHEBI:33369

praseodymium atom
type: Class
subclass of: atom
see also: CHEBI:49828

neodymium atom
type: Class
subclass of: atom
see also: CHEBI:33372

promethium atom
type: Class
subclass of: atom
see also: CHEBI:33373

samarium atom
type: Class
subclass of: atom
see also: CHEBI:33374

europium atom
type: Class
subclass of: atom
see also: CHEBI:32999

gadolinium atom
type: Class
subclass of: atom
see also: CHEBI:33375

terbium atom
type: Class
subclass of: atom
see also: CHEBI:33376

dysprosium atom
type: Class
subclass of: atom
see also: CHEBI:33377

holmium atom
type: Class
subclass of: atom
see also: CHEBI:49648

erbium atom
type: Class
subclass of: atom
see also: CHEBI:33379

thulium atom
type: Class
subclass of: atom
see also: CHEBI:33380

ytterbium atom
type: Class
subclass of: atom
see also: CHEBI:33381

lutetium atom
type: Class
subclass of: atom
see also: CHEBI:33382

thorium atom
type: Class
subclass of: atom
see also: CHEBI:33385

protactinium atom
type: Class
subclass of: atom
see also: CHEBI:33386

uranium atom
type: Class
subclass of: atom
see also: CHEBI:27214

neptunium atom
type: Class
subclass of: atom
see also: CHEBI:33387

plutonium atom
type: Class
subclass of: atom
see also: CHEBI:33388

americium atom
type: Class
subclass of: atom
see also: CHEBI:33389

curium atom
type: Class
subclass of: atom
see also: CHEBI:33390

berkelium atom
type: Class
subclass of: atom
see also: CHEBI:33391

californium atom
type: Class
subclass of: atom
see also: CHEBI:33392

einsteinium atom
type: Class
subclass of: atom
see also: CHEBI:33393

fermium atom
type: Class
subclass of: atom
see also: CHEBI:33394

mendelevium atom
type: Class
subclass of: atom
see also: CHEBI:33395

nobelium atom
type: Class
subclass of: atom
see also: CHEBI:33396

lawrencium atom
type: Class
subclass of: atom
see also: CHEBI:33397

covalent bond
type: Class
subclass of: strong submolecular component
subclass of: Restriction
  on property: has component part
  qualified cardinality: 2
  on class: atom
description: A covalent bond is a strong submolecular interaction between atoms.
see also: CHEMINF:000063

biomolecular structure descriptor
type: Class
subclass of: molecular structure descriptor
subclass of: Restriction
  on property: is about
  some values from: organic molecule
description: A biomolecular structure descriptor is structure description for organic compounds.

molecular structure file
type: Class
subclass of: file
subclass of: Restriction
  on property: has part
  some values from: cartesian coordinate
subclass of: Restriction
  on property: has part
  some values from: molecular structure descriptor
subclass of: Restriction
  on property: is concretization of
  some values from: biomolecular structure descriptor
description: A molecular structure file is a file that contains a description of molecular structure.

molecular structure descriptor
type: Class
subclass of: chemical quality
subclass of: Restriction
  on property: represents
  some values from: molecular structure
subclass of: Restriction
  on property: is about
  some values from: molecule
description: molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity.
see also: CHEMINF:000085

chemical data
type: Class
subclass of: scientific data
description: A chemical datum is a scientific data item which conforms to some specification, either for how it is calculated or for how it is measured, and is commonly used in the domain of chemistry to name and differentiate different numeric properties (both calculated and measured) which are about chemical entities.
see also: CHEMINF:000123

molecule
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: has part
  some values from: atom
description: A molecule is single chemical entity composed of fully covalently bonded atoms.
see also: CHEBI:23367

chemical substance
type: Class
equivalent class: Class
  union of: heterogeneous substance
  union of: homogeneous substance
subclass of: chemical entity
description: A chemical substance is a chemical entity composed of two or more weakly interacting chemical entities.
alternative: mixture
see also: CHEMINF:440533

PDB file
type: Class
subclass of: molecular structure file
description: A PDB file is a molecular structure file specified by the Protein DataBank (PDB).

collection of 3d molecular structure models
type: Class
subclass of: collection
subclass of: Restriction
  on property: has member
  some values from: 3d structure model
description: A collection of 3D molecular structure models is just that.

min exclusive: 0.0

max exclusive: 0.0