INO: Interaction Network Ontology
type: Ontology
editor note: Product version
Contributor: Yu Lin (YL)
creator: Arzucan Ozgur
creator: Junguk Hur
creator: Yongqun "Oliver" He (YH)
creator: Zuoshuang "Allen" Xiang
date: 2022-03-27
description: he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.
Format: OWL-DL
subject: An ontology of interactions and interaction networks
version info: 1.1.13

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

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

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred term: example
editor preferred term: example of usage
has curation status: IAO_0000122
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

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

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: IAO_0000122
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: IAO_0000122
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: IAO_0000122
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative term
type: AnnotationProperty
editor preferred term: alternative term
has curation status: IAO_0000125
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: IAO_0000122
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

imported from
type: AnnotationProperty

expand expression to
type: AnnotationProperty

OBO foundry unique label
type: AnnotationProperty
has curation status: IAO_0000125

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

has associated axiom(nl)
type: AnnotationProperty

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

has literature mining keywords
type: AnnotationProperty
definition: an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition.
term editor: Yongqun He

example of literature mining keyword usage
type: AnnotationProperty
alternative term: literature mining example
creator: Yongqun He
creator: an example of usage for literature mining
sub property of: example of usage

has keyword dependency pattern
type: AnnotationProperty
definition: an annotation property that specifies the dependency pattern of the literature keywords that match to the ontology interaction type.
term editor: Arzucan Ozgur, Junguk Hur, Yongqun He

temporal interpretation
type: AnnotationProperty
definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

logical macro assertion
type: AnnotationProperty
definition: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

logical macro assertion on a property
type: AnnotationProperty
definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty
sub property of: logical macro assertion on a property

is direct form of
type: AnnotationProperty
definition: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
editor note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
definition: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is directional form of
type: AnnotationProperty
definition: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created by: cjm
creation date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created by: cjm
creation date: 2018-03-14T00:03:24Z
sub property of: is directional form of

is homeomorphic for
type: AnnotationProperty
example of usage: part-of is homeomorphic for independent continuants.
definition: R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
created by: cjm
creation date: 2018-10-21T19:46:34Z
comment: R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
sub property of: logical macro assertion on an object property

has_rank
type: AnnotationProperty
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in_subset
type: AnnotationProperty

label
type: AnnotationProperty

part of
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: ro.owl
temporal interpretation: RO_0001901
is homeomorphic for: continuant
is homeomorphic for: occurrent
is homeomorphic for: independent continuant
is homeomorphic for: realizable entity
is homeomorphic for: quality
is homeomorphic for: specifically dependent continuant
is homeomorphic for: generically dependent continuant
in_subset: valid for go annotation extension
in_subset: valid for go gp2term
in_subset: valid for go ontology
in_subset: valid for gocam

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
imported from: ro.owl
temporal interpretation: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

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

preceded by
type: ObjectProperty
sub property of: ends after
type: TransitiveProperty
editor preferred term: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
imported from: ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
editor preferred term: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
imported from: ro.owl
in_subset: ro-eco

has activator
type: ObjectProperty
definition: an object property between an activation process and a material entity that acts as an activator during the process.
term editor: Yongqun He

has_controller
type: ObjectProperty

controls
type: ObjectProperty

has_next_step
type: ObjectProperty

lacks part
type: ObjectProperty

has interaction type
type: ObjectProperty
example of usage: A host-pathogen interaction that has a specific interaction type (e.g., activation).
definition: An object property that represents a relation between an interaction process (domain) and another interaction process (range) where the interaction proces (domain) has a specific type of the other interaction process (range)
term editor: Yongqun He

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

before or simultaneous with
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
alternative term: <=
imported from: ro.owl
in_subset: ro-eco
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
term editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
term editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

during which ends
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
type: TransitiveProperty
term editor: David Osumi-Sutherland
alternative term: di
imported from: ro.owl
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
term editor: David Osumi-Sutherland
alternative term: starts_at_end_of
imported from: ro.owl
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

starts before
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
term editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco

immediately precedes
type: ObjectProperty
sub property of: precedes
term editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
imported from: ro.owl
is direct form of: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
alternative term: io
imported from: ro.owl
in_subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: starts during
sub property of: ends during
type: TransitiveProperty
term editor: David Osumi-Sutherland
alternative term: d
alternative term: during
imported from: ro.owl
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporally related to
term editor: David Osumi-Sutherland
alternative term: o
alternative term: overlaps
imported from: ro.owl
in_subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
has curation status: IAO_0000125
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: ro.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for gocam
in_subset: ro-eco

regulates
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
has curation status: IAO_0000125
definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
term editor: Chris Mungall
term editor: David Hill
term editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
imported from: ro.owl
OBO foundry unique label: regulates (processual)
elucidation: false
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
term editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: negatively regulates (process to process)
is negative form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
type: TransitiveProperty
definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
term editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: positively regulates (process to process)
is positive form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

temporally related to
type: ObjectProperty
has curation status: IAO_0000125
term editor: Chris Mungall
definition source: Allen's interval algebra
curator note: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
imported from: ro.owl
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

starts
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
has curation status: IAO_0000125
definition: inverse of starts with
term editor: Chris Mungall
definition source: Allen
imported from: ro.owl
in_subset: ro-eco

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: IAO_0000125
definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
term editor: Chris Mungall
alternative term: started by
imported from: ro.owl
in_subset: ro-eco

ends
type: ObjectProperty
sub property of: part of
sub property of: temporally related to
has curation status: IAO_0000125
definition: inverse of ends with
term editor: Chris Mungall
imported from: ro.owl
in_subset: ro-eco

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporally related to
type: TransitiveProperty
has curation status: IAO_0000125
definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
term editor: Chris Mungall
alternative term: finished by
imported from: ro.owl
in_subset: ro-eco

has input
type: ObjectProperty
has curation status: IAO_0000125
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
term editor: Chris Mungall
alternative term: consumes
imported from: ro.owl
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

has output
type: ObjectProperty
has curation status: IAO_0000125
definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
term editor: Chris Mungall
alternative term: produces
imported from: ro.owl
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam
in_subset: ro-eco

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
imported from: ro.owl
is positive form of: causally upstream of
creator: cjm
in_subset: valid for go annotation extension
in_subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
imported from: ro.owl
is negative form of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
term editor: Chris Mungall
curator note: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
imported from: ro.owl
temporal interpretation: RO_0001901

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
has curation status: IAO_0000428
definition: inverse of upstream of
term editor: Chris Mungall
imported from: ro.owl

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
has curation status: IAO_0000428
term editor: Chris Mungall
imported from: ro.owl

directly activates
type: ObjectProperty
sub property of: directly positively regulates
has curation status: IAO_0000428
definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
term editor: Chris Mungall
alternative term: directly positively regulates
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly activates (process to process)

indirectly activates
type: ObjectProperty
sub property of: positively regulates
type: TransitiveProperty
definition: p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.
term editor: Chris Mungall
alternative term: indirectly positively regulates
imported from: ro.owl
is indirect form of: positively regulates

directly inhibits
type: ObjectProperty
sub property of: directly negatively regulates
term editor: Chris Mungall
alternative term: directly negatively regulates
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly inhibits (process to process)

indirectly inhibits
type: ObjectProperty
sub property of: negatively regulates
type: TransitiveProperty
has curation status: IAO_0000428
term editor: Chris Mungall
alternative term: indirectly negatively regulates
imported from: ro.owl
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
has curation status: IAO_0000428
definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
term editor: Chris Mungall
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: ro.owl

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
has curation status: IAO_0000428
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
term editor: Chris Mungall
imported from: ro.owl
in_subset: valid for go annotation extension
in_subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
has curation status: IAO_0000428
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
term editor: Chris Mungall
imported from: ro.owl
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
has curation status: IAO_0000428
definition: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
editor note: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
term editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
has curation status: IAO_0000428
definition: transitive form of directly_provides_input_for
term editor: Chris Mungall
curator note: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
imported from: ro.owl
OBO foundry unique label: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
term editor: Chris Mungall
alternative term: influences (processual)
imported from: ro.owl
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
term editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
in_subset: RO_0002259

causal relation between processes
type: ObjectProperty
sub property of: causally related to
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
term editor: Chris Mungall
definition source: causal-relations
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: ro.owl

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
term editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly regulates (processual)
is direct form of: regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly positively regulates (process to process)
is positive form of: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly negatively regulates (process to process)
is negative form of: directly regulates
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: ro.owl
is negative form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: ro.owl
is positive form of: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

has coefficient
type: DatatypeProperty
example of usage: The coefficient tells us how many molecules of a given formula are present. For example, 2 H2O means we have 2 molecules of water.
definition: An data property that represents the coefficient value in a chemical reaction equation. Specifically, the cofficent is the number in front of a formula in a chemical equation.
term editor: YH

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

continuant
type: Class
subclass of: entity
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: bfo.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

occurrent
type: Class
subclass of: entity
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
imported from: bfo.owl
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

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

temporal region
type: Class
subclass of: occurrent
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
imported from: bfo.owl
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

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

disposition
type: Class
subclass of: realizable entity
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
imported from: bfo.owl
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
imported from: bfo.owl
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: bfo.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: bfo.owl
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

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

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
imported from: bfo.owl
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
imported from: bfo.owl
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: bfo.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
imported from: bfo.owl
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

one-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
imported from: bfo.owl
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

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

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

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
imported from: bfo.owl
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl
has_alternative_id: CHEBI:13302
has_alternative_id: CHEBI:21123
has_alternative_id: CHEBI:33698
has_alternative_id: CHEBI:4291
database_cross_reference: CAS:9007-49-2
database_cross_reference: KEGG:C00039
has_exact_synonym: Deoxyribonucleic acid
has_exact_synonym: deoxyribonucleic acids
has_obo_namespace: chebi_ontology
has_related_synonym: (Deoxyribonucleotide)m
has_related_synonym: (Deoxyribonucleotide)n
has_related_synonym: (Deoxyribonucleotide)n+m
has_related_synonym: DNA
has_related_synonym: DNAn
has_related_synonym: DNAn+1
has_related_synonym: DNS
has_related_synonym: Desoxyribonukleinsaeure
has_related_synonym: deoxyribonucleic acids
has_related_synonym: desoxyribose nucleic acid
has_related_synonym: thymus nucleic acid
id: CHEBI:16991
in_subset: 3 STAR

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
imported from: chebi.owl
has_exact_synonym: molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: entidad molecular
has_related_synonym: entidades moleculares
has_related_synonym: entite moleculaire
has_related_synonym: molecular entities
has_related_synonym: molekulare Entitaet
id: CHEBI:23367
in_subset: 3 STAR

nucleic acid
type: Class
subclass of: molecular entity
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl
has_exact_synonym: nucleic acids
has_obo_namespace: chebi_ontology
has_related_synonym: NA
has_related_synonym: Nukleinsaeure
has_related_synonym: Nukleinsaeuren
has_related_synonym: acide nucleique
has_related_synonym: acides nucleiques
has_related_synonym: acido nucleico
has_related_synonym: acidos nucleicos
id: CHEBI:33696
in_subset: 3 STAR

ribonucleic acid
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl
database_cross_reference: CAS:63231-63-0
has_exact_synonym: ribonucleic acid
has_exact_synonym: ribonucleic acids
has_obo_namespace: chebi_ontology
has_related_synonym: RNA
has_related_synonym: RNS
has_related_synonym: Ribonukleinsaeure
has_related_synonym: pentosenucleic acids
has_related_synonym: ribonucleic acids
has_related_synonym: ribose nucleic acid
has_related_synonym: yeast nucleic acid
id: CHEBI:33697
in_subset: 3 STAR

cell
type: Class
subclass of: material entity
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
has_obo_namespace: cell
in_subset: upper level
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).

epithelial cell
type: Class
subclass of: cell
definition: A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
imported from: cl.owl
database_cross_reference: BTO:0000414
database_cross_reference: CALOHA:TS-2026
database_cross_reference: CARO:0000077
database_cross_reference: FBbt:00000124
database_cross_reference: FMA:66768
database_cross_reference: WBbt:0003672
has_exact_synonym: epitheliocyte
has_obo_namespace: cell

macrophage
type: Class
subclass of: material entity
subclass of: cell
definition: A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
imported from: cl.owl
database_cross_reference: BTO:0000801
database_cross_reference: CALOHA:TS-0587
database_cross_reference: FMA:63261
database_cross_reference: FMA:83585
has_exact_synonym: histiocyte
has_obo_namespace: cell
comment: Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.

protein acetylation
type: Class
subclass of: up-regulation of secretion
definition: The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
imported from: go.owl
has_exact_synonym: protein amino acid acetylation
has_obo_namespace: biological_process
id: GO:0006473

apoptotic process
type: Class
subclass of: programmed cell death
definition: A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
imported from: go.owl
has_exact_synonym: apoptotic cell death
has_exact_synonym: apoptotic programmed cell death
has_exact_synonym: programmed cell death by apoptosis
has_narrow_synonym: activation of apoptosis
has_narrow_synonym: apoptosis
has_narrow_synonym: apoptosis signaling
has_narrow_synonym: apoptotic program
has_narrow_synonym: type I programmed cell death
has_obo_namespace: biological_process
id: GO:0006915

biological_process
type: Class
subclass of: process
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_obo_namespace: biological_process
id: GO:0008150

cell death
type: Class
subclass of: biological_process
definition: Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
imported from: go.owl
has_obo_namespace: biological_process
id: GO:0008219

programmed cell death
type: Class
subclass of: cell death
definition: A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
imported from: go.owl
has_narrow_synonym: caspase-independent cell death
has_narrow_synonym: non-apoptotic programmed cell death
has_narrow_synonym: nonapoptotic programmed cell death
has_obo_namespace: biological_process
id: GO:0012501

phosphorylation
type: Class
subclass of: up-regulation
definition: The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
imported from: go.owl
has_obo_namespace: biological_process
id: GO:0016310

protein myristoylation
type: Class
subclass of: lipid addition
definition: The covalent attachment of a myristoyl group to a protein.
imported from: go.owl
has_exact_synonym: protein amino acid myristoylation
has_obo_namespace: biological_process
id: GO:0018377

protein complex oligomerization
type: Class
subclass of: biological_process
definition: The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
imported from: go.owl
has_exact_synonym: protein oligomer assembly
has_exact_synonym: protein oligomer formation
has_exact_synonym: protein oligomerization
has_obo_namespace: biological_process
id: GO:0051259

data item
type: Class
subclass of: information content entity
editor preferred term: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
editor preferred term: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl

pathogen role
type: Class
subclass of: role
definition: A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl
comment: Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles.

pathogen
type: Class
subclass of: material entity
definition: A material entity with a pathogenic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

host role
type: Class
subclass of: role
definition: A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: ido.owl

interaction network
type: Class
subclass of: process
definition: Interaction network is a process that includes a network of at least two interactions.
editor note: If the interaction is physical and molecular, the interaction network is molecular interactions usually found in cells.
term editor: YH, ZX
definition source: http://en.wikipedia.org/wiki/Interaction_network

interaction
type: Class
subclass of: process
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has role
      some values from: interactor role
definition: Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.
term editor: YH, ZX
has literature mining keywords: interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts

pathway
type: Class
subclass of: interaction network
definition: an interaction network that includes at least two interactions and has a start point(s) and an end point(s).
term editor: YH, ZX

Bayesian network
type: Class
subclass of: interaction network model
definition: an interaction network model that is represented by a probabilistic graphical model (a type of statistical model) that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG).
term editor: YH, ZX
definition source: WEB: http://en.wikipedia.org/wiki/Bayesian_network

regulator role
type: Class
subclass of: interactor role
definition: an regulator role that is borne by a material entity that regulates an interaction.
term editor: YH

up-regulation
type: Class
subclass of: positive regulation
definition: a positive regulation that one interactor up-regulates another.
term editor: YH
has literature mining keywords: up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating

interaction regulator
type: Class
equivalent class: Restriction
  on property: has role
  some values from: regulator role
subclass of: interactor
definition: an interactor that regulates an interaction.
term editor: YH

input interactor role
type: Class
subclass of: interactor role
definition: an interactor role that is borne by a material entity that acts as an input of an interaction.
term editor: YH, ZX
alternative term: interaction input role

output interactor role
type: Class
subclass of: interactor role
definition: an interactor role that is borne by a material entity that acts as an output of an interaction.
term editor: YH, ZX
alternative term: interaction output role

activator role
type: Class
subclass of: positive regulator role
definition: a positive regulator role that is borne by a material entity that activates an interaction.
term editor: YH

mutual information network
type: Class
subclass of: interaction network model
definition: an interaction network model that is represented by at least two mutual information interactions.
term editor: YH, ZX
definition source: WEB: http://en.wikipedia.org/wiki/Mutual_information

node
type: Class
subclass of: object
definition: a node is an object that represents an interactor in a graph of an interaction or interaction network.
term editor: YH, ZX
comment: is node equal to interactor?? (YL)

edge
type: Class
subclass of: object
definition: an edge is an object that represents a graphic line that links two interactors in an interaction.
term editor: YH, ZX

interactor role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  some values from: interaction
definition: a role that is borne by a material entity to act as a participant in an interaction process.
term editor: YH, ZX

interactor
type: Class
equivalent class: Restriction
  on property: has role
  some values from: interactor role
subclass of: material entity
definition: an interactor is a material entity that participates in an interaction.
creator: YL. YH. ZX.

activator
type: Class
equivalent class: Restriction
  on property: has role
  some values from: activator role
subclass of: positive regulator
definition: a positive interaction regulator that activates an interaction.
term editor: YH

organism-organism interaction
type: Class
subclass of: interaction
definition: a biological interaction that occurs in the organism level.
editor note: Examples: a bacterium interacts with a mouse, a cat interacts with a dog
creator: YL.YH. ZX.

two-way interaction
type: Class
subclass of: interaction
definition: A two-way interaction is an interaction that includes two different directions among two interactors.
term editor: YH

human molecular pathway
type: Class
subclass of: pathway
definition: a pathway that exists in human body.
term editor: YH, ZX

up-regulation of secretion
type: Class
subclass of: up-regulation
definition: an up-regulation that one interactor up-regulates the secretion of another interactor.
term editor: YH
has literature mining keywords: up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating

human molecular interaction
type: Class
subclass of: interaction
definition: an interaction involving human molecules
term editor: YH, ZX
comment: YH: This branch may be made obsolete since we now have human INO (HINO).

activation
type: Class
subclass of: positive regulation
definition: a positive regulation that one interactor activates another.
term editor: YH, ZX
has literature mining keywords: activate, activated, activates, activating, activation, activator, activators, activity

gene-cell interaction
type: Class
subclass of: interaction
definition: an interaction that includes a gene and a cell as interactors.
creator: YL.YH. ZX.

protein activation
type: Class
subclass of: activation
definition: an activation process where one protein is activated by a material entity
term editor: YH
has literature mining keywords: protein activation, protein activated, activates protein, activating protein, activated protein
comment: YH: in literature mining, the protein can be any specific protein symbol or protein name.

cell-cell interaction
type: Class
subclass of: interaction
definition: a biological interaction that involves two cells as interactors.
creator: YL.YH. ZX.

protein activation by mutant
type: Class
subclass of: protein activation
definition: an activation process where one protein is activated by a gene mutant
term editor: YH
alternative term: protein activation by gene mutant
has literature mining keywords: protein activation by mutant, protein activated by mutant, mutant activates protein, activating protein by mutant, mutant activated protein
comment: YH: in literature mining, the protein can be any specific protein symbol or protein name. In addition, the mutant can be a mutant of any gene and the name of the mutant can be any specific name given by the research who generated the mutant.

antagonism
type: Class
subclass of: direct interaction
definition: a biochemical binding where a substance binds to the same site an agonist would bind to without causing activation of the receptor
term editor: YH, ZX
definition source: WEB: http://en.wikipedia.org/wiki/Receptor_antagonist
has literature mining keywords: antagonise, antagonised, antagonises, antagonising, antagonist, antagonists, antagonize, antagonized, antagonizes, antagonizing

gene-enviroment interaction
type: Class
subclass of: interaction
definition: an interaction that involves a gene and its environment (e.g., calcium in blood).
creator: YL.YH. ZX.

regulation of protein location
type: Class
subclass of: regulation
definition: a regulation process that regulates the location of a protein
term editor: YH, AO
has literature mining keywords: location // (protein) // dependent, location // (protein) // depends
example of literature mining keyword usage: "Localization of SpoIIE was shown to be dependent on the essential cell division protein FtsZ" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10747015)

regulation of transcription
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: gene transcription
subclass of: gene expression regulation
definition: a gene expression regulation process that involves the regulation of a gene transcription.
term editor: YH, AO, JH
alternative term: regulation of gene transcription
has literature mining keywords: transcribed, transcribed by, regulates the transcription of, regulated the transcription of, regulates // transcription, regulated // transcription, under the control of // transcription, essential for // transcription, trascription depends, transcription // dependent, control // transcription, controlling // transcription, requires // transcription
has keyword dependency pattern: amod(transcription, controlling), amod(transcription, dependent), amod(expression, dependent), nsubj(dependent, transcription), nsubj(control, expression), nmod:for(regulator, transcription), nmod:of(activator, transcription), nsubjpass(recognized, promoter)

attenuation
type: Class
subclass of: negative regulation
definition: a negative regulation that attenuates the virulence of a pathogenic microbe.
term editor: YH, ZX
has literature mining keywords: attenuate, attenuated, attenuates, attenuating

regulation of translation
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: protein translation
subclass of: gene expression regulation
definition: a gene expression regulation process that involves the regulation of a protein translation process.
term editor: YH, AO
alternative term: regulation of gene translation
alternative term: regulation of protein translation
has literature mining keywords: translation depends, translation // dependent, regulates // translation, regulated // translation, regulates the translation of, regulated the translation of, regulation // production, regulated // production, regulate // production
example of literature mining keyword usage: "Transcription of ydhD was dependent on SigE" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148)

autophosphorylation
type: Class
subclass of: phosphorylation
definition: a phosphorylation process that adds a phosphate to a protein kinase (possibly affecting its activity) by virtue of its own enzymic activity.
term editor: YH, ZX
has literature mining keywords: autophosphorylate, autophosphorylated, autophosphorylates, autophosphorylating, autophosphorylation

regulation of gene activation
type: Class
subclass of: regulation
subclass of: Restriction
  on property: regulates
  some values from: gene activation
definition: a regulation process that regulates the activation of a gene so that the gene is expressed at a particular time
term editor: YH, AR, JH
definition source: WEB: http://www.medilexicon.com/medicaldictionary.php?t=970
has literature mining keywords: essential for // activation, essential for // activation, activated // expression, activates // expression, control // activation, controlling // activation, requires // activation, requiredd // activation
example of literature mining keyword usage: "sequestration of SpoIIE protein into the prespore plays an important role in the control of sigmaF activation and in coupling this activation to septation." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10476035)

positive regulation of gene expression
type: Class
equivalent class: Restriction
  on property: positively regulates
  some values from: gene expression
subclass of: gene expression regulation
definition: a regulation process that positively regulates gene expression level
term editor: YH, AR
has literature mining keywords: positive regulation // expression, increase // expression, induced // dependent, induced // via, induced // by, induced // dependent // presence
example of literature mining keyword usage: "YtxH and YvyD seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10913081)

negative regulation of gene expression
type: Class
equivalent class: Restriction
  on property: negatively regulates
  some values from: gene expression
subclass of: gene expression regulation
definition: a regulation process that negatively regulates gene expression level
term editor: YH, AR
has literature mining keywords: essential for // negative regulation, negatively regulated // expression, negatively regulates // expression, negative regulator // transcription
example of literature mining keyword usage: "These results suggest that YfhP may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and yfhP." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10463184)

human biochemical reaction
type: Class
subclass of: human molecular conversion
definition: a human molecular reaction that is specifically a biochemical reaction
term editor: YH. ZX

physical entity - obsolete
type: Class
subclass of: obsolete class
editor note: place holder for physical entities
comment: Obsolete note: This class is replaced by CHEBI term: molecular entity

negative regulation of gene transcription
type: Class
equivalent class: Restriction
  on property: negatively regulates
  some values from: gene transcription
subclass of: regulation of transcription
definition: a negative regulation process that down-regulates gene expression level
term editor: YH, AO
has literature mining keywords: negatively regulated // transcription, negatively regulates // transcription, negatively controls // transcription, negatively controled // transcription
has keyword dependency pattern: dobj(preventing,transcription)

negative regulation of protein translation
type: Class
equivalent class: Restriction
  on property: negatively regulates
  some values from: protein translation
subclass of: regulation of translation
definition: a negative regulation process that down-regulates protein translation level
term editor: YH, AO
has literature mining keywords: negatively regulated // translation, negatively regulates // translation, limits // production, limited // production

gene expression regulation
type: Class
equivalent class: Restriction
  on property: regulates
  some values from: gene expression
subclass of: regulation
subclass of: Restriction
  on property: has input
  some values from: Class
    intersection of: gene
    intersection of: Restriction
      on property: has role
      some values from: input interactor role
definition: a regulation process that regulates gene expression level
term editor: YH, AO, JH
alternative term: regulation of gene expression
has literature mining keywords: regulated // expression, regulates // expression, essential // expression, control // expression, controlled // expression, controlling // expression, controls // expression, expression under control, essential for // expression, responsible for production, essential for production, regulates the production of, regulated the production of, responsible // production, responsible // production, affect // production, affected // production, depend // expression, dependent // expression, level // (gene) // dependent, requires // expression, required // expression, regulated by // pathway // relying on, regulon // includes, member of // regulon
example of literature mining keyword usage: "SigK and GerE were essential for ykvP expression" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148)
has keyword dependency pattern: amod(expression, dependent)

protein translation
type: Class
subclass of: gene expression
definition: a gene expression process that results in protein production from a gene DNA sequence.
term editor: YH, ZX
alternative term: gene translation
definition source: WEB: http://en.wikipedia.org/wiki/Translation_%28biology%29
has literature mining keywords: translation, translated, translating, encoding, encodes, protein production

inhibition of gene transcription
type: Class
subclass of: negative regulation of gene transcription
definition: a negative regulation of gene transcription process that specifiies the negative regulation being an inhibition.
term editor: YH, AO
has literature mining keywords: inhibited // transcription, inhibits // transcription, repressed // transcription, repress // transcription, prevented // transcription, prevents // transcription, prevent // transcription
example of literature mining keyword usage: "GerE protein inhibits transcription in vitro of the sigK gene." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)

chemical reaction catalyst
type: Class
equivalent class: Restriction
  on property: has role
  some values from: chemical reaction catalyst role
subclass of: interactor
definition: an interactor that starts or speeds up a chemical reaction while undergoing no permanent change itself.
term editor: YH

coimmunoprecipitation
type: Class
subclass of: coprecipitation
definition: a coprecipitation that occurs through an immunoprecipitation process.
term editor: YH, ZX
alternative term: co-immunoprecipitation
has literature mining keywords: coimmunoprecipitate, coimmunoprecipitated, coimmunoprecipitates, coimmunoprecipitating, coimmunoprecipitation, coimmunopreticipate, coimmunopreticipated, coimmunopreticipates, coimmunopreticipating, co-immunoprecipitate, co-immunoprecipitated, co-immunoprecipitates, co-immunoprecipitating, co-immunoprecipitation, co-immunopreticipate, co-immunopreticipated, co-immunopreticipates, co-immunopreticipating

positive regulation of gene transcription
type: Class
equivalent class: Restriction
  on property: positively regulates
  some values from: gene transcription
subclass of: regulation of transcription
definition: a regulation of transcription process that inviolves a positive regulation.
term editor: YH, AO
has literature mining keywords: positively regulated // transcription, negatively regulates // transcription, stimulating // transcription, stimulates // transcription, stimulated // transcription, induction // transcription, induced // transcription, induces // transcription, inducing // transcription, driven // transcription, drives // transcription
has keyword dependency pattern: dobj(stimulating,transcription)

competition
type: Class
subclass of: association
definition: an indirect association that one interactor competes with another interactor in a specfiic process.
term editor: YH, ZX
has literature mining keywords: compete, competed, competes, competing

activation of gene transcription
type: Class
subclass of: positive regulation of gene transcription
definition: a positive regulation of gene transcription process that inviolves an activation of the gene transcription.
term editor: YH, AO
has literature mining keywords: activated // transcription, activates // transcription
example of literature mining keyword usage: "Transcription of the cotB, cotC, and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called GerE." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10788508)

activation of gene transcription by low level protein
type: Class
subclass of: activation of gene transcription
definition: an activation of gene transcription that is achieved by a low level of a protein
term editor: YH, AO
has literature mining keywords: low level // activated // transcription, low level // activates // transcription, low concentration // activated // transcription
example of literature mining keyword usage: "A low level of GerE activated transcription of cotD by sigmaK." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)

positive regulation of protein translation
type: Class
equivalent class: Restriction
  on property: positively regulates
  some values from: protein translation
subclass of: regulation of translation
definition: a regulation of translation process that positively regulates protein translation level
term editor: YH, AO
has literature mining keywords: positively regulated // translation, positively regulates // translation, increases // production, increased // production, increasing // production, increasing // production
example of literature mining keyword usage: "ComK ... thereby increasing the production of the FlgM." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775)

antigen-antibody interaction
type: Class
subclass of: direct interaction
definition: a direct interaction where an antigen interacts with an antibody physically.
term editor: YH
definition source: WEB: http://en.wikipedia.org/wiki/Antigen-antibody_interaction

regulation of protein activity
type: Class
subclass of: regulation
definition: a regulation process that regulates an activity of a protein
term editor: YH, AO
alternative term: protein activity regulation
has literature mining keywords: regulated // activity, regulates // activity, essential // activity, controlled // activity, controls // activity, activity under control, essential for // activity
comment: If you can detect your protein on a western blot, and it is migrating to the apparent molecular weight that you expect, you can say for definite that the protein is being expressed. This means that the primary structure (i.e. the amino acid chain) has been synthesised. Activity depends on, for example, correct folding of the enzyme, the presence of any required cofactors, proper targetting (e.g. if its a membrane protein) and that there are mutations crucial catalytic residues. Western blotting tells you nothing about these things. (Reference: http://www.protocol-online.org/biology-forums/posts/30248.html)

downexpression
type: Class
subclass of: gene expression
definition: a gene expression that has decreased volume.
term editor: YH, ZX
alternative term: decreased gene expression

controling
type: Class
subclass of: dominant regulation
definition: a regulation that one interactor controls the quality of another interactor to a specific range
term editor: YH, ZX
has literature mining keywords: control, controled, controling, controlled, controlling, controls

conversion
type: Class
subclass of: direct interaction
definition: a direct physical association that one interactor is converted from another interactor.
term editor: YH, ZX
has literature mining keywords: conversion, convert, converted, converting, converts, derived, derives, derivation

cooperation
type: Class
subclass of: association
definition: an indirect association that one interactor cooperates with another interactor in a specfiic process.
term editor: YH, ZX
has literature mining keywords: cooperate, cooperated, cooperates, cooperating

coprecipitation
type: Class
subclass of: colocalization
definition: a colocalization that two interactors are precipitated together.
term editor: YH, ZX
alternative term: co-precipitation
has literature mining keywords: coprecipitate, coprecipitated, coprecipitates, coprecipitating, coprecipitation, copreticipate, copreticipated, copreticipates, copreticipating, co-precipitate, co-precipitated, co-precipitates, co-precipitating, co-precipitation, co-preticipate, co-preticipated, co-preticipates, co-preticipating

correlation
type: Class
subclass of: association
definition: an indirect association that two interactors are correlated in a process without defined influence of each other.
term editor: YH, ZX
has literature mining keywords: correlate, correlated, correlating

costimulation
type: Class
subclass of: synergization
editor note: Example: A and B costimulate C. The relations between A and C or between B and C are regulation. However, the relation between A and B is an association.
term editor: YH, ZX, AO
has literature mining keywords: costimulate, costimulated, costimulating

cell-environment interaction
type: Class
subclass of: interaction
definition: an interaction that involves a cell and its environment as interactors
creator: YH

cross-immunoprecipitation interaction
type: Class
subclass of: immuno-precipitation
definition: an immuno-precipitation that one interactor is precipitated based on an cross- immunological precipitation process.
term editor: YH, ZX
has literature mining keywords: cross-immunoprecipitate, cross-immunoprecipitated, cross-immunoprecipitates, cross-immunoprecipitating, cross-immunoprecipitation, crossimmunoprecipitate, crossimmunoprecipitated, crossimmunoprecipitates, crossimmunoprecipitating, crossimmunoprecipitation

organism-environment interaction
type: Class
subclass of: interaction
definition: an interaction that involves an organism and its environment as interactors
creator: YH

immunological cross-reaction
type: Class
subclass of: antigen-antibody interaction
term editor: YH, ZX
definition source: an antigen-antibody interaction where an antibody interats with an antigen that differs from the immunogen used to generate antibody.

negative regulation of protein activity
type: Class
subclass of: regulation of protein activity
definition: a regulation of protein activitiy process that involves a negative regulation
term editor: YH, AO
alternative term: negative protein activity regulation
has literature mining keywords: negatively regulated // activity, negatively regulates // activity

negative regulation
type: Class
subclass of: regulation
definition: a regulation in which one interactor has a negative effect on another interactor
editor note: YH: different types of negative regulations exist. These types are related to different qualities and phenotyes of regulated targets.
term editor: YH, ZX
has literature mining keywords: down-regulate, down-regulations, down-regulated, down-regulating, downregulate, downregulations, downregulated, downregulating

chemical reaction catalyst role
type: Class
subclass of: interactor role
definition: an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself.
term editor: YH

inhibition of protein activity
type: Class
subclass of: negative regulation of protein activity
definition: a negative regulation of protein activitiy process that involves an inhibition of a protein activity
term editor: YH, AO
has literature mining keywords: inhibited // activity, inhibites // activity, inhibition // activity
example of literature mining keyword usage: "... FlgM antisigma factor that inhibits sigmaD activity." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775)

regulation of transcription by binding to promoter
type: Class
subclass of: promoter-based regulation of transcription
definition: a regulation of transcription process that occurs through the binding to a promotor of a gene
term editor: YH, AO
has literature mining keywords: binds // promoter, bound to // promoter, binding // promoter, recognize // promoter, recognized // promoter, expressed // promoter, dependent // promoter. depdenent // promoter of (or proceding, procedes), repress // promoter, activate // promoter, regulate // promoter, regulated // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter
example of literature mining keyword usage: "We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
comment: Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor).

positive regulation of transcription by binding to promoter
type: Class
subclass of: regulation of transcription by binding to promoter
subclass of: Restriction
  on property: positively regulates
  some values from: gene transcription
definition: a regulation of transcription by binding to promoter that is further classified as a positive regulation
term editor: YH, AO
has literature mining keywords: induce // expression // promoter, induced // transcription // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter, activated // transcription // promoter, activated // promoter, dependent // promoter // drives // expression, dependent // promoter // responsible // transcription, expressed // controlled // promoter
example of literature mining keyword usage: "We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
comment: Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor).

decrease
type: Class
subclass of: negative regulation
definition: a negative regulation that results in the decrease of one interactor volume.
term editor: YH, ZX
alternative term: reduction
has literature mining keywords: decrease, decreased, decreases, decreasing, decreasing, reduce, reduced, reduces, reducing, diminish, diminished, diminishes, diminishing, declining, declines, declination, limit, limited, limiting, limits

negative regulation of transcription by binding to promoter
type: Class
subclass of: regulation of transcription by binding to promoter
subclass of: Restriction
  on property: negatively regulates
  some values from: gene transcription
definition: a regulation of transcription by binding to promoter that is further classified as a positive regulation
term editor: YH, AO
has literature mining keywords: negatively regulate // promoter, negatively regulated // promoter, repressed // promoter, represses // promoter, repress // promoter, binds // transcriptional start site // repressor, bound // transcriptional start site // repressor
example of literature mining keyword usage: "We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
comment: Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor).

gene activation
type: Class
subclass of: positive regulation of gene expression
definition: a positive regulation of gene expression process that activates a gene so that the gene is expressed at a particular time
term editor: YH, AR, JH
definition source: WEB: http://www.medilexicon.com/medicaldictionary.php?t=970
has literature mining keywords: activation // (gene), activated // (gene), activates // // (gene), activated // action

biochemical degradation
type: Class
subclass of: enzymatic reaction
definition: an enzymatic reaction that leads to the breakdown of a biochemical entity.
term editor: YH, ZX
has literature mining keywords: degradation, degradations, degrade, degraded, degrades, degrading

co-regulation of transcription
type: Class
subclass of: regulation of transcription
definition: a regulation of transcription process where two or more regulators regulate a gene transcription
term editor: YH, AO
has literature mining keywords: transcription // combined action, transcription // results from // combined action
example of literature mining keyword usage: "In vitro transcription experiments suggest that the differential pattern of cot gene expression results from the combined action of GerE and another transcription factor, SpoIIID." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10788508)

activation of gene transcription by high level protein
type: Class
subclass of: activation of gene transcription
definition: an activation of gene transcription that is achieved by a high level of a protein
term editor: YH, AO
has literature mining keywords: high level // activated // transcription, high level // activate // transcription, high concentration // activated // transcription
example of literature mining keyword usage: "A low concentration of GerE activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)

promoter-based regulation of transcription
type: Class
subclass of: regulation of transcription
definition: a regulation of transcription process through binding to a promoter or regulating the promoter binding activity
term editor: YH, AO
has literature mining keywords: recognize // promoter, recognized // promoter, expressed // promoter, dependent // promoter. depdenent // promoter of (or proceding, procedes), repress // promoter, activate // promoter, regulate // promoter, regulated // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter
example of literature mining keyword usage: "The -10 and -35 sequences of the sigmaB- and sigmaF-dependent promoters of katX overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10503549)
comment: Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor).

activation of gene transcription by phosphorylated protein
type: Class
subclass of: activation of gene transcription
definition: an activation of gene transcription that is achieved by a phosphorylated protein
term editor: YH, AO
has literature mining keywords: phosphorylated // activator // transcription, phosphorylated // activates // transcription, phosphorylated // activate // transcription, phosphorylated // activated // transcription
example of literature mining keyword usage: "Spo0A, which when phosphorylated is an activator of sigE transcription." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10383978)

human molecular catalysis
type: Class
subclass of: human molecular control interaction
term editor: YH

destabilization
type: Class
subclass of: negative regulation
definition: a negative regulation that results in a destabilization.
term editor: YH, ZX
has literature mining keywords: destabilization, destabilize, destabilized, destabilizes, destabilizing

gene expression inhibition
type: Class
subclass of: negative regulation of gene expression
definition: a negative regulation process that inhibits gene expression level
term editor: YH
has literature mining keywords: inhibits // expression, inhibited // expression, suppressor // expression, suppress // expression, repress // expression, acts // repressor
example of literature mining keyword usage: "CtsR protein acts as a global repressor of the clpC operon." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9852015)

dominant regulation
type: Class
subclass of: regulation
definition: a regulation that one interactor has a dominant effect on the quality of another interactor. This differs from the accessory regulation.
term editor: YH, ZX
has literature mining keywords: determine, determined, determines, determining, cause, caused, causes, causing, lead, leading, leads, led, govern, governed, governing, governs

protein dimerization
type: Class
subclass of: GO_0006461
definition: a protein complex assembly that involves two proteins that form a dimer.
term editor: YH, ZX
has literature mining keywords: dimerize, dimerized, dimerizes, dimerizing

co-regulation
type: Class
subclass of: regulation
definition: a regulation process that involves in two interactors co-regulate a third interactor.
term editor: YH
has literature mining keywords: co-regulation, co-regulated, co-regulate, co-regulating

molecular complex
type: Class
subclass of: molecular entity

disruption
type: Class
subclass of: negative regulation
definition: a negative regulation that results in a disruption.
term editor: YH, ZX
has literature mining keywords: disrupt, disrupted, disrupting, disrupts

dissociation
type: Class
subclass of: direct interaction
term editor: YH, ZX
has literature mining keywords: dissociate, dissociated, dissociating, dissociation

down-regulation
type: Class
subclass of: negative regulation
definition: a negative regulation that one interactor down-regulates another.
term editor: YH, ZX
has literature mining keywords: down-regulate, down-regulated, down-regulates, down-regulating, down-regulation, downregulate, downregulated, downregulates, downregulating, downregulation, downmodulation, depress, depressed, depresses, depressing, suppress, suppressed, suppresses, suppressing, suppression, suppressor, repress, repressed, represses, repressing, repression, repressor, repressors

gene expression up-regulation
type: Class
subclass of: positive regulation of gene expression
definition: a positive regulation of gene expression process that up-regulates gene expression level
term editor: YH, AR
has literature mining keywords: essential for // up-regulation, up-regulated // expression, up-regulates // expression

gene expression down-regulation
type: Class
subclass of: negative regulation of gene expression
definition: a negative regulation process that down-regulates gene expression level
term editor: YH
has literature mining keywords: down-regulated // expression, down-regulates // expression

induction of production
type: Class
subclass of: induction
definition: an induction that leads to the production of an entity
editor note: YH: For example, "IL-2 and IL-15 induced the production of IL-17 and IFN-γ in a dose dependent manner by PBMCs.”
term editor: YH
has literature mining keywords: induction of the production, induces the production, induced the production

elimination
type: Class
subclass of: negative regulation
definition: a negative regulation that one interactor eliminates another.
term editor: YH, ZX
has literature mining keywords: eliminate, eliminated, eliminates, eliminating, abolish, abolished, abolishes, abolishing, abrogation

bacterial conjugation
type: Class
subclass of: cell-cell interaction
definition: a cell-cell interaction that the transfers genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells.
term editor: YH
definition source: WEB: http://en.wikipedia.org/wiki/Bacterial_conjugation

hydrogen binding
type: Class
subclass of: direct interaction
definition: Interaction leading to the formation of hydrogen bond between two molecules
term editor: YH
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK22567/

regulation of assembly
type: Class
subclass of: regulation
subclass of: Restriction
  on property: regulates
  some values from: gene activation
definition: a regulation process where one gene product regulates an assembly process which forms an assembly having another gene product.
term editor: YH, AR, JH
has literature mining keywords: regulated // assembly

human molecular control interaction
type: Class
subclass of: human molecular interaction
definition: a human molecular interaction where one molecule controls another molecule.
term editor: YH

gene expression
type: Class
subclass of: interaction
definition: a biological interaction that uses the information from a gene to synthesize a functional gene product.
term editor: YH, ZX
has literature mining keywords: express, expressed, expresses, expressing, expression, expressions

accessory regulation
type: Class
subclass of: regulation
definition: a positive regulation that one interactor facilitates a phenomenon such as a phenotype. This is an accessory effect not a major one.
term editor: YH, ZX
has literature mining keywords: facilitate, facilitates, facilitating, faciliteted, help, helps, helped

positive regulation of protein activity
type: Class
subclass of: regulation of protein activity
definition: a regulation of protein activitiy process that involves a positive regulation
term editor: YH, AO
alternative term: negative protein activity regulation
has literature mining keywords: positively regulated // activity, positively regulates // activity, dependent // stimulation

host-pathogen interaction
type: Class
equivalent class: Class
  intersection of: interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: pathogen
  intersection of: Restriction
    on property: RO_0000057
    some values from: host
subclass of: interaction
subclass of: Restriction
  on property: has interaction type
  some values from: interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: pathogen
subclass of: Restriction
  on property: RO_0000057
  some values from: host
definition: An interaction that involves a host (host organism or host cell) and pathogen organism at a specific condition.
term editor: YH

gene fusion
type: Class
subclass of: genetic interaction
definition: a genetic interaction that forms a hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion.
term editor: YH, ZX
definition source: WEB: http://en.wikipedia.org/wiki/Gene_fusion
has literature mining keywords: gene AND (fuse, fused, fuses, fusing)

host cell-pathogen interaction
type: Class
equivalent class: Class
  intersection of: host-pathogen interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: cell
      intersection of: Restriction
        on property: has role
        some values from: host role
subclass of: host-pathogen interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: cell
    intersection of: Restriction
      on property: has role
      some values from: host role
definition: An host-pathogen interaction where the host is a cell.
term editor: YH

induction by binding to protein
type: Class
subclass of: induction
example of usage: The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1
definition: an induction that is achieved by binding to a protein
has literature mining keywords: induction ... by binding to // induces .. through binding// induced ... by binding to // caused ... by binding to // causes ... through ... binding
has keyword dependency pattern: YH, AO, JH

macrophage-pathogen interaction
type: Class
equivalent class: Class
  intersection of: host cell-pathogen interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: macrophage
      intersection of: Restriction
        on property: has role
        some values from: host role
subclass of: host cell-pathogen interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: macrophage
definition: An host cell-pathogen interaction where the host cell is a macrophage.
term editor: YH

human molecular degradation
type: Class
subclass of: human molecular conversion
term editor: YH

protein heterodimerization
type: Class
subclass of: protein dimerization
definition: a protein dimerization where two proteins are different.
term editor: YH, ZX
has literature mining keywords: heterodimerize, heterodimerized, heterodimerizes, heterodimerizing

protein homodimerization
type: Class
subclass of: protein dimerization
definition: a protein dimerization where two proteins are the same.
term editor: YH, ZX
has literature mining keywords: homodimerize, homodimerized, homodimerizes, homodimerizing

macrophage-pathogen protein-protein interaction
type: Class
subclass of: macrophage-pathogen interaction
example of usage: The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26795/
definition: A macrophage-pathogen interaction that involves a macrophage protein and a pathogen protein.
term editor: YH
alternative term: macrophage-pathogen PPI

overexpression
type: Class
subclass of: gene expression
definition: a gene expression that has increased volume.
term editor: YH, ZX
alternative term: increased gene expression
alternative term: overexpression
has literature mining keywords: hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression

hyperphosphorylation
type: Class
subclass of: phosphorylation
term editor: YH, ZX
has literature mining keywords: hyperphosphorylate, hyperphosphorylated, hyperphosphorylates, hyperphosphorylation

immuno-precipitation
type: Class
subclass of: translocation
definition: a translocation that one interactor is precipitated based on an immunological precipitation process.
term editor: YH, ZX
has literature mining keywords: immuno-precipitate, immuno-precipitated, immuno-precipitates, immuno-precipitating, immuno-precipitation, immunoprecipitate, immunoprecipitated, immunoprecipitates, immunoprecipitating, immunoprecipitation, immunopreticipate, immunopreticipated, immunopreticipates, immunopreticipating

positive regulation
type: Class
subclass of: regulation
editor note: YH: different types of positive regulations exist. These types are related to different qualities and phenotyes of regulated targets.
term editor: YH, ZX
has literature mining keywords: positively regulate, positive regulations, positively regulated, positively regulating, promote, promoted, promotes, promoting

impairment
type: Class
subclass of: negative regulation
definition: A negative regulation that disables, damages, or impairs the functioning of another entity.
term editor: YH, ZX
has literature mining keywords: impair, impaired, impairing, impairs, cripple, crippled, cripples, crippling, sever, severed, severs

inactivation
type: Class
subclass of: negative regulation
definition: a negative regulation that one interactor inactivates another.
term editor: YH, ZX
has literature mining keywords: inactivate, inactivated, inactivates, inactivating, inactivation

increase
type: Class
subclass of: positive regulation
definition: a positive regulation that leads to the increase of a quality of an entity.
term editor: YH, ZX
alternative term: augmentation
alternative term: elavation
alternative term: enhancement
has literature mining keywords: increase, increased, increases, increasing, augment, augmented, augmenting, augments, elavating, elevate, elevated, elevates, elevating, raise, raised, raises, raising, enhance, enhanced, enhances, enhancing, enhancement

human molecular synthesis
type: Class
subclass of: human molecular interaction

induction
type: Class
subclass of: positive regulation
definition: a positive regulation that leads to the induction of a new interactor due to the presence of another interactor.
term editor: YH, ZX
alternative term: leading
alternative term: triggering
has literature mining keywords: induce, induced, induces, inducing, induction, trigger, triggered, triggering, triggerring, triggers, initiate, initiated, initiates, initiating, stimulate, stimulation, stimulated, stimulating, dependent // inducible

human molecular regulatory reaction
type: Class
subclass of: human molecular interaction

inhibition
type: Class
subclass of: negative regulation
definition: a negative regulation that one interactor inhibites another.
term editor: YH, ZX
has literature mining keywords: inhibit, inhibited, inhibiting, inhibition, inhibitor, inhibitors, inhibits, block, blocked, blocking, blocks

input interactor
type: Class
equivalent class: Restriction
  on property: has role
  some values from: input interactor role
subclass of: interactor
definition: an interactor that is an input of an interaction.
term editor: YH

interference
type: Class
subclass of: negative regulation
definition: a negative regulation that one interactor interferes a process.
term editor: YH, ZX
has literature mining keywords: interfere, interferes, interfered, interfering, perturb, perturbed, perturbing, perturbs, obstruction

human molecular modulation
type: Class
subclass of: human molecular control interaction
term editor: YH

human template reaction regulation
type: Class
subclass of: human molecular control interaction
term editor: YH

host gene mutant-pathogen interaction
type: Class
equivalent class: Class
  intersection of: host-pathogen interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: host
      intersection of: Restriction
        on property: lacks part
        some values from: gene
subclass of: host-pathogen interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: host
    intersection of: Restriction
      on property: lacks part
      some values from: gene
definition: An host-pathogen interaction where the host is a gene mutant
term editor: YH

human molecular conversion
type: Class
subclass of: human molecular interaction
definition: a human molecular interaction where one molecule converts to another molecule.
term editor: YH

human molecular template reaction
type: Class
subclass of: human molecular interaction

small molecule
type: Class
subclass of: molecular entity

host
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: host role
subclass of: material entity
subclass of: Restriction
  on property: has role
  some values from: host role
definition: An organism bearing a host role.

positive regulator role
type: Class
subclass of: regulator role
definition: an interactor role that is borne by a material entity that positively regulates an interaction.
term editor: YH

pathway step
type: Class
subclass of: data item
definition: An data item that indicates the step number of a pathway.
term editor: Oliver He

negative regulator role
type: Class
subclass of: regulator role
definition: an interactor role that is borne by a material entity that negatively regulates an interaction.
term editor: YH

macrophage-pathogen PPI inducing cell death
type: Class
subclass of: macrophage-pathogen protein-protein interaction
subclass of: Restriction
  on property: causally upstream of
  some values from: cell death
example of usage: The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26795/
definition: A macrophage-pathogen protein-protein interaction that induces cell death.
term editor: YH

neutralization
type: Class
subclass of: direct interaction
definition: a biochemical reaction that one interactor neutrolizes another.
term editor: YH, ZX
has literature mining keywords: neutralise, neutralised, neutralises, neutralising, neutralize, neutralized, neutralizes, neutralizing

positive regulator
type: Class
equivalent class: Restriction
  on property: has role
  some values from: positive regulator role
subclass of: interaction regulator
definition: an interaction regulator that positively regulates an interaction.
term editor: YH

oxidation
type: Class
subclass of: enzymatic reaction
editor note: an enzymatic reaction where a molecule gains oxygen.
term editor: YH, ZX
has literature mining keywords: oxidate, oxidated, oxidates, oxidating, oxidation, oxidise, oxidised, oxidises, oxidising, oxidize, oxidized, oxidizes, oxidizing

host-pathogen mutant interaction
type: Class
equivalent class: Class
  intersection of: host-pathogen interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: pathogen
      intersection of: Restriction
        on property: lacks part
        some values from: gene
subclass of: host-pathogen interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: pathogen
    intersection of: Restriction
      on property: lacks part
      some values from: gene
definition: An host-pathogen interaction where the pathogen is a gene mutant
term editor: YH

negative regulator
type: Class
equivalent class: Restriction
  on property: has role
  some values from: negative regulator role
subclass of: interaction regulator
definition: an interaction regulator that negatively regulates an interaction.
term editor: YH

deactivator role
type: Class
subclass of: negative regulator role
definition: a negative regulator role that is borne by a material entity that deactivates, inhibits, blocks, or disrupts the action of a biological agent (e.g., enzyme).
term editor: YH

macrophage-pathogen interaction
type: Class
equivalent class: Class
  intersection of: host cell-pathogen interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: macrophage
      intersection of: Restriction
        on property: has role
        some values from: host role
subclass of: host cell-pathogen interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: macrophage
definition: An host cell-pathogen interaction where the host is a macrophage cell
term editor: YH

motivator role
type: Class
subclass of: input interactor role
definition: an input interactor role that is borne by a material entity that motivates a process.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory

precedence
type: Class
subclass of: association
definition: an indirect association that one interactor is preceded by another interactor.
term editor: YH, ZX
has literature mining keywords: precede, preceded, precedes, preceding

prevention
type: Class
subclass of: negative regulation
term editor: YH, ZX
has literature mining keywords: prevent, prevented, preventing, prevents

hygiene factor role
type: Class
subclass of: input interactor role
definition: an input interactor role that is borne by a material entity (e.g. status, job security, salary and fringe benefits) that do not motivate if present, but, if absent, result in demotivation.
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Motivation#Herzberg's_two-factor_theory

output interactor
type: Class
equivalent class: Restriction
  on property: has role
  some values from: output interactor role
subclass of: interactor
definition: an interactor that is an output of an interaction.
term editor: YH

epithelial cell-pathogen interaction
type: Class
equivalent class: Class
  intersection of: host cell-pathogen interaction
  intersection of: Restriction
    on property: RO_0000057
    some values from: Class
      intersection of: epithelial cell
      intersection of: Restriction
        on property: has role
        some values from: host role
subclass of: host cell-pathogen interaction
subclass of: Restriction
  on property: RO_0000057
  some values from: epithelial cell
definition: An host cell-pathogen interaction where the host is an epithelial cell
term editor: YH

reactivation
type: Class
subclass of: activation
definition: an activation that repeats.
term editor: YH, ZX
has literature mining keywords: reactivate, reactivated, reactivates, reactivating, reactivation

recruitment
type: Class
subclass of: regulation
definition: a positive regulation that leads the recruitment of one interactor from one location to another.
term editor: YH, ZX
has literature mining keywords: recruit, recruite, recruited, recruites, recruiting, recruits

epithelial cell-pathogen protein-protein interaction
type: Class
subclass of: epithelial cell-pathogen interaction
example of usage: We show that caspase-2 functions as an initiator caspase during Staphylococcus aureus α-toxin- and Aeromonas aerolysin-mediated apoptosis in epithelial cells. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365430/
term editor: YH
alternative term: epithelial cell-pathogen PPI

regulation
type: Class
subclass of: association
subclass of: Restriction
  on property: RO_0000057
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has role
      some values from: regulator role
definition: A regulation represents a regulatory interaction between two interactors.
term editor: YH, ZX, AO, JH
has literature mining keywords: regulate, regulated, regulates, regulating, regulation, regulator, modulate, modulated, modulates, modulating, modulation, mediate, mediated, mediates, mediating, influence, influenced, influences, influencing, affect, affected, affecting, affects, impact, impacted, impacting, impacts, effect, effected, effecting, effects, require, required, requires, requiring, respond, responded, responding, responds, responsive, change, changed, changes, changing, alter, altered, altering, alters, modified, modifies, modify, modifying, depend, depended, depending, depends, direct, directed, directing, directs, drive, driven, drives, driving, cause, caused, causes, causing, lead, leading, leads, led, target, targeted, targeting, targets, dependent, essential for
see also: GO: GO_0065007

interaction network model
type: Class
subclass of: information content entity
definition: An information content entity that models interaction network
term editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Interactome

obsolete class
type: Class

stabilization
type: Class
subclass of: positive regulation
definition: a postive interaction that one interactor increases the stability of another interactor.
term editor: YH, ZX
has literature mining keywords: stabilization, stabilize, stabilized, stabilizes, stabilizing

synergization
type: Class
subclass of: co-regulation
definition: a regulation process that involves in two interactors that are synergized in affecting a phenomenon (e.g., phenotype).
term editor: YH, ZX
has literature mining keywords: synergise, synergised, synergises, synergising, synergize, synergized, synergizes, synergizing

termination
type: Class
subclass of: negative regulation
definition: a negative regulation that leads to a process termination.
term editor: YH, ZX
has literature mining keywords: terminate, terminated, terminates, terminating

transactivation
type: Class
subclass of: gene expression regulation
definition: a gene expression regulation that leads to an increased rate of gene expression triggered either by biological processes or by artificial means.
term editor: YH, ZX
definition source: WEB: http://en.wikipedia.org/wiki/Transactivation
has literature mining keywords: trans-activate, trans-activated, trans-activates, trans-activating, trans-activation, trans-activator, trans-activators, transactivate, transactivated, transactivates, transactivating, transactivation, transactivator, transactivators

gene transcription
type: Class
subclass of: gene expression
subclass of: Restriction
  on property: has input
  some values from: gene
definition: an interaction process that creates a complementary RNA copy of a sequence of DNA.
term editor: YH
definition source: WEB: http://en.wikipedia.org/wiki/Transcription_%28genetics%29
has literature mining keywords: transcribe, transcribed, transcribes, transcribing, transcription

genetic transduction
type: Class
subclass of: cell-cell interaction
definition: a cell-cell interaction that transfers viral, bacterial, or both bacterial and viral DNA from one cell to another using a bacteriophage vector.
term editor: YH, ZX
has literature mining keywords: transduce, transduced, transducer, transducers, transduces, transducing, transduction

translocation
type: Class
subclass of: process
definition: A process that changes the location of a material entity.
term editor: YH, ZX
has literature mining keywords: translocation, transloated, translocating, translocates, migrated, migration, migrates migrating, mobilization, mobilize, mobilized, mobilizes, mobilizing, mobilisation, mobilise, mobilised, mobilises, mobilising

tyrosine-phosphorylation
type: Class
subclass of: phosphorylation
term editor: YH, ZX
has literature mining keywords: tyrosine-phosphorylated

co-expression
type: Class
subclass of: correlation
editor note: a correlation association that two genes are co-expressed in a system.
term editor: YH

deregulation
type: Class
subclass of: negative regulation
definition: a negative regulation that results in the deregulation of one interactor on a process.
term editor: YH

one-way interaction
type: Class
subclass of: interaction
definition: A one-way interaction is an interaction that shows one direction between interactors.
term editor: YH

export
type: Class
subclass of: translocation
definition: a translocation that one interactor exports from one location
term editor: YH

import
type: Class
subclass of: translocation
definition: a translocation that one interactor imports from one location
term editor: YH

secretion
type: Class
subclass of: translocation
definition: a translocation that one interactor secretes from the inside of another interactor
term editor: YH

protein-protein interaction
type: Class
subclass of: interaction
definition: an interaction between two proteins.
term editor: YH, ZX

gene-protein interaction
type: Class
subclass of: interaction
definition: an interaction that involves in a gene DNA and a protein
term editor: YH, ZX

organism
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: cell
definition: An organism is an individual entity that exhibits the properties of life, including reproduction, growth and development, maintenance, and response to stimuli. All organisms are composed of one or more cells.
definition source: https://en.wikipedia.org/wiki/Organism
creator: Oliver He
comment: An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction, growth or metabolism.

acetylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
imported from: mi.owl
has_exact_synonym: acetylation
has_obo_namespace: PSI-MI
id: MI:0192
in_subset: PSI-MI slim

amidation reaction
type: Class
subclass of: enzymatic reaction
definition: Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
imported from: mi.owl
has_exact_synonym: amidation
has_obo_namespace: PSI-MI
id: MI:0193
in_subset: PSI-MI slim

cleavage reaction
type: Class
subclass of: enzymatic reaction
definition: Covalent bond breakage in a molecule leading to the formation of smaller molecules.
imported from: mi.owl
has_exact_synonym: cleavage
has_obo_namespace: PSI-MI
id: MI:0194
in_subset: PSI-MI slim

covalent binding
type: Class
subclass of: direct interaction
definition: Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0195
in_subset: PSI-MI slim

deacetylation reaction
type: Class
subclass of: enzymatic reaction
definition: N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
imported from: mi.owl
has_exact_synonym: deacetylation
has_obo_namespace: PSI-MI
id: MI:0197
in_subset: PSI-MI slim

defarnesylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: S-farnesyl-L-cysteined is cleaved and returns a C residue.
imported from: mi.owl
has_exact_synonym: defarnesylation
has_obo_namespace: PSI-MI
id: MI:0198
in_subset: PSI-MI slim

deformylation reaction
type: Class
subclass of: enzymatic reaction
definition: N6-formyl-L-lysine is cleaved and returns a K residue.
imported from: mi.owl
has_exact_synonym: deformylation
has_obo_namespace: PSI-MI
id: MI:0199
in_subset: PSI-MI slim

degeranylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
imported from: mi.owl
has_exact_synonym: degeranylation
has_obo_namespace: PSI-MI
id: MI:0200
in_subset: PSI-MI slim

demyristoylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: N6-myristoyl-L-lysine is cleaved and returns a K residue.
imported from: mi.owl
has_exact_synonym: demyristoylation
has_obo_namespace: PSI-MI
id: MI:0201
in_subset: PSI-MI slim

depalmitoylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
imported from: mi.owl
has_exact_synonym: depalmitoylation
has_obo_namespace: PSI-MI
id: MI:0202
in_subset: PSI-MI slim

dephosphorylation reaction
type: Class
subclass of: enzymatic reaction
definition: Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
imported from: mi.owl
has_exact_synonym: dephosphorylation
has_obo_namespace: PSI-MI
id: MI:0203
in_subset: PSI-MI slim

deubiquitination reaction
type: Class
subclass of: enzymatic reaction
definition: Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
imported from: mi.owl
has_exact_synonym: deubiquitination
has_obo_namespace: PSI-MI
id: MI:0204
in_subset: PSI-MI slim

farnesylation reaction
type: Class
subclass of: lipid addition
definition: Reversible reaction that can affect C residue.
imported from: mi.owl
has_exact_synonym: farnesylation
has_obo_namespace: PSI-MI
id: MI:0206
in_subset: PSI-MI slim

formylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
imported from: mi.owl
has_exact_synonym: formylation
has_obo_namespace: PSI-MI
id: MI:0207
in_subset: PSI-MI slim

genetic interaction
type: Class
subclass of: interaction
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0208
in_subset: PSI-MI slim

geranylgeranylation reaction
type: Class
subclass of: lipid addition
definition: Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
imported from: mi.owl
has_exact_synonym: geranylgeranylation
has_obo_namespace: PSI-MI
id: MI:0209
in_subset: PSI-MI slim

hydroxylation reaction
type: Class
subclass of: enzymatic reaction
definition: Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
imported from: mi.owl
has_exact_synonym: hydroxylation
has_obo_namespace: PSI-MI
id: MI:0210
in_subset: PSI-MI slim

lipid addition
type: Class
subclass of: enzymatic reaction
definition: Covalent or non covalent binding of lipid group on a protein residue.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0211
in_subset: PSI-MI slim

lipoprotein cleavage reaction
type: Class
subclass of: cleavage reaction
definition: Cleavage of a lipid group covalently bound to a protein residue.
imported from: mi.owl
has_exact_synonym: lipid cleavage
has_obo_namespace: PSI-MI
id: MI:0212
in_subset: PSI-MI slim

methylation reaction
type: Class
subclass of: enzymatic reaction
definition: The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
imported from: mi.owl
has_exact_synonym: methylation
has_obo_namespace: PSI-MI
id: MI:0213
in_subset: PSI-MI slim

myristoylation reaction
type: Class
subclass of: lipid addition
definition: Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
imported from: mi.owl
has_exact_synonym: myristoylation
has_obo_namespace: PSI-MI
id: MI:0214
in_subset: PSI-MI slim

palmitoylation reaction
type: Class
subclass of: lipid addition
definition: Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
imported from: mi.owl
has_exact_synonym: palmitoylation
has_obo_namespace: PSI-MI
id: MI:0216
in_subset: PSI-MI slim

phosphorylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that can affect D,C,H,S,T,Y,R residues.
imported from: mi.owl
has_exact_synonym: phosphorylation
has_obo_namespace: PSI-MI
id: MI:0217
in_subset: PSI-MI slim

ubiquitination reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
imported from: mi.owl
has_exact_synonym: ubiquitination
has_obo_namespace: PSI-MI
id: MI:0220
in_subset: PSI-MI slim

colocalization
type: Class
subclass of: interaction
definition: Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0403
in_subset: PSI-MI slim

direct interaction
type: Class
subclass of: physical association
definition: Interaction between molecules that are in direct contact with each other.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0407
in_subset: PSI-MI slim

disulfide bond
type: Class
subclass of: covalent binding
definition: Covalent bond mediated by 2 sulfur atoms.
imported from: mi.owl
has_exact_synonym: SS-bond
has_exact_synonym: disulfide bridge
has_obo_namespace: PSI-MI
id: MI:0408
in_subset: PSI-MI slim

enzymatic reaction
type: Class
subclass of: direct interaction
definition: terms aiming to represent biochemical reactions referring to their resulting product modifications.
imported from: mi.owl
has_exact_synonym: Biochemical reaction
has_obo_namespace: PSI-MI
id: MI:0414
in_subset: PSI-MI slim

transglutamination reaction
type: Class
subclass of: covalent binding
definition: Gln-Lys cross-link catalyzed by a transglutaminase.
imported from: mi.owl
has_exact_synonym: transglutamination
has_obo_namespace: PSI-MI
id: MI:0556
in_subset: PSI-MI slim

adp ribosylation reaction
type: Class
subclass of: enzymatic reaction
definition: Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
imported from: mi.owl
has_exact_synonym: adp ribosylation
has_obo_namespace: PSI-MI
id: MI:0557
in_subset: PSI-MI slim

deglycosylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
imported from: mi.owl
has_exact_synonym: deglycosylation
has_obo_namespace: PSI-MI
id: MI:0558
in_subset: PSI-MI slim

glycosylation reaction
type: Class
subclass of: enzymatic reaction
definition: The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
imported from: mi.owl
has_exact_synonym: glycosylation
has_obo_namespace: PSI-MI
id: MI:0559
in_subset: PSI-MI slim

sumoylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
imported from: mi.owl
has_exact_synonym: sumoylation
has_obo_namespace: PSI-MI
id: MI:0566
in_subset: PSI-MI slim

neddylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
imported from: mi.owl
has_exact_synonym: neddylation
has_obo_namespace: PSI-MI
id: MI:0567
in_subset: PSI-MI slim

desumoylation reaction
type: Class
subclass of: enzymatic reaction
definition: Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
imported from: mi.owl
has_exact_synonym: desumoylation
has_obo_namespace: PSI-MI
id: MI:0568
in_subset: PSI-MI slim

deneddylation reaction
type: Class
subclass of: enzymatic reaction
definition: Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
imported from: mi.owl
has_exact_synonym: deneddylation
has_obo_namespace: PSI-MI
id: MI:0569
in_subset: PSI-MI slim

protein cleavage
type: Class
subclass of: cleavage reaction
definition: Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0570
in_subset: PSI-MI slim

mrna cleavage
type: Class
subclass of: rna cleavage
definition: Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0571
in_subset: PSI-MI slim

dna cleavage
type: Class
subclass of: nucleic acid cleavage
definition: Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0572
in_subset: PSI-MI slim

dna strand elongation
type: Class
subclass of: nucleic acid strand elongation reaction
definition: The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
imported from: mi.owl
has_exact_synonym: DNA replication elongation
has_exact_synonym: dna elongation
has_obo_namespace: PSI-MI
id: MI:0701
in_subset: PSI-MI slim

synthetic
type: Class
subclass of: negative genetic interaction
definition: An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (to any degree) as a result of any of the individual perturbations. wt = a = b = E (not=) ab
imported from: mi.owl
has_exact_synonym: synthetic genetic interaction (sensu inequality)
has_exact_synonym: synthetic genetic interaction defined by inequality
has_obo_namespace: PSI-MI
id: MI:0794
in_subset: PSI-MI slim

asynthetic
type: Class
subclass of: positive genetic interaction
definition: An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
has_exact_synonym: asynthetic
has_exact_synonym: asynthetic genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0795
in_subset: PSI-MI slim

suppression
type: Class
subclass of: positive genetic interaction
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
has_exact_synonym: suppression
has_exact_synonym: suppressive genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
has_related_synonym: Alleviating interaction
id: MI:0796
in_subset: PSI-MI slim

epistasis
type: Class
subclass of: genetic interaction
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
imported from: mi.owl
has_exact_synonym: epistatic
has_exact_synonym: epistatic genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0797
in_subset: PSI-MI slim

phosphotransfer reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
imported from: mi.owl
has_exact_synonym: phosphotransfer
has_obo_namespace: PSI-MI
id: MI:0844
in_subset: PSI-MI slim

demethylation reaction
type: Class
subclass of: enzymatic reaction
definition: The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
imported from: mi.owl
has_exact_synonym: demethylation
has_obo_namespace: PSI-MI
id: MI:0871
in_subset: PSI-MI slim

nucleoside triphosphatase reaction
type: Class
subclass of: enzymatic reaction
definition: Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
imported from: mi.owl
has_exact_synonym: triphosphatase react
has_obo_namespace: PSI-MI
id: MI:0881
in_subset: PSI-MI slim

atpase reaction
type: Class
subclass of: nucleoside triphosphatase reaction
definition: Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0882
in_subset: PSI-MI slim

gtpase reaction
type: Class
subclass of: nucleoside triphosphatase reaction
definition: Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0883
in_subset: PSI-MI slim

rna cleavage
type: Class
subclass of: nucleic acid cleavage
definition: Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0902
in_subset: PSI-MI slim

nucleic acid cleavage
type: Class
subclass of: cleavage reaction
definition: Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
imported from: mi.owl
has_exact_synonym: ncl acid cleavage
has_obo_namespace: PSI-MI
id: MI:0910
in_subset: PSI-MI slim

association
type: Class
subclass of: interaction
definition: Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0914
in_subset: PSI-MI slim

physical association
type: Class
subclass of: association
definition: Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0915
in_subset: PSI-MI slim

noninteractive
type: Class
subclass of: neutral genetic interaction
definition: The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
imported from: mi.owl
has_exact_synonym: noninteractive genetic interaction (sensu inequality)
has_exact_synonym: noninteractive genetic interaction defined by inequality
has_obo_namespace: PSI-MI
id: MI:0932
in_subset: PSI-MI slim

negative genetic interaction
type: Class
subclass of: genetic interaction
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
has_exact_synonym: negative gen int
has_obo_namespace: PSI-MI
id: MI:0933
in_subset: PSI-MI slim

neutral genetic interaction
type: Class
subclass of: genetic interaction
definition: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.
imported from: mi.owl
has_exact_synonym: neutral gent int
has_obo_namespace: PSI-MI
id: MI:0934
in_subset: PSI-MI slim

positive genetic interaction
type: Class
subclass of: genetic interaction
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
has_exact_synonym: positive gent int
has_obo_namespace: PSI-MI
id: MI:0935
in_subset: PSI-MI slim

oxidoreductase activity electron transfer reaction
type: Class
subclass of: enzymatic reaction
definition: An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
imported from: mi.owl
has_exact_synonym: redox reaction
has_obo_namespace: PSI-MI
id: MI:0945
in_subset: PSI-MI slim

phosphopantetheinylation
type: Class
subclass of: enzymatic reaction
definition: The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
imported from: mi.owl
created by: orchard
creation date: 2009-10-28T01:20:40Z
has_exact_synonym: p_patetheinylation
has_obo_namespace: PSI-MI
id: MI:0971
in_subset: PSI-MI slim

deamination reaction
type: Class
subclass of: enzymatic reaction
definition: The removal of an amine group from a molecule.
imported from: mi.owl
created by: orchard
creation date: 2010-04-26T10:49:06Z
has_exact_synonym: deamination
has_obo_namespace: PSI-MI
id: MI:0985
in_subset: PSI-MI slim

nucleic acid strand elongation reaction
type: Class
subclass of: enzymatic reaction
definition: The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
imported from: mi.owl
created by: orchard
creation date: 2010-04-26T10:52:22Z
has_exact_synonym: strand elongation
has_obo_namespace: PSI-MI
id: MI:0986
in_subset: PSI-MI slim

rna strand elongation
type: Class
subclass of: nucleic acid strand elongation reaction
definition: The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
imported from: mi.owl
created by: orchard
creation date: 2010-04-26T11:00:08Z
has_exact_synonym: rna elongation
has_obo_namespace: PSI-MI
id: MI:0987
in_subset: PSI-MI slim

diphtamidation reaction
type: Class
subclass of: enzymatic reaction
definition: A modification that converts an L-histidine residue to diphthamide.
imported from: mi.owl
created by: orchard
creation date: 2010-11-11T12:36:51Z
has_exact_synonym: diphthamidation
has_obo_namespace: PSI-MI
id: MI:1027
in_subset: PSI-MI slim

predicted interaction
type: Class
subclass of: interaction
definition: Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
imported from: mi.owl
created by: orchard
creation date: 2011-08-03T11:14:11Z
has_exact_synonym: predicted
has_obo_namespace: PSI-MI
id: MI:1110
in_subset: PSI-MI slim

self interaction
type: Class
subclass of: direct interaction
definition: Intra-molecular interaction between two or more regions of the same molecule.
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T01:19:22Z
has_obo_namespace: PSI-MI
id: MI:1126
in_subset: PSI-MI slim
comment: The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.

putative self interaction
type: Class
subclass of: direct interaction
definition: Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T01:21:58Z
has_obo_namespace: PSI-MI
id: MI:1127
in_subset: PSI-MI slim
comment: The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.

carboxylation reaction
type: Class
subclass of: enzymatic reaction
definition: Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T03:24:05Z
has_exact_synonym: carboxylation
has_obo_namespace: PSI-MI
id: MI:1139
in_subset: PSI-MI slim

decarboxylation reaction
type: Class
subclass of: enzymatic reaction
definition: Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T03:31:42Z
has_exact_synonym: decarboxylation
has_obo_namespace: PSI-MI
id: MI:1140
in_subset: PSI-MI slim

aminoacylation reaction
type: Class
subclass of: enzymatic reaction
definition: Aminoacylation is the process of adding an aminoacyl group to a compound.
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T03:49:50Z
has_exact_synonym: aminoacylation
has_obo_namespace: PSI-MI
id: MI:1143
in_subset: PSI-MI slim

phospholipase reaction
type: Class
subclass of: enzymatic reaction
definition: Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T04:08:14Z
has_obo_namespace: PSI-MI
id: MI:1146
in_subset: PSI-MI slim

ampylation reaction
type: Class
subclass of: enzymatic reaction
definition: AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
imported from: mi.owl
created by: orchard
creation date: 2012-01-03T04:21:12Z
has_exact_synonym: ampylation
has_obo_namespace: PSI-MI
id: MI:1148
in_subset: PSI-MI slim

uridylation reaction
type: Class
subclass of: enzymatic reaction
definition: The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
imported from: mi.owl
created by: orchard
creation date: 2012-08-10T07:50:08Z
has_exact_synonym: uridylation
has_obo_namespace: PSI-MI
has_related_synonym: umpylation
id: MI:1230
in_subset: PSI-MI slim

proline isomerization reaction
type: Class
subclass of: isomerase reaction
definition: The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
imported from: mi.owl
created by: orchard
creation date: 2012-08-10T09:02:28Z
has_obo_namespace: PSI-MI
id: MI:1237
in_subset: PSI-MI slim

isomerase reaction
type: Class
subclass of: enzymatic reaction
definition: The catalysis of the structural rearrangement of isomers.
imported from: mi.owl
created by: orchard
creation date: 2012-08-10T12:51:00Z
has_obo_namespace: PSI-MI
id: MI:1250
in_subset: PSI-MI slim

methylmalonyl-CoA isomerase reaction
type: Class
subclass of: isomerase reaction
definition: The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
imported from: mi.owl
created by: orchard
creation date: 2012-08-10T01:23:35Z
has_obo_namespace: PSI-MI
id: MI:1251
in_subset: PSI-MI slim

enhancement
type: Class
subclass of: negative genetic interaction
definition: An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T19:12:17Z
has_obo_namespace: PSI-MI
has_related_synonym: Aggravating interaction
id: MI:1271
in_subset: PSI-MI slim

positive epistasis
type: Class
subclass of: epistasis
subclass of: positive genetic interaction
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:05:15Z
has_obo_namespace: PSI-MI
id: MI:1272
in_subset: PSI-MI slim

maximal epistasis
type: Class
subclass of: positive epistasis
subclass of: quantitative epistasis
definition: An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:11:27Z
has_obo_namespace: PSI-MI
id: MI:1273
in_subset: PSI-MI slim

minimal epistasis
type: Class
subclass of: positive epistasis
subclass of: mutual suppression (partial)
subclass of: quantitative epistasis
definition: An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:13:14Z
has_obo_namespace: PSI-MI
id: MI:1274
in_subset: PSI-MI slim

neutral epistasis
type: Class
subclass of: epistasis
subclass of: neutral genetic interaction
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:22:53Z
has_obo_namespace: PSI-MI
id: MI:1275
in_subset: PSI-MI slim

opposing epistasis
type: Class
subclass of: neutral epistasis
subclass of: quantitative epistasis
definition: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:25:26Z
database_cross_reference: psi-mi:MI:1285
has_obo_namespace: PSI-MI
id: MI:1276
in_subset: PSI-MI slim

qualitative epistasis
type: Class
subclass of: neutral epistasis
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:26:38Z
has_obo_namespace: PSI-MI
id: MI:1277
in_subset: PSI-MI slim

mutual enhancement
type: Class
subclass of: enhancement
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:31:30Z
has_obo_namespace: PSI-MI
id: MI:1278
in_subset: PSI-MI slim

unilateral enhancement
type: Class
subclass of: enhancement
definition: An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:33:13Z
has_obo_namespace: PSI-MI
id: MI:1279
in_subset: PSI-MI slim

mutual suppression
type: Class
subclass of: suppression
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:35:53Z
has_obo_namespace: PSI-MI
id: MI:1280
in_subset: PSI-MI slim

mutual suppression (complete)
type: Class
subclass of: mutual suppression
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:37:41Z
has_obo_namespace: PSI-MI
id: MI:1281
in_subset: PSI-MI slim

mutual suppression (partial)
type: Class
subclass of: mutual suppression
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:39:12Z
has_obo_namespace: PSI-MI
id: MI:1282
in_subset: PSI-MI slim

suppression-enhancement
type: Class
subclass of: mutual suppression (partial)
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:43:52Z
has_obo_namespace: PSI-MI
id: MI:1283
in_subset: PSI-MI slim

quantitative epistasis
type: Class
subclass of: epistasis
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T20:47:35Z
has_obo_namespace: PSI-MI
id: MI:1284
in_subset: PSI-MI slim

over-suppression
type: Class
subclass of: neutral genetic interaction
definition: An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:04:18Z
has_obo_namespace: PSI-MI
id: MI:1286
in_subset: PSI-MI slim

mutual over-suppression
type: Class
subclass of: over-suppression
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:06:09Z
has_obo_namespace: PSI-MI
id: MI:1287
in_subset: PSI-MI slim

over-suppression-enhancement
type: Class
subclass of: neutral genetic interaction
definition: An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:11:03Z
has_obo_namespace: PSI-MI
id: MI:1288
in_subset: PSI-MI slim

phenotype bias
type: Class
subclass of: neutral genetic interaction
definition: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:15:34Z
has_obo_namespace: PSI-MI
id: MI:1289
in_subset: PSI-MI slim

suppression (complete)
type: Class
subclass of: suppression
definition: An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:34:57Z
has_obo_namespace: PSI-MI
id: MI:1290
in_subset: PSI-MI slim

suppression (partial)
type: Class
subclass of: suppression
definition: An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:36:07Z
has_obo_namespace: PSI-MI
id: MI:1291
in_subset: PSI-MI slim

unilateral suppression
type: Class
subclass of: suppression
definition: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:37:28Z
has_obo_namespace: PSI-MI
id: MI:1292
in_subset: PSI-MI slim

unilateral suppression (complete)
type: Class
subclass of: unilateral suppression
definition: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:38:36Z
has_obo_namespace: PSI-MI
id: MI:1293
in_subset: PSI-MI slim

unilateral suppression (partial)
type: Class
subclass of: unilateral suppression
definition: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:39:32Z
has_obo_namespace: PSI-MI
id: MI:1294
in_subset: PSI-MI slim

unilateral over-suppression
type: Class
subclass of: over-suppression
definition: An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
imported from: mi.owl
created by: orchard
creation date: 2013-06-05T21:54:08Z
has_obo_namespace: PSI-MI
id: MI:1295
in_subset: PSI-MI slim

de-ADP-ribosylation reaction
type: Class
subclass of: enzymatic reaction
definition: Measure of hydrolytic reactions that release ADP-ribose.
imported from: mi.owl
created by: orchard
creation date: 2013-06-06T10:34:18Z
has_obo_namespace: PSI-MI
has_related_synonym: mono-ADP-ribosylhydrolase reaction
id: MI:1310
in_subset: PSI-MI slim

sulfurtransfer reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction where a sulfate group is transferred between two proteins
imported from: mi.owl
created by: orchard
creation date: 2014-01-08T11:16:12Z
has_exact_synonym: sulfurtransfer
has_exact_synonym: sulphurtransfer reaction
has_obo_namespace: PSI-MI
id: MI:1327
in_subset: PSI-MI slim

lipid cleavage
type: Class
subclass of: cleavage reaction
definition: Reaction monitoring the cleavage (hydrolysis) or a lipid molecule.
imported from: mi.owl
created by: orchard
creation date: 2015-02-03T13:25:21Z
has_obo_namespace: PSI-MI
id: MI:1355
in_subset: PSI-MI slim

guanine nucleotide exchange factor reaction
type: Class
subclass of: enzymatic reaction
definition: The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP.
imported from: mi.owl
created by: ppm
creation date: 2017-01-19T16:13:36Z
has_exact_synonym: GEF reaction
has_obo_namespace: PSI-MI
id: MI:2252
in_subset: PSI-MI slim

s-nitrosylation
type: Class
subclass of: enzymatic reaction
definition: Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine.
imported from: mi.owl
created by: ppm
creation date: 2017-01-19T17:11:46Z
has_exact_synonym: s-nitrosylation
has_obo_namespace: PSI-MI
id: MI:2263
in_subset: PSI-MI slim

tyrosinylation
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that add a tyrosine residue to an amino-acid.
imported from: mi.owl
created by: ppm
creation date: 2017-01-26T15:21:43Z
database_cross_reference: GO:GO:0018322
has_exact_synonym: tyrosinylation
has_obo_namespace: PSI-MI
id: MI:2272
in_subset: PSI-MI slim

tyrosination
type: Class
subclass of: tyrosinylation
definition: Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin.
imported from: mi.owl
created by: ppm
creation date: 2017-01-26T15:22:39Z
database_cross_reference: GO:GO:0018166
has_exact_synonym: tyrosination
has_obo_namespace: PSI-MI
id: MI:2273
in_subset: PSI-MI slim

deamidation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline).
imported from: mi.owl
created by: ppm
creation date: 2017-08-08T14:38:29Z
has_exact_synonym: deamidation
has_obo_namespace: PSI-MI
id: MI:2280
in_subset: PSI-MI slim

Mycobacterium tuberculosis
type: Class
subclass of: Bacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:2528440
database_cross_reference: GC_ID:11
database_cross_reference: PMID:29205127
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus tuberculosis
has_related_synonym: Bacterium tuberculosis
has_related_synonym: Mycobacterium tuberculosis typus humanus
has_related_synonym: Mycobacterium tuberculosis var. hominis
has_related_synonym: Mycobacterium tuberculosis variant tuberculosis

Bacteria
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11542017
database_cross_reference: PMID:11542087
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:270744
database_cross_reference: PMID:7520741
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8186100
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: PMID:9336922
has_exact_synonym: eubacteria
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: bacteria
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Archaea
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10425795
database_cross_reference: PMID:10425796
database_cross_reference: PMID:10425797
database_cross_reference: PMID:10490293
database_cross_reference: PMID:10843050
database_cross_reference: PMID:10939651
database_cross_reference: PMID:10939673
database_cross_reference: PMID:10939677
database_cross_reference: PMID:11211268
database_cross_reference: PMID:11321083
database_cross_reference: PMID:11321113
database_cross_reference: PMID:11411719
database_cross_reference: PMID:11540071
database_cross_reference: PMID:11541975
database_cross_reference: PMID:11542064
database_cross_reference: PMID:11542149
database_cross_reference: PMID:11760965
database_cross_reference: PMID:12054223
database_cross_reference: PMID:2112744
database_cross_reference: PMID:25527841
database_cross_reference: PMID:270744
database_cross_reference: PMID:8123559
database_cross_reference: PMID:8590690
database_cross_reference: PMID:9103655
database_cross_reference: PMID:9336922
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Archaebacteria
has_related_synonym: Mendosicutes
has_related_synonym: Metabacteria
has_related_synonym: Monera
has_related_synonym: Procaryotae
has_related_synonym: Prokaryota
has_related_synonym: Prokaryotae
has_related_synonym: archaea
has_related_synonym: prokaryote
has_related_synonym: prokaryotes

Eukaryota
type: Class
subclass of: organism
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
database_cross_reference: PMID:30257078
has_exact_synonym: eucaryotes
has_exact_synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes

Escherichia coli
type: Class
subclass of: Bacteria
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
has_alternative_id: NCBITaxon:1637691
has_alternative_id: NCBITaxon:1806490
has_alternative_id: NCBITaxon:469598
has_alternative_id: NCBITaxon:662101
has_alternative_id: NCBITaxon:662104
database_cross_reference: GC_ID:11
database_cross_reference: PMID:10319482
has_exact_synonym: E. coli
has_exact_synonym: Escherichia/Shigella coli
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Bacillus coli
has_related_synonym: Bacterium coli
has_related_synonym: Bacterium coli commune
has_related_synonym: Enterococcus coli

Homo sapiens
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has_exact_synonym: human
has_obo_namespace: ncbi_taxonomy

gene
type: Class
subclass of: material entity
definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
term editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
imported from: ogg.owl

protein
type: Class
subclass of: molecular entity
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: pr.owl
has_exact_synonym: natural protein
has_narrow_synonym: native protein
has_obo_namespace: protein
id: PR:000000001
comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].

pathway
type: Class
subclass of: interaction network
definition: A pathway is a set of inter-connected reactions and interactions whose delineation and scope are used as a model for exploring and studying, describing and understanding the working of and relationships between biomolecules within a context.
imported from: pw.owl
has_obo_namespace: pathway
id: PW:0000001

classic metabolic pathway
type: Class
subclass of: pathway
definition: The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics.
imported from: pw.owl
has_obo_namespace: pathway
id: PW:0000002
comment: The definition was compiled based on a number of available defintions in various dictionaries.

signaling pathway
type: Class
subclass of: pathway
definition: The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways.
imported from: pw.owl
has_obo_namespace: pathway
id: PW:0000003
comment: The definition was compiled based on a number of definitions available in various dictionaries.

regulatory pathway
type: Class
subclass of: pathway
definition: The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning.
imported from: pw.owl
has_obo_namespace: pathway
id: PW:0000004
comment: The definition was complied based on a number of definitions available in several dictionaries

disease pathway
type: Class
subclass of: pathway
definition: Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition.
imported from: pw.owl
has_obo_namespace: pathway
has_related_synonym: complex human diseases
id: PW:0000013

drug pathway
type: Class
subclass of: pathway
definition: The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. The systems involved in drug processing and responses are also those handling exogenous, xenobiotic compounds in the cellular detoxification pathway. The distinction between a random encounter with a foreign compound and the processing of a substance administered for treatment along with the importance of genetic variation for the individual responses to particular drugs warrant their separate consideration.
imported from: pw.owl
created by: VPetri
creation date: 2010-03-15T11:01:15Z
has_obo_namespace: pathway
id: PW:0000754